Miracle-dz/UniFAR-FTUs huggingface dataset:
Extraction of recombinant proteins from Escherichia coli by cell disruption with aqueous solutions of surface-active compounds

BACKGROUND: Green fluorescent protein (GFP) is used extensively as a biomarker due to its unique spectral and fluorescence characteristics. GFP is usually obtained from recombinant strains of Escherichia coli (E. coli) producing the protein intracellularly. However, the common methods of extraction are cumbersome leading to an increase in the downstream process costs and complexity, sometimes leading to a higher risk of biomolecule degradation. RESULTS: This work proposes a new method to extract recombinant intracellular GFP from E. coli BL21 by using aqueous solutions of surface-active compounds. CONCLUSION: By comparing the fluorescence intensity of the extracted GFP, it was concluded that some of these compounds, namely ionic liquids with an alkyl chain of 10 or more carbons (best solvent being tributyl-1-tetradecylphosphonium, [P4,4,4,14]Cl) are more effective than an ultrasonic-assisted extraction, even at low concentrations, being able to extract the whole GFP content from the cells. © 2018 Society of Chemical Industry Supporting information may be found in the online version of this article.
OpenSeqSLAM2.0: An Open Source Toolbox for Visual Place Recognition Under Changing Conditions

Visually recognising a traversed route - regardless of whether seen during the day or night, in clear or inclement conditions, or in summer or winter - is an important capability for navigating robots. Since SeqSLAM was introduced in 2012, a large body of work has followed exploring how robotic systems can use the algorithm to meet the challenges posed by navigation in changing environmental conditions. The following paper describes OpenSeqSLAM2.0, a fully open-source toolbox for visual place recognition under changing conditions. Beyond the benefits of open access to the source code, OpenSeqSLAM2.0 provides a number of tools to facilitate exploration of the visual place recognition problem and interactive parameter tuning. Using the new open source platform, it is shown for the first time how comprehensive parameter characterisations provide new insights into many of the system components previously presented in ad hoc ways and provide users with a guide to what system component options should be used under what circumstances and why.
Variability in Modified Rankin Scoring Across a Large Cohort of International Observers

Background and Purpose— The modified Rankin scale (mRS) is the most commonly used outcome measure in stroke trials. However, substantial interobserver variability in mRS scoring has been reported. These studies likely underestimate the variability present in multicenter clinical trials, because exploratory work has only been undertaken in single centers by a few observers, all of similar training. We examined mRS variability across a large cohort of international observers using data from a video training resource. Methods— The mRS training package includes a series of “real-life” patient interviews for grading. Training data were collected centrally and analyzed for variability using kappa statistics. We examined variability against a standard of “correct” mRS grades; examined variability by country; and for UK assessors, examined variability by center and by professional background of the observer. Results— To date, 2942 assessments from 30 countries have been submitted. Overall reliability for mRS grading has been moderate to good with substantial heterogeneity across countries. Native English language has had little effect on reliability. Within the United Kingdom, there was no significant variation by profession. Conclusion— Our results confirm interobserver variability in mRS assessment. The heterogeneity across countries is intriguing because it appears not to be related solely to language. These data highlight the need for novel strategies to improve reliability.
Blind Source Separation: The Location of Local Minima in the Case of Finitely Many Samples

Cost functions used in blind source separation are often defined in terms of expectations, i.e., an infinite number of samples is assumed. An open question is whether the local minima of finite sample approximations to such cost functions are close to the minima in the infinite sample case. To answer this question, we develop a new methodology of analyzing the finite sample behavior of general blind source separation cost functions. In particular, we derive a new probabilistic analysis of the rate of convergence as a function of the number of samples and the conditioning of the mixing matrix. The method gives a connection between the number of available samples and the probability of obtaining a local minimum of the finite sample approximation within a given sphere around the local minimum of the infinite sample cost function. This shows the convergence in probability of the nearest local minima of the finite sample approximation to the local minima of the infinite sample cost function. We also answer a long-standing problem of the mean-squared error (MSE) behavior of the (finite sample) least squares constant modulus algorithm (LS-CMA), namely whether there exist LS-CMA receivers with good MSE performance. We demonstrate how the proposed techniques can be used to determine the required number of samples for LS-CMA to exceed a specified performance. The paper concludes with simulations that validate the results.
A Study on Optimization of Process Parameters in EDM Using Taguchi's Doe Technique

