Miracle-dz/UniFAR-FTUs huggingface dataset:
Tuning RNA folding and function through rational design of junction topology

Abstract Structured RNAs such as ribozymes must fold into specific 3D structures to carry out their biological functions. While it is well-known that architectural features such as flexible junctions between helices help guide RNA tertiary folding, the mechanisms through which junctions influence folding remain poorly understood. We combine computational modeling with single molecule Förster resonance energy transfer (smFRET) and catalytic activity measurements to investigate the influence of junction design on the folding and function of the hairpin ribozyme. Coarse-grained simulations of a wide range of junction topologies indicate that differences in sterics and connectivity, independent of stacking, significantly affect tertiary folding and appear to largely explain previously observed variations in hairpin ribozyme stability. We further use our simulations to identify stabilizing modifications of non-optimal junction topologies, and experimentally validate that a three-way junction variant of the hairpin ribozyme can be stabilized by specific insertion of a short single-stranded linker. Combined, our multi-disciplinary study further reinforces that junction sterics and connectivity are important determinants of RNA folding, and demonstrates the potential of coarse-grained simulations as a tool for rationally tuning and optimizing RNA folding and function.
Inhibition of ovarian cancer cell proliferation by a cell cycle inhibitory peptide fused to a thermally responsive polypeptide carrier

Current treatment of solid tumors is limited by normal tissue tolerance, resulting in a narrow therapeutic index. To increase drug specificity and efficacy and to reduce toxicity in normal tissues, we have developed a polypeptide carrier for a cell cycle inhibitory peptide, which has the potential to be thermally targeted to the tumor site. The design of this polypeptide is based on elastin‐like polypeptide (ELP). The coding sequence of ELP was modified by the addition of the cell penetrating peptide Bac‐7 at the N‐terminus and a 23 amino acid peptide derived from p21 at the C‐terminus (Bac‐ELP1‐p21). Bac‐ELP1‐p21 is soluble in aqueous solutions below physiological temperature (37°C) but aggregates when the temperature is raised above 39°C, making it a promising thermally responsive therapeutic carrier that may be actively targeted to solid tumors by application of focused hyperthermia. While Bac‐ELP1‐p21 at 37°C did not have any effect on SKOV‐3 cell proliferation, the use of hyperthermia increased the antiproliferative effect of Bac‐ELP1‐p21 compared with a thermally unresponsive control polypeptide. Bac‐ELP1‐p21 displayed both a cytoplasmic and nuclear distribution in the SKOV‐3 cells, with nuclear‐localized polypeptide enriched in the heated cells, as revealed by confocal microscopy. Using Western blotting, we show that Bac‐ELP1‐p21 caused a decrease in Rb phosphorylation levels in cells treated at 42°C. The polypeptide also induced caspase activation, PARP cleavage, and cell cycle arrest in S‐phase and G2/M‐phase. These studies indicate that ELP is a promising macromolecular carrier for the delivery of cell cycle inhibitory peptides to solid tumors.
Happiness, Personal Income, and National Income: New Evidence from Taiwan

This study explores the relationship between income and happiness using data from Taiwan. It also proposes a two-stage estimation method for studying the macroeconomics of happiness. The study finds that while personal income has a strong positive effect on individual happiness, national income fails to have any significant effect in either the short run or the long run. This finding agrees with the Easterlin paradox, and suggests that recessions do not reduce happiness in Taiwan.
Reduction of the Posterior Column in Displaced Acetabulum Fractures Through the Anterior Intrapelvic Approach

Summary: The anterior intrapelvic approach can be used for the reduction and fixation of displaced fractures of the acetabulum. Reduction techniques and options for placement of fixation deviate to some degree from those used with the traditional ilioinguinal approach secondary to the surgeon's perspective and available vectors. Here, we present several techniques for the application of reduction clamps, reduction techniques, and fixation options for the posterior column in displaced fractures of the acetabulum treated through the anterior intrapelvic approach.
The Stochastic Volatility Model, Regime Switching and Value-at-Risk (VaR) in International Equity Markets

In this paper, we estimate two stochastic volatility models applied to international equity markets. The two models are the log-normal stochastic volatility (SV) model and the two-regime switching model. Then based on the one-day-ahead forecasted volatility from each model, we calculate the Value-at-Risk (VaR) in each market. The estimated VaR measures from the SV are higher than those obtained from the regime-switching model for all markets and over all horizons. The exception is the Japanese market, where the stochastic volatility model generates low VaR estimates. Comparing those estimates with the unconditional return distribution, the two models generate smaller VaR measures; an evidence of the two models capturing volatility changes in international equity markets. Finally, we backtest each model and find that the performance of both models is the worst for the Canadian stock market, while the regime switching model does poorly for Germany. The results have significant implications for risk management, trading and hedging activities as well as in the pricing of equity derivatives.
Glutathione Oxidation Is Associated With Airway Macrophage Functional Impairment in Children With Severe Asthma

