Miracle-dz/UniFAR-FTUs huggingface dataset:
ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms

MOTIVATION RNA-Seq technology is promising to uncover many novel alternative splicing events, gene fusions and other variations in RNA transcripts. For an accurate detection and quantification of transcripts, it is important to resolve the mapping ambiguity for those RNA-Seq reads that can be mapped to multiple loci: >17% of the reads from mouse RNA-Seq data and 50% of the reads from some plant RNA-Seq data have multiple mapping loci. In this study, we show how to resolve the mapping ambiguity in the presence of novel transcriptomic events such as exon skipping and novel indels towards accurate downstream analysis. We introduce ORMAN ( O ptimal R esolution of M ultimapping A mbiguity of R N A-Seq Reads), which aims to compute the minimum number of potential transcript products for each gene and to assign each multimapping read to one of these transcripts based on the estimated distribution of the region covering the read. ORMAN achieves this objective through a combinatorial optimization formulation, which is solved through well-known approximation algorithms, integer linear programs and heuristics. RESULTS On a simulated RNA-Seq dataset including a random subset of transcripts from the UCSC database, the performance of several state-of-the-art methods for identifying and quantifying novel transcripts, such as Cufflinks, IsoLasso and CLIIQ, is significantly improved through the use of ORMAN. Furthermore, in an experiment using real RNA-Seq reads, we show that ORMAN is able to resolve multimapping to produce coverage values that are similar to the original distribution, even in genes with highly non-uniform coverage. AVAILABILITY ORMAN is available at http://orman.sf. net
Economic Valuation of R&D Programs in Consideration of Strategic Flexibility

Under the circumstances of increasing uncertainty, strategic flexibility has become an essential element on which any R&D management system should be based. Unfortunately, however, the present R&D management system for government sponsored R&D programs cannot be said to be flexible enough to effectively respond to various threats such as technological failure, significant changes in competition environment, and so on. This paper presents a new scheme for R&D planning and economic assessment with strategic flexibility, which has been applied to a real R&D program. According to the newly presented R&D management system, economic valuation has been conducted for various alternative scenarios based on real option theory. Each of the alternative scenarios has different scheme for R&D process and the assessment results has been fed back to choose superior strategic scheme. In conclusion, introducing strategic flexibility into R&D planning and economic assessment can enhance the value of R&D project remarkably.
Delta-neutral dynamic hedging of the HS300 stock index futures and option portfolio — The evidence from simulation

The launch of Shanghai-Shenzhen 300 index futures can not only supply the hedging tools and liquidity, but also bring some new kind of risk. The principal of this research is to analyze the risk hedging policy of the index futures using various kinds of dynamic hedging portfolios of index futures and index options with the same underlying index. Firstly, we developed a delta-neutral dynamic hedging model of the stock index futures/option portfolio in a perfect market; Secondly, we completed the daily and weekly adjusting of dynamic delta-neutral hedging and proposed the dynamic-neutral adjusting strategy: adjusting continuously the stock index futures position to achieve zero-delta of the portfolios on the basis of the prerequisite of keeping the stock index option position constant. The results of this analysis show that a protective “delta-neutral” strategy produces a more effective hedge than the other hedging examined, daily adjusting is optimal. Thus, we further suggest that with the steady operation of Shanghai-Shenzhen 300 stock index futures, China could launch the stock index options in due time, thus to provide developing strategy for the stock index derivatives markets.
Bond Supply and Excess Bond Returns in Zero�?Lower Bound and Normal Environments: Evidence from Japan

We estimate a discrete-time version of Vayanos and Vila’s (2009) preferred habitat model, using Japanese government bond yield data. The estimated results indicate that bond excess returns become more sensitive to supply factors in the absence of a zero lower bound constraint unless arbitrageurs become willing to take on more risk.
A Reliable Method for Disseminating Safety Information in Vehicular Ad Hoc Networks Considering Fragmentation Problem