Non-conventional machining processes such as electrical discharge machining (EDM) are being widely used to machine hard tool and die materials used in the industries. EDM is a process whereby metal is removed by the action of electrical discharge between the tool (cathode) and the work piece (anode). Literally thousands of electrical discharges per second are generated and each electrical discharge produces a tiny crater by melting and vaporization thus reproducing the shape of the tool in to the work piece. A di-electric fluid flushes out the 'chips' and confines the electrical discharge. Materials of any hardness can be cut as long as the material can conduct electricity. Many complex shapes can be reproduced in the work piece. A small amount of material up to 15% is expelled violently from the surface melt and the remaining liquid resolidifies. The recast structure is typically very fine grained and hard, and may be alloyed with carbon from the cracked dielectric or with material transferred from the tool 111. The machining parameters, including peak current, pulse on-time, gap voltage, fluid pressure etc. should be chosen properly so that a better performance 151 can be obtained. However, the selection of appropriate machining parameters for EDM is difficult and relies heavily on the operators experience and machining parameters tables provided by the machine-tool builder. The purpose of this paper is to present an efficient method by means of which to determine appropriate machining parameters so as to be able to achieve the
Effects of dexmedetomidine postconditioning on myocardial ischemia and the role of the PI3K/Akt-dependent signaling pathway in reperfusion injury

The present study aimed to determine whether post-ischemic treatment with dexmedetomidine (DEX) protected the heart against acute myocardial ischemia/reperfusion (I/R)-induced injury in rats. The phosphatidylinositol-3 kinase/protein kinase B(PI3K/Akt)-dependent signaling pathway was also investigated. Male Sprague Dawley rats (n=64) were subjected to ligation of the left anterior descending artery (LAD), which produced ischemia for 25 min, followed by reperfusion. Following LAD ligation, rats were treated with DEX (5, 10 and 20 µg/kg) or underwent post-ischemic conditioning, which included three cycles of ischemic insult. In order to determine the role of the PI3K/Akt signaling pathway, wortmannin (Wort), a PI3K inhibitor, was used to treat a group of rats that had also been treated with DEX (20 µg/kg). Post-reperfusion, lactate dehydrogenase (LDH), cardiac troponin I (cTnI), creatine kinase isoenzymes (CK-MB), superoxide dismutase (SOD) and malondialdehyde (MDA) serum levels were measured using an ultraviolet spectrophotometer. The protein expression levels of phosphorylated (p)-Akt, Ser9-p-glycogen synthase kinase-3β (p-GSK-3β) and cleaved caspase-3 were detected in heart tissue by western blotting. The mRNA expression levels of B-cell lymphoma 2 (Bcl-2) and Bcl-2-associated X protein (Bax) were detected using reverse transcription-polymerase chain reaction. At the end of the experiment, the hearts were removed and perfused in an isolated perfusion heart apparatus with Evans blue (1%) in order to determine the non-ischemic areas. The risk and infarct areas of the heart were not dyed. As expected, I/R induced myocardial infarction, as determined by the increased serum levels of cTnI, CK-MB and MDA, and the decreased levels of SOD. Post-ischemic treatment with DEX increased the expression levels of p-Akt and p-GSK-3β, whereas caspase-3 expression was reduced following DEX treatment compared with in the I/R group. Compared with the I/R group, the ratio of Bcl-2/Bax at the mRNA level was elevated in the DEX and ischemic post-conditioning groups, whereas the expression levels of Bax were decreased. Conversely, the effects of DEX were attenuated by Wort. These results indicated that, similar to post-ischemic conditioning, post-ischemic treatment with DEX protects the heart against I/R via the PI3K/Akt-dependent signaling pathway, possibly by activating GSK-3β.
Personality in women with endometriosis: temperament and character dimensions and pelvic pain.