Airway cellular dysfunction is a differentiating feature of severe asthma in children that may be related to an imbalance of the antioxidant, glutathione (GSH). We hypothesized that oxidation of GSH to glutathione disulfide (GSSG) in the epithelial lining fluid (ELF) of children with severe asthma would contribute to altered airway macrophage (AM) GSH homeostasis and AM cellular dysfunction. Bronchoalveolar lavage (BAL) was performed in 64 asthmatic children (severe asthma, n = 43). GSH, GSSG, markers of lipid peroxidation and DNA oxidation, and IL-8 were quantified in the BAL supernatant. GSH, GSSG, activities of histone deacetylase (HDAC) and histone acetyltransferase, apoptosis, and phagocytosis were assessed in isolated AMs. Children with severe asthma had increased GSSG, lipid peroxidation, byproducts of DNA oxidation, and inflammation in the ELF. This imbalance of GSH homeostasis was also noted intracellularly within the AMs and was associated with decreased HDAC activities, increased apoptosis, and impaired phagocytosis. In vitro GSH supplementation inhibited apoptosis and rescued phagocytosis in children with severe asthma. Severe asthma in children is characterized by altered airway and intracellular AM GSH homeostasis that translates to impaired AM function. Interventions to restore airway GSH homeostasis may be warranted in children with severe asthma.
Assessing patient safety culture in New Zealand primary care: a pilot study using a modified Manchester Patient Safety Framework in Dunedin general practices.

INTRODUCTION Patient safety is a major concern, both in hospitals and in primary care settings. The current focus internationally is on the prospect of improving patient safety through cultural transformation. There are no tools designed to assess and strengthen safety culture in New Zealand (NZ) general practices, but a United Kingdom (UK) group have developed a tool--the Manchester Patient Safety Framework (MaPSaF)--to assess safety culture in UK Primary Care Trusts. We aimed to modify the MaPSaF and test its acceptability and utility in the NZ primary care setting. METHODS We modified the MaPSaF to suit the NZ context and then used it in 12 Dunedin general practices at baseline and at three months. Participants were all practice personnel present in the practice on the day. Participants rated their practice individually on each of the nine MaPSaF dimensions of safety culture, then discussed the dimensions and their scores and chose a practice-wide consensus score for each dimension in turn. These discussions were recorded, transcribed and analysed to determine acceptability and utility of the modified framework in NZ practices. FINDINGS The framework process took about one hour. Most participants found the process acceptable and useful. The framework directed team discussion about patient safety issues and facilitated communication and prompted some practices to make changes. Some participants from smaller practices deemed the systems advocated in the framework superfluous. CONCLUSION The framework can be adapted and used in NZ practices to stimulate learning about safety culture and to facilitate team communication.
A generic construction of ciphertext-policy attribute-based encryption supporting attribute revocation

Attribute-based encryption is drawing more attention with its inherent attractive properties which are potential to be widely used in the newly developing cloud computing. However, one of the main obstacles for its application is how to revoke the attributes of the users, though some ABE schemes have realized revocation, they mostly focused on the user revocation that revokes the user's whole attributes, or attribute revocation under the indirect revocation model such that all the users' private keys will be affected by the revocation. In this paper,we define the model of CP-ABE supporting the attribute revocation under the direct revocation model, in which the revocation list is embed in the ciphertext and none of the users' private keys will be affected by the revocation process. Then we propose a generic construction, and prove its security with the decision q-BDHE assumption.
Application of Decision-Tree Induction Techniques to Personalized Advertisements on Internet Storefronts

Customization and personalization services are a critical success factor for Internet stores and Web service providers. This paper studies personalized recommendation techniques that suggest products or services to the customers of Internet storefronts based on their demographics or past purchasing behavior. The underlining theories of recommendation techniques are statistics, data mining, artificial intelligence, and rule-based matching. In the rule-based approach to personalized recommendation, marketing rules for personalization are usually obtained from marketing experts and used to perform inferencing based on customer data. However, it is difficult to extract marketing rules from marketing experts, and to validate and maintain the constructed knowledge base. This paper proposes a marketing rule-extraction technique for personalized recommendation on Internet storefronts using machine learning techniques, and especially decisiontree induction techniques. Using tree induction techniques, data-mining tools can generate marketing rules that match customer demographics to product categories. The extracted rules provide personalized advertisement selection when a customer visits an Internet store. An experiment is performed to evaluate the effectiveness of the proposed approach with preference scoring and random selection.
Intrinsic Liquidity in Conditional Volatility Models