Many of applications in vehicular ad hoc networks (VANET) are based on dissemination of information, so broadcasting is a fundamental service in these networks. Broadcasting is a difficult task since vehicular networks often lack continuous end-to-end connectivity and have large variations in node densities. In this paper we present a method that improves the reception rates of broadcast messages by overcoming problem of connectivity gaps. In our method, every forwarder of message when facing a gap sends small messages periodically. These methods are used to understand entrance of a new vehicle that can be selected as the next forwarder of message. We have evaluated the performance of proposed protocol in NS2 under various network conditions.
Association of overweight with increased risk of coronary heart disease partly independent of blood pressure and cholesterol levels: a meta-analysis of 21 cohort studies including more than 300 000 persons.

BACKGROUND The extent to which moderate overweight (body mass index [BMI], 25.0-29.9 [calculated as weight in kilograms divided by height in meters squared]) and obesity (BMI, >/= 30.0) are associated with increased risk of coronary heart disease (CHD) through adverse effects on blood pressure and cholesterol levels is unclear, as is the risk of CHD that remains after these mediating effects are considered. METHODS Relative risks (RRs) of CHD associated with moderate overweight and obesity with and without adjustment for blood pressure and cholesterol concentrations were calculated by the members of a collaboration of prospective cohort studies of healthy, mainly white persons and pooled by means of random-effects models (RRs for categories of BMI in 14 cohorts and for continuous BMI in 21 cohorts; total N = 302 296). RESULTS A total of 18 000 CHD events occurred during follow-up. The age-, sex-, physical activity-, and smoking-adjusted RRs (95% confidence intervals) for moderate overweight and obesity compared with normal weight were 1.32 (1.24-1.40) and 1.81 (1.56-2.10), respectively. Additional adjustment for blood pressure and cholesterol levels reduced the RR to 1.17 (1.11-1.23) for moderate overweight and to 1.49 (1.32-1.67) for obesity. The RR associated with a 5-unit BMI increment was 1.29 (1.22-1.35) before and 1.16 (1.11-1.21) after adjustment for blood pressure and cholesterol levels. CONCLUSIONS Adverse effects of overweight on blood pressure and cholesterol levels could account for about 45% of the increased risk of CHD. Even for moderate overweight, there is a significant increased risk of CHD independent of these traditional risk factors, although confounding (eg, by dietary factors) cannot be completely ruled out.
Multifunctional role of Tyr 108 in the catalytic mechanism of human glutathione transferase P1-1. Crystallographic and kinetic studies on the Y108F mutant enzyme.

The possible role of the hydroxyl group of Tyr 108 in the catalytic mechanism of human glutathione transferase P1-1 has been investigated by means of site-directed mutagenesis, steady-state kinetic analysis, and crystallographic studies. Three representative cosubstrates have been used, i.e. ethacrynic acid, 7-chloro-4-nitrobenz-2-oxa-1,3-diazole, and 1-chloro-2,4-dinitrobenzene. In the presence of ethacrynic acid, the enzyme follows a rapid equilibrium random bi-bi mechanism with a rate-limiting step which occurs after the addition of the substrates and before the release of products. The replacement of Tyr 108 with Phe yields a 14-fold decrease of k(cat), while it does not change appreciably the affinity of the H site for the substrate. In this case, it would appear that the role of the hydroxyl function is to stabilize the transition state for the chemical step, i.e. the Michael addition of GSH to the electrophilic substrate. Crystallographic data are compatible with this conclusion showing the hydroxyl group of Y108 in hydrogen bonding distance of the ketone moiety of ethacrynic acid [Oakley, A. J., Rossjohn, J., Lo Bello, M. , Caccuri, A. M. , Federici, G. , & Parker, M. W. (1997) Biochemistry 36, 576-585]. Moreover, no structural differences are observed between the Y108F mutant and the wild type, suggesting that the removal of the hydroxyl group is solely responsible for the loss of activity. A different involvement of Tyr 108 appears in the catalyzed conjugation of 7-chloro-4-nitrobenz-2-oxa-1,3-diazole with GSH in which the rate-limiting step is of a physical nature, probably a structural transition of the ternary complex. The substitution of Tyr 108 yields an approximately 7-fold increase of k(cat) and a constant k(cat)/Km(NBD-Cl) value. Lack of a critical hydrogen bond between 7-chloro-4-nitrobenz-2-oxa-1,3-diazole and Tyr 108 appears to be the basis of the increased k(cat). In the 1-chloro-2,4-dinitrobenzene/GSH system, no appreciable changes of kinetics parameters are found in the Y108F mutant. We conclude that Y108 has a multifunctional role in glutathione transferase P1-1 catalysis, depending on the nature of the electrophilic cosubstrate.
Concept-based query language approach to enterprise information systems