STUDY QUESTION Is pelvic pain due to endometriosis associated with temperament and character dimensions? SUMMARY ANSWER Women with endometriosis and pelvic pain do not clearly exhibit a specific personality profile; however, personality is associated with pelvic pain perception. WHAT IS KNOWN ALREADY There is research evidence suggesting that endometriosis patients with pelvic pain are more likely to present psychological disruption. Little is known about the association between subjective factors, such as personality traits, and pelvic pain. STUDY DESIGN, SIZE, DURATION This cross-sectional study (N = 133) is part of a larger research on the association between endometriosis and several psychological variables carried out between 2012 and 2014. PARTICIPANTS/MATERIALS, SETTINGS, METHODS The participants were 82 endometriosis patients and 51 healthy controls. Endometriosis patients indicated on a dichotomous scale (yes/no) whether they were suffering from pelvic pain and were divided in two study groups: painful endometriosis group (N = 58) and pain-free endometriosis group (N = 24). The severity of pelvic pain (chronic pelvic pain, dysmenorrhoea, dyspareunia, and dyschezia) was rated on a 0-10 point numerical rating scale. All participants completed a 240-item psychometric test (TCI-R) evaluating personality in terms of temperament and character dimensions. MAIN RESULTS AND THE ROLE OF CHANCE Women with painful endometriosis had lower novelty seeking compared with the control group (P = 0.017) and higher harm avoidance (P = 0.007) and lower exploratory excitability (P = 0.034) and responsibility (P = 0.027) compared with the pain-free endometriosis group, as well as higher fatigability compared with the pain-free endometriosis group (P = 0.001) and the control group (P = 0.032). Higher harm avoidance (B = 0.081; P = 0.002) and lower self-directedness (B = -0.053; P = 0.015) were associated with a greater severity of chronic pelvic pain. LIMITATIONS, REASONS FOR CAUTION These study findings should be taken cautiously for several methodological reasons such as small sample size, differences in group sizes and cultural homogeneity. More research is needed to further investigate the association between personality and pelvic pain related to endometriosis. WIDER IMPLICATIONS OF THE FINDINGS Our findings suggest new avenues for future research and treatment of endometriosis. The association between the severity of chronic pelvic pain and personality may help clarify the lack of a direct correlation between pain severity and the type and stage of endometriosis, as well as the inconsistencies in patients' response to medical and/or surgical treatment. Therapeutic strategies should be specifically targeted on individual women and involve an integrated approach to the treatment of chronic pelvic pain related to endometriosis. STUDY FUNDING/COMPETING INTERESTS There was no external funding for this study and the authors have no conflicts of interest. TRIAL REGISTRATION NUMBER Not applicable to this study.
The effect of methotrexate on bone metabolism markers in patients with rheumatoid arthritis