Until recently the liquidity of financial assets has typically been viewed as a second-order consideration. Liquidity was frequently associated with simple transaction costs that impose ? temporary if any ? effect on asset prices, and whose shocks could be easily diversified away. Yet the evidence ? especially the recent liquidity crisis ? suggests that liquidity is now a primary concern. This paper aims at disentangling market risk and liquidity risk in the context of conditional volatility models. Our approach allows the isolation of the intrisic liquidity of any asset, and thus makes it possible to deduce a liquidity risk even when volumes are not observed.
Load modeling in power system studies: WECC progress update

This paper provides an update on a composite load model development in Western Electricity Coordinating Council (WECC). A composite load model structure is described. The two salient features of the new load model are: (a) the model recognizes electrical distance between the transmission bus and the end-uses and (b) the model represents the diversity in composition and dynamic characteristics of various electrical end-uses. The load model data includes (a) data for a distribution equivalent model, (b) load component model data and (c) load component fractions. The paper presents tests and modeling of various electrical end-uses. The paper in particular focuses on modeling compressor motors in single-phase air-conditioners. Load composition methodology is also discussed. The model structure was implemented and tested in a production-level grid simulator.
Use of “Knowledge House”, DWS, DMS and DSS methodology by completing a competitors' analysis in the railway sector

In completing a competitors’ analysis in the railway sector by using the “Knowledge House” method, there is frequently a problem of data and information accessibility. The quality of primary information has direct influence on the quality of analytical conclusions. One more condition for the qualitative application of this method is the intellectual capital and experience of the analyst. One should note that in this regard we face another problem, that of selection of proper personnel, on the qualification of whom depends the accuracy of the evaluation and final results, on the basis of which strategic decisions are taken. The main aim of the paper is to assess the opportunities for applications of competitive intelligence methods in the railway sector. The study is using “Knowledge House”, DWS, DMS, DSS methodologies.Having analysed the scientific works the direct scientific sources of information, which are oriented to the application of the methods of competitive intelligence to the railway sector, have not been identified. The paper is absolutely original in that until now the competitive intelligence techniques have not been applied for the railway sector companies.Considering the fact that foreign companies, which compete for freighting at the international level, are regarded as the main competitors of the railway sector, the use of the methods of the competitive intelligence becomes more important while fighting for the part of the market. The competitive intelligence methods and their application to the railway sector companies are little studied. In accordance with application of the relevant methods in other sectors, it can be assumed that these innovative approaches could have a positive impact on the competitiveness of companies in the railway sector and their income.
Conformational and biochemical analysis of the cyclic peptides which modulate serine protease activity

Prostate‐specific antigen (PSA), a member of the kallikrein sub‐group of the trypsin serine protease family, is a widely used marker for prostate cancer. Several sequences with specific binding to PSA have been identified by using phage display peptide libraries. The GST‐fusion proteins of the characterized sequences have been shown to increase the enzyme activity of PSA to a synthetic substrate. The corresponding three cyclic synthetic analogues CVFTSNYAFC (A‐1), CVFAHNYNYLVC (B‐2) and CVAYCIEHHCWTC (C‐4) have similar PSA promoting activity. Despite differences in the amino acid sequences, all three peptides bind to the same region of PSA. The conformation of the peptides was investigated by proton NMR spectroscopy. In addition, alanine replacement was used to characterize the prerequisites for binding. It is proposed that interactions with PSA are based on the aromatic and hydrophobic features of the amino acid side chains. Furthermore, it is suggested that peptides form β–turn structures forced by cysteine bridges directing important aromatic side chains to the same side of the turn‐structure. Copyright © 2004 European Peptide Society and John Wiley & Sons, Ltd.
Dichloroacetate- and trichloroacetate-induced modulation of superoxide dismutase, catalase, and glutathione peroxidase activities and glutathione level in the livers of mice after subacute and subchronic exposures

Dichloroacetate (DCA) and trichloroacetate (TCA) were previously found to induce various levels of oxidative stress in the hepatic tissues of mice after subacute and subchronic exposures. The cells are known to have several protective mechanisms against production of oxidative stress by different xenobiotics. To assess the roles of the antioxidant enzymes and glutathione (GSH) in DCA- and TCA-induced oxidative stress, groups of B6C3F1 mice were administered either DCA or TCA at doses of 7.7, 77, 154, and 410 mg kg−1 day−1, by gavage for 4 weeks (4-W) and 13 weeks (13-W), and superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-Px) activities, as well as GSH were determined in the hepatic tissues. DCA at doses ranging between 7.7–410, and 7.7–77 mg kg−1 day−1, given for 4-W and 13-W, respectively, resulted in either suppression or no change in SOD, CAT, and GSH-Px activities, but doses of 154–410 mg DCA kg−1 day−1 administered for 13-W were found to result in a significant induction of the three enzyme activities. TCA administration on the other hand, resulted in increases in the SOD and CAT activities, but caused suppression of GSH-Px activity in both the periods. Except for the DCA doses of 77–154 mg kg−1 day−1 administered for 13-W that resulted in a significant reduction in the GSH levels, all other DCA as well as TCA treatments produced no changes in GSH. Since these enzymes are involved in the detoxification of the reactive oxygen species (ROS), superoxide anion (SA), and H2O2, it is concluded that SA is the main contributor to DCA-induced oxidative stress, while both ROS contribute to that of TCA. The increase in the enzyme activities associated with 154–410 mg DCA kg1− day−1 in the 13-W period suggest their role as protective mechanisms contributing to the survival of cells modified in response to those treatments.
Remote condition monitoring of a PV system using an embedded web server