In enterprise information systems (EISs) it is necessary to model, integrate and compute very diverse data. In advanced EISs the stored data often are based both on structured (e.g. relational) and semi-structured (e.g. XML) data models. In addition, the ad hoc information needs of end-users may require the manipulation of data-oriented (structural), behavioural and deductive aspects of data. Contemporary languages capable of treating this kind of diversity suit only persons with good programming skills. In this paper we present a concept-oriented query language approach to manipulate this diversity so that the programming skill requirements are considerably reduced. In our query language, the features which need technical knowledge are hidden in application-specific concepts and structures. Therefore, users need not be aware of the underlying technology. Application-specific concepts and structures are represented by the modelling primitives of the extended RDOOM (relational deductive object-oriented modelling) which contains primitives for all crucial real world relationships (is-a relationship, part-of relationship, association), XML documents and views. Our query language also supports intensional and extensional–intensional queries, in addition to conventional extensional queries. In its query formulation, the end-user combines available application-specific concepts and structures through shared variables.
Early Breastfeeding Experiences and Postpartum Depression

BACKGROUND: The first weeks after childbirth are a critical period for mother and newborn. Women may present with lactation failure and postpartum depression. It is unclear how a woman's early breastfeeding experiences relate to postpartum depression. OBJECTIVE: We estimated the association between early breastfeeding experiences and postpartum depression at 2 months. METHODS: We modeled this association with logistic regression in a secondary analysis of data from the Infant Feeding Practices Study II. We assessed postpartum depression status with the Edinburgh Postnatal Depression Scale. RESULTS: In the neonatal period, 2,586 women reported ever breastfeeding, among whom 223 (8.6%) met criteria for major depression (Edinburgh Postnatal Depression Scale 13 or greater) at 2 months postpartum. Women who disliked breastfeeding in the first week were more likely to experience postpartum depression at 2 months (odds ratio [OR] 1.42, 95% confidence interval [CI] 1.04–1.93) adjusting for maternal age, parity, education, ethnicity, and postnatal WIC participation. Women with severe breastfeeding pain in the first day (adjusted OR 1.96, 95% CI 1.17–3.29), the first week (adjusted OR 2.13, 95% CI 0.74–6.15 compared with no pain), and the second week (adjusted OR 2.24, 95% CI 1.18–4.26 compared with no pain) were more likely to be depressed. Breastfeeding help appeared protective among women with moderate (adjusted OR 0.22, 95% CI 0.05–0.94) or severe (adjusted OR 0.17, 95% CI 0.04–0.75) pain with nursing. CONCLUSION: Women with negative early breastfeeding experiences were more likely to have depressive symptoms at 2 months postpartum. Women with breastfeeding difficulties should be screened for depressive symptoms. LEVEL OF EVIDENCE: II
All-Optical Generation of Two IEEE802.11n Signals for 2  $\times$ 2 MIMO-RoF via MRR System

