Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction of Conserved Precursors of miRNAs and Their Mature Forms by Integrating Position-Specific Structural Features

MicroRNA (miRNA) precursor hairpins have a unique secondary structure, nucleotide length, and nucleotide content that are in most cases evolutionarily conserved. The aim of this study was to utilize position-specific features of miRNA hairpins to improve their identification. To this end, we defined the evolutionary and structurally conserved features in each position of miRNA hairpins with heuristically derived values, which were successfully integrated using a probabilistic framework. Our method, miRRim2, can not only accurately detect miRNA hairpins, but infer the location of a mature miRNA sequence. To evaluate the accuracy of miRRim2, we designed a cross validation test in which the whole human genome was used for evaluation. miRRim2 could more accurately detect miRNA hairpins than the other computational predictions that had been performed on the human genome, and detect the position of the 5′-end of mature miRNAs with sensitivity and positive predictive value (PPV) above 0.4. To further evaluate miRRim2 on independent data, we applied it to the Ciona intestinalis genome. Our method detected 47 known miRNA hairpins among top 115 candidates, and pinpointed the 5′-end of mature miRNAs with sensitivity and PPV about 0.4. When our results were compared with deep-sequencing reads of small RNA libraries from Ciona intestinalis cells, we found several candidates in which the predicted mature miRNAs were in good accordance with deep-sequencing results.
Geometry of abstraction in quantum computation

Quantum algorithms are sequences of abstract operations, per­ formed on non-existent computers. They are in obvious need of categorical semantics. We present some steps in this direction, following earlier contribu­ tions of Abramsky, Goecke and Selinger. In particular, we analyze function abstraction in quantum computation, which turns out to characterize its clas­ sical interfaces. Intuitively, classical data can be recognized as just those data that can be manipulated using variables, i.e. copied, deleted, and abstracted over. A categorical framework of polynomial extensions provides a convenient language for specifying quantum algorithms, with a clearly distinguished clas­ sical fragment, familiar from functional programming. As a running example, we reconstruct Simon's algorithm, which is a sim­ ple predecessor of Shor's quantum algorithms for factoring and discrete loga­ rithms. The abstract specification in the framework of polynomial categories displays some of the fundamental program transformations involved in devel­ oping quantum algorithms, and points to the computational resources, whether quantum or classical, which are necessary for the various parts of the execution. The relevant resources are characterized as categorical structures. They are normally supported by the standard Hilbert space model of quantum mechan­ ics, but in some cases they can also be found in other, nonstandard models. We conclude the paper by sketching an implementation of Simon's algorithm using just abelian groups and relations.
Standard dynamic programming applied to time aggregated Markov decision processes

In this note we address the time aggregation approach to ergodic finite state Markov decision processes with uncontrollable states. We propose the use of the time aggregation approach as an intermediate step toward constructing a transformed MDP whose state space is comprised solely of the controllable states. The proposed approach simplifies the iterative search for the optimal solution by eliminating the need to define an equivalent parametric function, and results in a problem that can be solved by simpler, standard MDP algorithms.
Association between asthma and physical activity in Korean adolescents: the 3rd Korea Youth Risk Behavior Web-based Survey (KYRBWS-III).

BACKGROUND Asthma is the leading chronic illness among children and adolescents in several nations. This study investigated the association between asthma and physical activity (PA). METHODS The findings in this study are based on the data obtained from the 2007 3rd Korea Youth Risk Behavior Web-Based Survey (KYRBWS-III), a cross-sectional survey of health-risk behaviours among a representative sample of Korean middle- and high-school students aged 13-18 years. This survey is conducted annually by the Korea Centers for Disease Control and Prevention. The 72 943 study subjects were selected using the complex sampling design of the survey. The association between asthma and PA was assessed by conducting multiple logistic regression analyses of the data by using the statistical software SPSS 17.0 Complex Sample. RESULTS Compared with the adolescents without current asthma, significantly fewer adolescents with current asthma had a sedentary time of 3 h or less per day (odds ratio, 0.86; 95% confidence interval, 0.75-0.97). Sedentary time was defined as time spent watching television, surfing the Internet, or playing computer games and excluded the time spent doing homework or study during leisure time. The analysis was adjusted for age, gender, family affluence level (FAL), obesity, allergic rhinitis, atopy and smoking. With regard to participation in adequate vigorous or moderate PA, strengthening exercise or physical education class, no significant differences were found between the adolescent students with current asthma and those without current asthma. In addition, it was found that all PA had no significant differences in their effects on asthma severity (medication, inability to work and absence from school). CONCLUSION Our results show that the amount of sedentary time influenced asthma prevalence; however, PA did not influence asthma prevalence in Korean adolescents.
Prediction and assessment of extrapyramidal side effects induced by risperidone based on dopamine D2 receptor occupancy

In the present study, we attempted to predict the risk of extrapyramidal side effects of a selective monoaminergic antagonist, risperidone, by analyzing the correlation between the dopamine D2 receptor occupancy and the degree of extrapyramidal side effects of the drug. The occupancies of D2 and 5‐HT2 receptors at various doses of risperidone were calculated by means of a receptor occupancy theory. The extrapyramidal side effects after administration of risperidone were attempted to predict by theoretical analysis of the correlation between the calculated occupancies and the evidence of extrapyramidal symptoms using a ternary complex model. The pharmacokinetic/pharmacodynamic analysis utilized the data concerning the pharmacokinetics of risperidone and 9‐hydroxyrisperidone (active metabolite), their binding affinities with D2 and 5‐HT2 receptors, and the clinical evidence of extrapyramidal symptoms (Extrapyramidal Symptom Rating Scale: ESRS), gathered from the literature. The mean occupancy of 5‐HT2 receptors after the administration of regular doses of risperidone was suggested to be more than 90%, whereas the mean occupancy of D2 receptors varied between 50–80%, depending on the dose. The correlation between the occupancy of D2 receptors and the extrapyramidal symptoms could be successfully analyzed with a ternary complex model, showing the predictability of the model for the extrapyramidal side effects of risperidone. Since the estimated risk of the extrapyramidal side effects varied with the dose, the present method of predicting the extrapyramidal side effects of risperidone may provide a basis for developing a rational dosing regimen for the drug. Synapse 46:32–37, 2002. © 2002 Wiley‐Liss, Inc.
Metadata of the chapter that will be visualized online

