Miracle-dz/UniFAR-FTUs huggingface dataset:
Refolding and Structural Characteristic of TRAIL/Apo2L Inclusion Bodies from Different Specific Growth Rates of Recombinant Escherichia coli

TNF‐related apoptosis‐inducing ligand (TRAIL/Apo2L) was produced mainly as inclusion bodies (IBs) by recombinant Escherichia coli with a temperature‐inducible expression system. The yield of TRAIL type 2 IBs at higher preinduction specific growth rate (μ = 0.15 h‐1) was higher than that of TRAIL type 1 IBs at lower preinduction specific growth rate (μ = 0.05 h‐1). With the same optimized refolding protocols, two types of IBs exhibited different refolding features. Refolded type 1 IBs had higher recovery of more than 80% compared with type 2 IBs (57–63%). By the measurements of fluorescence and CD spectroscopy, type 1 TRAIL IBs dissolved by urea appeared to be a closer secondary structure to the native TRAIL than type 2. Furthermore, with trypsin treatment, the striking decrease in stability of type 1 IBs against protease digestion cannot be attributed to their small size particles observed by scanning electron microscope and probably depend on different protein structure properties between the two IBs. Different properties of inclusion bodies were mainly influenced by different physiological states of the cells just prior to the induction.
Capacity-achieving rateless polar codes

A rateless coding scheme transmits incrementally more and more coded bits over an unknown channel until all the information bits are decoded reliably by the receiver. We propose a new rateless coding scheme based on polar codes, and we show that this scheme is capacity-achieving, i.e. its information rate is as good as the best code specifically designed for the unknown channel. Previous rateless coding schemes are designed for specific classes of channels such as AWGN channels, binary erasure channels, etc. but the proposed rateless coding scheme is capacity-achieving for broad classes of channels as long as they are ordered via degradation. Moreover, it inherits the conceptual and computational simplicity of polar codes.
In Vivo Screening of Hepatocellular Carcinoma Using AC Susceptibility of Anti-Alpha Fetoprotein-Activated Magnetic Nanoparticles

With antibody-mediated magnetic nanoparticles (MNPs) applied in cancer examinations, patients must pay at least twice for MNP reagents in immunomagnetic reduction (IMR) of in vitro screening and magnetic resonance imaging (MRI) of in vivo tests. This is because the high maintenance costs and complex analysis of MRI have limited the possibility of in vivo screening. Therefore, this study proposes novel methods for in vivo screening of tumors by examining the AC susceptibility of bound MNPs using scanning superconducting-quantum-interference-device (SQUID) biosusceptometry (SSB), thereby demonstrating high portability and improved economy. The favorable agreement between in vivo tests using SSB and MRI demonstrated the feasibility of in vivo screening using SSB for hepatocellular carcinoma (HCC) targeted by anti-alpha fetoprotein (AFP)-mediated MNPs. The magnetic labeling was also proved by in vitro tests using SSB and biopsy assays. Therefore, patients receiving bioprobe-mediated MNPs only once can undergo in vivo screening using SSB in the future.
Applications of Lagrangian-Based Alternating Direction Methods and Connections to Split Bregman

Analogous to the connection between Bregman iteration and the method of multipliers that was pointed out in [59], we show that a similar connection can be made between the split Breg-man algorithm [32] and the alternating direction method of multipliers (ADMM) of ([29], [31]). Existing convergence theory for ADMM [23] can therefore be used to justify both the alternating step and inexact minimizations used in split Bregman for the cases in which the algorithms are equivalent. Application of these algorithms to diﬀerent image processing problems is simpliﬁed by rewriting these problems in a general form that still includes constrained and unconstrained total variation, (TV), and l 1 minimization as was investigated in [32]. Numerical results for the application to TV-l 1 minimization [12] are presented. We also discuss applications of two related methods, the alternating minimization algorithm (AMA) of [56] and the Bregman operator splitting algorithm (BOS) of [61], which are sometimes better suited for problems where further decoupling of variables is useful.
Airway inflammation during stable and acutely exacerbated chronic obstructive pulmonary disease