A radio-over-fiber system capable of very spectrally efficient data transmission and based on multiple-input multiple-output (MIMO) and orthogonal frequency-division multiplexing (OFDM) is presented here. Carrier generation is the basic building block for implementation of OFDM transmission, and multicarriers can be generated using the microring resonator (MRR) system. A series of MRRs incorporated with an add/drop filter system was utilized to generate multicarriers in the 193.00999-193.01001-THz range, which were used to all-optically generate two MIMO wireless local area network radio frequency (RF) signals suitable for the IEEE802.11n standard communication systems, and single wavelengths at frequencies of 193.08, 193.1, and 193.12 THz with free spectral range of 20 GHz used to optically transport the separated MIMO signals over a single-mode fiber (SMF). The error vector magnitude (EVM) and bit error rate of the overall system performance are discussed. Results show that the generated RF signals wirelessly propagated through the MIMO channel using the 2 × 2 MIMO Tx antennas. There is an acceptable EVM variation for wireless distance lower than 70, 30, and 15 m. It can be concluded that the transmission of both MIMO RF signals is feasible for up to a 50-km SMF path length and a wireless distance of 15 m.
The Moderating Effect of Marijuana Use on the Relationship Between Delinquent Behavior and HIV Risk Among Adolescents in Foster Care

Adolescents in foster care experience mental health and substance use problems that place them at risk for HIV, yet the exact nature of the relationship remains unclear. This study examined the co-occurring influences of mental health problems and substance use on HIV risk and determined whether substance use moderated the effect of mental health problems on HIV risk behaviors among adolescents in foster care. Regression analyses of cross-sectional data collected through structured interviews with 334 adolescents, aged 15 to 18 years, determined which mental health problems and substances increased HIV risk behaviors. Adolescents with delinquency and anxiety/depression engaged in significantly more HIV risk behaviors than their counterparts, controlling for race, gender, and type of childhood abuse. Further, any marijuana use significantly moderated the effects of delinquent behaviors on HIV risk, differentially increasing HIV risk among those who engaged in delinquent behaviors.
Multiple sugar: phosphotransferase system permeases participate in catabolite modification of gene expression in Streptococcus mutans

Streptococcus mutans is particularly well adapted for high‐affinity, high‐capacity catabolism of multiple carbohydrate sources. S. mutansenzyme II (EIILev), a fructose/mannose permease encoded by the levDEFG genes, and fruA, which encodes a hydrolase that releases fructose from fructan polymers, are transcriptionally regulated by the LevQRST four‐component signal transduction system. Here, we demonstrate that: (i) levDEFGX are co‐transcribed and the levE/F intergenic region is required for optimal expression of levFGX; (ii) D‐mannose is a potent inducer of the levD and fruA operons; (iii) CcpA regulates levD expression in a carbohydrate‐specific manner; (iv) deletion of the genes for the fructose/mannose‐EII enzymes of S. mutans (manL, fruI and levD) enhances levD expression; (v) repression of the LevQRST regulon by EII enzymes depends on the presence of their substrates and requires LevR, but not LevQST; and (vi) CcpA inhibits expression of the manL and fruI genes to indirectly control the LevQRST regulon. Further, the manL, ccpA, fruI/fruCD and levD gene products differentially exert control over the cellobiose and lactose operons. Collectively, the results reveal the existence of a global regulatory network in S. mutans that governs the utilization of non‐preferred carbohydrates in response to the availability and source of multiple preferred carbohydrates.
ACCOUNTING FOR TURBULENCE DESTRUCTION IN THE FLOW OVER FORESTS

Large-eddy simulations of the flow over a long homogeneous forest were used to calibrate the canopy related terms in a RaNS k−e turbulence model. It was found that the canopy drag always acts to decrease both the turbulent kinetic energy and its dissipation. The flow across a forest edge was used to see whether the model was also accurate in a more complex flow, with a finite length forest. The effects of the canopy were overestimated in an initial part, but, overall, the accuracy approached the levels found in the case of the long forest.
Corrupt Bureaucrats: The Response of Non-Elected Officials to Electoral Accountability