The aim of the present study was to evaluate the influence on urinary excretion levels of N-telopeptide of type I collagen (NTX) and deoxypyridinoline (DPD) as a useful marker for bone resorption, and on serum-bone alkaline phosphate (BAP) levels as a useful marker for bone formation and an early marker of osteoblast differentiation in patients with rheumatoid arthritis (RA) treated with methotrexate (MTX). Thirty patients with RA, diagnosed according to the criteria of the American College of Rheumatology, were involved in this study between March 2003 and January 2005. None of the patients had a history of hormone (estrogen) replacement therapy. All patients were treated with MTX. Methotrexate was administered perorally at a dosage of 4–10 mg/week. All patients underwent general and physical examinations and routine blood and urinary analysis at the baseline, 3 months and 6 months after the initial treatment. Then the levels of NTX and DPD in urine and BAP in serum were measured in all patients. For comparison with the effect of other DMARDs on bone metabolism markers in RA patients, we measured the levels of NTX and DPD in urine and BAP in serum of RA patients, 13 patients treated with salazosulfapyridine (SASP), and 14 patients treated with actarit (ACT). In patients treated with MTX, NTX levels decreased significantly at 3 months after the initial treatment and remained low at 6 months after the initial treatment, and DPD levels significantly decreased at 6 months after the initial treatment. The mean serum BAP levels changed without significant differences from the baseline at 3 months and 6 months. In patients treated with SASP and ACT, all bone metabolism markers had not changed significantly at the three time points. On disease activity erythrocyte sedimentation rate, C-reactive protein, the number of swollen joints and tender joints, and mHAQ score decreased significantly at 3 months after the initial treatment, and remained at low levels at 6 months after the initial treatment with MTX. Methotrexate therapy looks promising in inhibiting generalized bone loss in patients with RA. In addition, NTX is a more sensitive marker than DPD.
EnTagRec: An Enhanced Tag Recommendation System for Software Information Sites

Software engineers share experiences with modern technologies by means of software information sites, such as Stack Overflow. These sites allow developers to label posted content, referred to as software objects, with short descriptions, known as tags. However, tags assigned to objects tend to be noisy and some objects are not well tagged. To improve the quality of tags in software information sites, we propose EnTagRec, an automatic tag recommender based on historical tag assignments to software objects and we evaluate its performance on four software information sites, Stack Overflow, Ask Ubuntu, Ask Different, and Free code. We observe that that EnTagRec achieves Recall@5 scores of 0.805, 0.815, 0.88 and 0.64, and Recall@10 scores of 0.868, 0.876, 0.944 and 0.753, on Stack Overflow, Ask Ubuntu, Ask Different, and Free code, respectively. In terms of Recall@5 and Recall@10, averaging across the 4 datasets, EnTagRec improves Tag Combine, which is the state of the art approach, by 27.3% and 12.9% respectively.
ICCAD-2017 CAD contest in multi-deck standard cell legalization and benchmarks

An increasing number of multi-deck cells occupying multiple rows (e.g. multi-bit registers) are used in advanced node technologies to achieve low power and high performance. The multi-deck standard cell legalization not only should remove all overlaps between cells but also should satisfy delicate and complicated design rules with preserving the quality of the given placement by applying the minimal perturbation. In addition, the process must be fast and robust to handle the sheer number of cells in the state-of-the-art designs. For this purpose, we have defined an evaluation metric based on maximum, average cell movements, and Half Perimeter Wire Length (HPWL) as well as runtime of the legalization algorithm. In addition, we have introduced a set of benchmarks that include multi-deck cells with a range of heights (1–4 row heights).
Peripheral T-cell lymphoma (excluding anaplastic large-cell lymphoma): results from the Non-Hodgkin's Lymphoma Classification Project.