The aim of this study was to clarify the mechanism of increased airway inflammation during an acute exacerbation. A total of 68 chronic obstructive pulmonary disease patients in a stable phase were enrolled and followed-up for 2–3 yrs. Inflammatory cells were analysed, and interleukin (IL)-8, neutrophil elastase, eotaxin, tryptase and RANTES (regulated on activation, normal T-cell expressed and secreted) were measured in sputum, both in a stable phase and during acute exacerbation. Out of 68 patients, 30 (unstable group) developed an acute exacerbation and expectorated adequate sputum during exacerbation. Thirty-two patients (stable group) did not develop any exacerbation for 2–3 yrs. The number of neutrophils, lymphocytes and eosinophils, and the levels of IL-8, eosinophil cationic protein (ECP), eotaxin and tryptase in sputum obtained from patients in both groups during the stable phase were significantly higher than those from healthy nonsmokers. There were no significant differences in cell analysis and biomarkers between the two groups, but patients in the unstable group showed more severe airflow limitation. In the unstable group, total cells, lymphocytes, neutrophils and eosinophils, and IL-8, neutrophil elastase, ECP and RANTES levels were significantly increased during an exacerbation from values in a stable phase. These findings suggest that exacerbation of chronic obstructive pulmonary disease may associate with additional increases in airway inflammation mediated by neutrophils, lymphocytes, eosinophils, interleukin-8 and RANTES.
Rigid mode and harmonic response analysis of three-body vibrating screen

By using the ADAMS, the dynamic parameters of three-body vibrating screen are extracted, and the simple finite element model is established on the basis of parameters in ANSYS. The amplitude-frequency curve and phase-frequency curve is obtained by using the harmonic analysis. According to the error between the simulated amplitude of the vibrating screen and the actual magnitude, the correctness of vibrating screen model is verified. By analyzing the rigid-body modes of the vibrating screen, the natural frequencies, mode shapes and other dynamic parameters are obtained. The results show that: the natural frequencies of three-body vibrating screen modes are more concentrated; the damping bearing is the weak link of the vibrating screen.
Execution Strategies in Fixed Income Markets

Reducing trading costs and slippage is a universal concern of asset managers. Although the decision of what assets to hold is stil the most important aspect of investing, poor execution of trade decisions can subtract many basis points from overall return. Conversely, having an effective strategy to execute trades and to measure transaction costs can enhance returns: “A penny saved in slippage is a penny earned in alpha. ” Execution techniques in equities have advanced far ahead of those in other markets such as futures, options, foreign exchange, and fixed income. One reason for this is the overall size of the equity markets, and the widespread use of active investment strategies. A second reason is the simplicity of the products themselves: for trading a single name of stock you need very little information beyond its price. Relationships between different stocks are at best weak. As a consequence, quant researchers in equity markets have focused intensively on the details of the execution process. By contrast, fixed income products are inherently complex, and quantitatively minded researchers in the area have focused on such aspects as yield curve modeling, day counts, etc. Asset managers have not traditionally focused on measuring or managing execution costs, and have few effective tools to do so. However, the Securities Industry and Financial Markets Association (SIFMA) in 2008 (SIFMA Asset Management Group, 2008) noted that “It is clear that the duty to seek best execution imposed on an asset manager is the same regardless of whether the manager is undertaking equity or fixed-income transactions. ” This chapter discusses some details of the fixed income markets that present special challenges for best execution in general and automated trading in particular. The focus will be on interest rate mar-
A spiral model of software development and enhancement

A short description is given of software process models and the issues they address. An outline is given of the process steps involved in the spiral model, an evolving risk-driven approach that provides a framework for guiding the software process, and its application to a software project is shown. A summary is given of the primary advantages and implications involved in using the spiral model and the primary difficulties in using it at its current incomplete level of elaboration. <<ETX>>
BESS Control Strategies for Participating in Grid Frequency Regulation