The architecture and construction of a simple embedded web server system with due account of its application for remote condition monitoring of a photovoltaic (PV) installation is presented. The system, which is based on a PIC18 microcontroller, uses the Internet as a medium for communications between a central control point and a PV system. It allows various parameters of a PV installation such as the temperature of an individual PV module and its open-circuit voltage to be remotely accurately measured and monitored. This permits early detection of any technical problem such as a faulty PV module to be communicated over the Internet to a desired location. Inspection of the PV system is also possible from any Internet enabled computer terminal.
The safety and efficacy of anterior cervical discectomy and fusion with polyetheretherketone spacer and recombinant human bone morphogenetic protein-2: a review of 200 patients.

OBJECT The goal in this study was to demonstrate the safety and efficacy of anterior cervical discectomy and fusion ([ACDF]; single- or multilevel procedure) performed using titanium plates and polyetheretherketone (PEEK) spacers filled with recombinant human bone morphogenetic protein-2 (rhBMP-2) impregnated in a type I collagen sponge to achieve fusion. METHODS The authors retrospectively reviewed 200 patients who underwent a single- or multilevel ACDF with titanium plate fixation and PEEK spacer filled with a collagen sponge impregnated with low-dose rhBMP-2. Clinical outcomes were assessed using pre- and postoperative Nurick grades and the Odom criteria. Radiographic outcomes were assessed using dynamic radiographs and computed tomography (CT) scans. RESULTS The follow-up period ranged from 8 to 36 months (mean 16.7 months). A single-level ACDF was performed in 96 patients, 2-level ACDF in 62 patients, 3-level ACDF in 36 patients, and 4-level ACDF in 6 patients. Long-term follow-up was available for 193 patients. The Odom outcomes were rated as good to excellent in 165 patients (85%), fair in 24 (12.4%), and poor in 4 (2%). Among patients with myelopathy, Nurick grades improved from a preoperative mean of 1.42 to a postoperative mean of 0.26. All patients (100%) achieved solid radiographic fusion on dynamic radiographs and CT scans. Fourteen patients (7%) in this series experienced clinically significant dysphagia, and 4 (2%) required repeated operation for hematoma or seroma. CONCLUSIONS An ACDF performed using a PEEK spacer filled with rhBMP-2 leads to good to excellent clinical outcomes and solid fusion, even in multilevel cases and in patients who are smokers. The incidence of symptomatic dysphagia may be decreased with a lower dose of rhBMP-2 that is placed only within the PEEK spacer.
A Study on India Volatility Index (VIX) and its Performance as Risk Management Tool in Indian Stock Market

This study is aimed at examining the relationship between India VIX and NIFTY and to examine the usefulness of volatility index as risk management tool for stock market trading. It is found that relationship between NIFTY and VIX is strong when market is moving down and vice a versa. I observed that two indices moved in opposite direction. The linear association between the India VIX and NIFTY is statistically significant. The result indicated that statistically significant relationship exist between percentage change in the level of India VIX and rates of returns for various holding periods on index future contract on CNX Nifty Index and CNX midcap 50 Index. In terms of trading strategies it is found that portfolio performance can be improved by shifting the portfolio from midcap to large cap stocks when India VIX goes up and shifting the portfolio from large-cap to mid-cap when India VIX goes down.
On the Potential of Functional Relational Databases

Database management systems deal with numerous aspects of data storage: data versioning, access control, validation, querying etc. They may do so by offering features that allow the user to specify the data model and express the desired system behaviour: SQL, tables, views, triggers, stored procedures, user-defined types and functions. These features add complexity to the DBMS as well as the data model. We propose the “functional database” as a more generic and elegant solution to dealing with various database aspects. The “functional database” leverages features of the functional paradigm, such as function composition and treating functions as “first-class citizens”. We have adopted the relational data model as foundation for our functional database but we reckon other data models may be just as adequate. The relational model is implemented with a number of abstractions (contextdependence, lifting and decorating) to allow composition. Other database aspects, such as data validation and access control, may then be implemented with these abstractions, and composed (i.e., “stacked”) to create a more complete database system.