BACKGROUND Peripheral T-cell lymphoma (PTCL) is rare in most parts of the world. Therefore, we have evaluated the 96 cases of PTCL diagnosed within the Non-Hodgkin's Lymphoma Classification Project (NHLCP) (1378 cases) for their geographical distribution, pathologic features and diagnostic reliability, as well as clinical presentation and outcome. MATERIALS AND METHODS Diagnoses of all cases were rendered independently by five experienced hematopathologists based on morphology only, and after introduction of the immunophenotype and clinical data. Divergent diagnoses were jointly discussed and a final consensus diagnosis was established in each case. Reliability of the diagnoses was evaluated statistically, and the clinical features and outcome were analyzed according to the consensus diagnoses. RESULTS Seven per cent of all non-Hodgkin's lymphoma (NHL) cases reviewed were classified as PTCL and the frequency varied from 1.5% to 18.3% in different countries. The interobserver agreement with the consensus diagnosis of PTCL was 86% in the Revised European-American Lymphoma (REAL) classification, but the designation of subtypes was less reliable. Diagnostic reliability improved from 41% to 86% after immunophenotyping, but did not improve further with the addition of detailed clinical data. Clinically, angiocentric nasal lymphoma presented in young females (median age 49 years) at extranodal sites, but with few adverse risk factors, whereas angioimmunoblastic lymphoma presented most often in older males (median age 65 years) at nodal and extranodal sites with numerous risk factors. The 5-year overall and failure-free survivals for patients with PTCL treated with doxorubicin (Adriamycin)-containing regimens were only 26% and 20%, respectively. Both failure-free and overall survival were strongly correlated with the performance status and International Prognostic Index scores at presentation, but differences in survival were not observed between the major histological types. However, within the PTCL 'not otherwise specified' category, but not angioimmunoblastic lymphoma, the number of transformed blasts was prognostically relevant. CONCLUSIONS PTCLs can be diagnosed reliably by experienced hematopathologists, but immunophenotyping is absolutely necessary. Currently, all types of PTCL should be considered high-grade lymphomas. An increased ability to distinguish T-lymphocyte subsets is needed in order to better subclassify the PTCLs for therapeutic and prognostic purposes.
Outage Minimization for a Fading Wireless Link With Energy Harvesting Transmitter and Receiver

This paper studies online power control policies for outage minimization in a fading wireless link with energy harvesting transmitter and receiver. The outage occurs when either the transmitter or the receiver does not have enough energy, or the channel is in outage, where the transmitter only has the channel distribution information. Under infinite battery capacity and without retransmission, we prove that threshold-based power control policies are optimal. We thus propose disjoint/joint threshold-based policies with and without battery state sharing between the transmitter and receiver, respectively. We also analyze the impact of practical receiver detection and processing on the outage performance. When retransmission is considered, policy with linear power levels is adopted to adapt the power thresholds per retransmission. With finite battery capacity, a three dimensional finite state Markov chain is formulated to calculate the optimal parameters and corresponding performance of proposed policies. The energy arrival correlation between the transmitter and receiver is addressed for both finite and infinite battery cases. Numerical results show the impact of battery capacity, energy arrival correlation and detection cost on the outage performance of the proposed policies, as well as the tradeoff between the outage probability and the average transmission times.
A Compact 2-DOF Piezoelectric-Driven Platform Based on “Z-Shaped” Flexure Hinges

A compact 2-DOF (two degrees of freedom) piezoelectric-driven platform for 3D cellular bio-assembly systems has been proposed based on “Z-shaped” flexure hinges. Multiple linear motions with high resolution both in x and y directions are achieved. The “Z-shaped” flexure hinges and the parallel-six-connecting-rods structure are utilized to obtain the lowest working stress while compared with other types of flexure hinges. In order to achieve the optimized structure, matrix-based compliance modeling (MCM) method and finite element method (FEM) are used to evaluate both the static and dynamic performances of the proposed 2-DOF piezoelectric-driven platform. Experimental results indicate that the maximum motion displacements for x-stage and y-stage are lx = 17.65 μm and ly = 15.45 μm, respectively. The step response time for x-stage and y-stage are tx = 1.7 ms and ty = 1.6 ms, respectively.
Fully Nonparametric Estimation of Scalar Diffusion Models

We propose a functional estimation procedure for homogeneous stochastic differential equations based on a discrete sample of observations and with minimal requirements on the data generating process. We show how to identify the drift and diffusion function in situations where one or the other function is considered a nuisance parameter. The asymptotic behavior of the estimators is examined as the observation frequency increases and as the time span lengthens. We prove almost sure consistency and weak convergence to mixtures of normal laws, where the mixing variates depend on the chronological local time of the underlying diffusion process, that is the random time spent by the process in the vicinity of a generic spatial point. The estimation method and asymptotic results apply to both stationary and nonstationary recurrent processes.