Abstract Battery Energy Storage Systems (BESS) are very effective means of supporting system frequency by providing fast response to power imbalances in the grid. However, BESS are costly, and careful system design and operation strategies are needed in order to generate revenue for the system owner. We propose control strategies which will help to maintain BESS's State of Charge (SoC) in the optimal range and slow down battery aging significantly. A validation of these strategies using data from ENTSO-E (for the German regulation market) in Continental Europe and the PJM interconnection in the USA is presented in the results section.
Genetic Variant rs10757278 on Chromosome 9p21 Contributes to Myocardial Infarction Susceptibility

Large-scale genome-wide association studies (GWAS) have revealed that rs10757278 polymorphism (or its proxy rs1333049) on chromosome 9p21 is associated with myocardial infarction (MI) susceptibility in individuals of Caucasian ancestry. Following studies in other populations investigated this association. However, some of these studies reported weak or no significant association. Here, we reevaluated this association using large-scale samples by searching PubMed and Google Scholar databases. Our results showed significant association between rs10757278 polymorphism and MI with p = 6.09 × 10−22, odds ratio (OR) = 1.29, 95% confidence interval (CI) 1.22–1.36 in pooled population. We further performed a subgroup analysis, and found significant association between rs10757278 polymorphism and MI in Asian and Caucasian populations. We identified that the association between rs10757278 polymorphism and MI did not vary substantially by excluding any one study. However, the heterogeneity among the selected studies varies substantially by excluding the study from the Pakistan population. We found even more significant association between rs10757278 polymorphism and MI in pooled population, p = 3.55 × 10−53, after excluding the study from the Pakistan population. In summary, previous studies reported weak or no significant association between rs10757278 polymorphism and MI. Interestingly, our analysis suggests that rs10757278 polymorphism is significantly associated with MI susceptibility by analyzing large-scale samples.
Robustness of meta-analyses in finding gene × environment interactions

Meta-analyses that synthesize statistical evidence across studies have become important analytical tools for genetic studies. Inspired by the success of genome-wide association studies of the genetic main effect, researchers are searching for gene × environment interactions. Confounders are routinely included in the genome-wide gene × environment interaction analysis as covariates; however, this does not control for any confounding effects on the results if covariate × environment interactions are present. We carried out simulation studies to evaluate the robustness to the covariate × environment confounder for meta-regression and joint meta-analysis, which are two commonly used meta-analysis methods for testing the gene × environment interaction or the genetic main effect and interaction jointly. Here we show that meta-regression is robust to the covariate × environment confounder while joint meta-analysis is subject to the confounding effect with inflated type I error rates. Given vast sample sizes employed in genome-wide gene × environment interaction studies, non-significant covariate × environment interactions at the study level could substantially elevate the type I error rate at the consortium level. When covariate × environment confounders are present, type I errors can be controlled in joint meta-analysis by including the covariate × environment terms in the analysis at the study level. Alternatively, meta-regression can be applied, which is robust to potential covariate × environment confounders.
SUPEROVULATORY RESPONSE OF PRF- AND POSTPUBERTAL RABBITS TO COMMERCIALLY AVAILABLE GONADOTROPHINS