Modern state bureaucracies are designed to be insulated from political interference. Successful insulation implies that politicians' electoral incentives do not affect bureaucrats' corruption. I test this prediction by assembling a unique dataset on corruption, promotions and demotions for more than 4 million Indonesian local civil servants. To identify the effect of reelection incentives, I exploit the existence of term limits and a difference-indifference strategy. I find that reelection incentives decrease the corruption behaviour of both top and administrative bureaucrats, which constitutes new evidence of the deep, farreaching effects of politicians' accountability on local civil servants. I explore a mechanism where bureaucrats have career concerns and politicians facing reelection manipulate such concerns by increasing the turnover of top bureaucrats. Consistent with this mechanism, I find that reelection incentives increase demotions of top bureaucrats and promotions of administrative bureaucrats.
Microfluidic radiosynthesis and biodistribution of [18 F] 2-(5-fluoro-pentyl)-2-methyl malonic acid.

Microfluidics technology has emerged as a powerful tool for the radiosynthesis of positron emission tomography (PET) and single-photon emission computed tomography radiolabeled compounds. In this work, we have exploited a continuous flow microfluidic system (Advion, Inc., USA) for the [(18) F]-fluorine radiolabeling of the malonic acid derivative, [(18) F] 2-(5-fluoro-pentyl)-2-methyl malonic acid ([(18) F]-FPMA), also known as [(18) F]-ML-10, a radiotracer proposed as a potential apoptosis PET imaging agent. The radiosynthesis was developed using a new tosylated precursor. Radiofluorination was initially optimized by manual synthesis and served as a basis to optimize reaction parameters for the microfluidic radiosynthesis. Under optimized conditions, radio-thin-layer chromatography analysis showed 79% [(18) F]-fluorine incorporation prior to hydrolysis and purification. Following hydrolysis, the [(18) F]-FPMA was purified by C18 Sep-Pak, and the final product was analyzed by radio-HPLC (high-performance liquid chromatography). This resulted in a decay-corrected 60% radiochemical yield and ≥98% radiochemical purity. Biodistribution data demonstrated rapid blood clearance with less than 2% of intact [(18) F]-FPMA radioactivity remaining in the circulation 60 min post-injection. Most organs showed low accumulation of the radiotracer, and radioactivity was predominately cleared through kidneys (95% in 1 h). Radio-HPLC analysis of plasma and urine samples showed a stable radiotracer at least up to 60 min post-injection.
Accuracy evaluation of GEM5 simulator system

Design space exploration (DSE) of complex embedded systems that combine a number of CPUs, dedicated hardware and software is a tedious task for which a broad range of approaches exists, from the use of high-level models to hardware prototyping. Each of these entails different simulation speed/accuracy tradeoffs, and thereby enables exploring a certain subset of the design space in a given time. Some simulation frameworks devoted to CPU-centric systems have been developed over the past decade, that either feature near real-time simulation speed or moderate to high speed with quasi-cycle level accuracy, often by means of instruction-set simulators or binary translation techniques. This paper presents an evaluation in term of accuracy in modeling real systems using the GEM5 simulator that belong to the first class. Performance figures of a wide range of benchmarks (e.g. in domains such as scientific computing and media applications) are captured and compared to results obtained on real hardware.
Enhancing ISP network reliability with multi-criteria decision framework and genetic algorithm

This paper presents a multi-criteria decision model and multi-criteria genetic algorithm (MCGA) approach to improve backbone topology by leveraging the virtual link (VL) system in an hierarchical link-state (LS) routing domain. Given that the sound backbone topology structure has a great impact on the overall routing performance in an hierarchical LS domain, the importance of this research is evident. The proposed decision model is to find an optimal configuration of VLs that properly meets two-pronged engineering goals in installing and maintaining VLs: i.e., operational costs and network reliability. The experiment results clearly indicates that it is essential to the effective operations of hierarchical LS routing domain to consider not only engineering aspects but also specific benefits from systematical layout of VLs, thereby presenting the validity of the decision model and MCGA