The superovulatory response of Dutch-belted does injected with several standard gonadotrophin preparations twice daily for 3 days at 12, 16 and 20 weeks of age and in adult animals was examined to determine the relationship between age, dose and response. The effects of age and the age x treatment interaction were highly significant (P< 0\m=.\01). At 12 weeks of age 0\m=. \31mg and 0\m=. \50mg fsh/day resulted in over\x=req-\ stimulation without ovulation. Prepriming with progesterone apparently counteracted high fsh levels at this age because 0\m=. \125mg fsh with and without progesterone resulted in 16\m=. \8and 1\m=. \8ovulation points respectively. Similar results were obtained at 16 weeks of age, but at 20 weeks of age the number of ovulation points was lower in the progesterone-treated groups. Adult rabbits responded with a mean of 53\m=. \7 ovulations following administration of 0\m=. \50mg of fsh. Overstimulation reduced the rate of egg recovery. This was attributed partially to the effect of endogenous oestrogen production on the rate of egg transport and partially to eggs being trapped in follicles.
New approaches for domain transformation and parameter combination for improved accuracy in parallel model combination (PMC) techniques

Parallel model combination (PMC) techniques have been very successful and popularly used in many applications to improve the performance of speech recognition systems under noisy environments. However, it is believed that some assumptions and approximations made in this approach, primarily in the domain transformation and parameter combination processes, are not necessarily accurate enough in certain practical situations, which may degrade the achievable performance of PMC. In this paper, the possible sources that cause the performance degradation in these processes are carefully analyzed and discussed. Three new approaches, including the truncated Gaussian approach and the split mixture approach for the domain transformation process and the estimated cross-term approach for parameter combination process, are proposed in this paper in order to handle these problems, minimize such degradation, and improve the accuracy of the PMC techniques. These proposed approaches were analyzed and discussed with two recognition tasks, one relatively simple, and the other more complicated and realistic. Both sets of experiments showed that these proposed approaches are able to provide significant improvements over the original PMC method, especially when the SNR condition is worse.
Bacterial Growth Inhibitory Effect of Ceratonia siliqua L. Plant Extracts Alone and in Combination with Some Antimicrobial Agents

Objectives: To evaluate the antibacterial activity of the total extracts, methanolic and water extract of leaves with stems and the pods of Ceratonia siliqua L. each alone and in combination with some antimicrobials on some pathogens. As the wide use of antibiotics in the treatment of bacterial infections has led to the emergence and spread of resistant strains. Many studies showed that the efficacy of antimicrobials can be improved by combining them with crude plant extracts. Materials and Methods: the antibacterial activity of the total extracts, methanolic and water extract of leaves with stems and the pods of Ceratonia siliqua L. each alone and in combination with some antimicrobials was evaluated using well- diffusion method. Cytotoxicity of the total methanolic extract against Huh-7 liver and A-495 lung cancer cell lines was assessed using SRB method. Results: Well diffusion method demonstrates an in-vitro antibacterial activity of the tested extracts against tested microorganisms. Combination of the tested extracts with antimicrobials increased the activity of the tested antimicrobials. A dose dependant effect on both Huh-7 liver and A-495 lung cancer cells was observed. Conclusion: Our results revealed the importance of plant extracts when associated with antibiotics to control resistant bacteria that become a threat to human health. In addition, the tested plant extracts can be exposed for further investigation to be used as hepatoprotective agent.
Talker Discrimination by Prelingually Deaf Children with Cochlear Implants: Preliminary Results

Forty-four school-age children who had used a multichannel cochlear implant (CI) for at least 4 years were tested to assess their ability to discriminate differences between recorded pairs of female voices uttering sentences. Children were asked to respond “same voice” or “different voice” on each trial. Two conditions were examined. In one condition, the linguistic content of the sentence was always held constant and only the talker's voice varied from trial to trial. In another condition, the linguistic content of the utterance also varied so that to correctly respond “same voice,” the child needed to recognize that Two different sentences were spoken by the same talker. Data from normal-hearing children were used to establish that these tasks were well within the capabilities of children without hearing impairment. For the children with CIs, in the “fixed sentence condition” the mean proportion correct was 68%, which, although significantly different from the 50% score expected by chance, suggests that the children with CIs found this discrimination task rather difficult. In the “varied sentence condition,” however, the mean proportion correct was only 57%, indicating that the children were essentially unable to recognize an unfamiliar talker's voice when the linguistic content of the paired sentences differed. Correlations with other speech and language outcome measures are also reported.
Anaplasma marginale Infection with Persistent High-Load Bacteremia Induces a Dysfunctional Memory CD4+ T Lymphocyte Response but Sustained High IgG Titers

ABSTRACT Control of blood-borne infections is dependent on antigen-specific effector and memory T cells and high-affinity IgG responses. In chronic infections characterized by a high antigen load, it has been shown that antigen-specific T and B cells are vulnerable to downregulation and apoptosis. Anaplasma marginale is a persistent infection of cattle characterized by acute and chronic high-load bacteremia. We previously showed that CD4+ T cells primed by immunization with an A. marginale outer membrane protein were rapidly deleted following infection. Furthermore, peripheral blood T cell responses to bacteria were not observed after acute infection was controlled, suggesting dysfunctional T cell priming to other A. marginale antigens. The current study more closely investigated the kinetics of A. marginale-specific CD4+ T cell responses primed during infection. Frequent sampling of peripheral blood and spleens revealed that antigen-specific CD4+ T cell responses were first detected at 5 to 7 weeks, but the responses were sporadic and transient thereafter. A similar pattern was observed in animals sampled weekly for nearly 1 year. Paradoxically, by 2 weeks of infection, cattle had developed high titers of A. marginale-specific IgG, which remained high throughout persistent infection. This dysfunctional CD4+ T cell response to infection is consistent with continual downregulation or deletion of newly primed effector T cells, similar to what was observed for immunization-induced T cells following A. marginale infection. The failure to establish a strong memory T cell response during A. marginale infection likely contributes to bacterial persistence.
Advances in the theory of box integrals

Box integrals - expectations or over the unit n-cube (or n-box) - have over three decades been occasionally given closed forms for isolated n,s. By employing experimental mathematics together with a new, global analytic strategy, we prove that for n {le} 4 dimensions the box integrals are for any integer s hypergeometrically closed in a sense we clarify herein. For n = 5 dimensions, we show that a single unresolved integral we call K{sub 5} stands in the way of such hyperclosure proofs. We supply a compendium of exemplary closed forms that naturally arise algorithmically from this theory.
Cold Start Recommendations : A Non-negative Matrix Factorization Approach

Recommender systems suggest to users items that they might like (e.g., news articles, songs, movies) and, in doing so, they help users deal with information overload and enjoy a personalized experience. One of the main problems of these systems is the cold-start, i.e., when a new item or user is introduced in the system and no past information is available, no effective recommendation can be produced. The cold-start is a very common problem in practice: modern online platforms have hundreds of new items and millions of visits from logged-out users every day. Despite the importance of this problem not many solutions have been proposed in the literature. We contribute to closing this gap by studying whether it could be overcome without sacrificing performance. We do so by exploiting two aspects: the combination of the content and collaborative information, and the users’ location. First, we combine the properties of the items and past user preferences by introducing Joint NMF, a novel recommender system based on Non-negative Matrix Factorization (NMF). We also propose a variation, Joint NMF with Graph Regularization, which accounts for the local geometric structure of the data. We present two training strategies, based on multiplicative update rules and alternating least squares. The experimental results show that the two proposed methods outperform the existing content-based recommenders, which are often used for recommending newly introduced items (item cold-start). Second, to exploit user location, we test whether specific interests are linked to specific locations. To this end, we study the geography of user engagement in online news platforms on a random sample of 200K news articles and the corresponding 41M comments posted on the Yahoo! News website for the USA. We find that time zones play an important role on the user engagement: users from the same time zone preferentially engage with each other on the same articles about the same topics. Thus, we propose a time-zone-aware recommender that suggests the most popular articles not in the whole USA but in the users’ time zones, when no past information of the user preferences is available (user cold-start). We find that suggesting recommendations that are specific to time zones improves the recommendation accuracy by a factor of one point five.