Biological invasion is the process by which a species is introduced, deliberately or inadvertently, into a new geographic region where it proliferates and persists. Outside their natural range (in which they evolved) such species are described as nonnative (or nonindigenous, exotic, alien). For a variety of reasons, the vast majority of introduced nonnative organisms fail to persist. Many of those that do establish self-sustaining populations do not spread very far or very fast beyond their point of introduction, and they often do not have conspicuous impacts on their environment. However, a small proportion (but a large and growing number) of nonnative species becomes invasive – that is, they may spread aggressively and/or have strong environmental effects. Invasive species are a global problem that threatens native biodiversity, the normal functioning of ecosystems, natural resources, regional economies, and human health. As such, they pose a major concern for conservation and management, and are the focus of a highly productive multidisciplinary field called invasion ecology. Comp. by: GDurga Stage: Proof Chapter No.: 574 Title Name: ESST Page Number: 0 Date:8/12/11 Time:14:43:26
Incidence and Prognostic Value of the Systemic Inflammatory Response Syndrome and Organ Dysfunctions in Ward Patients.

RATIONALE Tools that screen inpatients for sepsis use the systemic inflammatory response syndrome (SIRS) criteria and organ dysfunctions, but most studies of these criteria were performed in intensive care unit or emergency room populations. OBJECTIVES To determine the incidence and prognostic value of SIRS and organ dysfunctions in a multicenter dataset of hospitalized ward patients. METHODS Hospitalized ward patients at five hospitals from November 2008 to January 2013 were included. SIRS and organ system dysfunctions were defined using 2001 International Consensus criteria. Patient characteristics and in-hospital mortality were compared among patients meeting two or more SIRS criteria and by the presence or absence of organ system dysfunction. MEASUREMENTS AND MAIN RESULTS A total of 269,951 patients were included in the study, after excluding 48 patients with missing discharge status. Forty-seven percent (n = 125,841) of the included patients met two or more SIRS criteria at least once during their ward stay. On ward admission, 39,105 (14.5%) patients met two or more SIRS criteria, and patients presenting with SIRS had higher in-hospital mortality than those without SIRS (4.3% vs. 1.2%; P < 0.001). Fourteen percent of patients (n = 36,767) had at least one organ dysfunction at ward admission, and those presenting with organ dysfunction had increased mortality compared with those without organ dysfunction (5.3% vs. 1.1%; P < 0.001). CONCLUSIONS Almost half of patients hospitalized on the wards developed SIRS at least once during their ward stay. Our findings suggest that screening ward patients using SIRS criteria for identifying those with sepsis would be impractical.
Effective Group Training for Patients with Unexplained Physical Symptoms: A Randomized Controlled Trial with a Non-Randomized One-Year Follow-Up

Background Although cognitive-behavioral therapy for Unexplained Physical Symptoms (UPS) is effective in secondary care, studies done in primary care produced implementation problems and conflicting results. We evaluated the effectiveness of a cognitive-behavioral group training tailored to primary care patients and provided by a secondary community mental-health service reaching out into primary care. Methodology/Principal Findings The effectiveness of this training was explored in a randomized controlled trial. In this trial, 162 patients with UPS classified as undifferentiated somatoform disorder or as chronic pain disorder were randomized either to the training or a waiting list. Both lasted 13 weeks. The preservation of the training's effect was analyzed in non-randomized follow-ups, for which the waiting group started the training after the waiting period. All patients attended the training were followed-up after three months and again after one year. The primary outcomes were the physical and the mental summary scales of the SF-36. Secondary outcomes were the other SF-36-scales and the SCL-90-R. The courses of the training's effects in the randomized controlled trial and the follow-ups were analyzed with linear mixed modeling. In the randomized controlled trial, the training had a significantly positive effect on the quality of life in the physical domain (Cohen's d = 0.38;p = .002), but this overall effect was not found in the mental domain. Regarding the secondary outcomes, the training resulted in reporting an improved physical (Cohen's d = 0.43;p = 0.01), emotional (Cohen's d = 0.44;p = .0.01), and social (Cohen's d = 0.36;p = 0.01) functioning, less pain and better functioning despite pain (Cohen's d = 0.51;p = <0.001), less physical symptoms (Cohen's d = −.23;p = 0.05) and less sleep difficulties (Cohen's d = −0.25;p = 0.04) than time in the waiting group. During the non-randomized follow-ups, there were no relapses. Conclusions/Significance The cognitive-behavioral group training tailored for UPS in primary care and provided by an outreaching secondary mental-health service appears to be effective and to broaden the accessibility of treatment for UPS. Trial Registration TrialRegister.nl NTR1609
Safety and Efficacy of Bimatoprost 0.03% versus Timolol Maleate 0.5%/Dorzolamide 2% Fixed Combination

Purpose To determine the efficacy and safety of bimatoprost given every evening versus the dorzolamide/timolol fixed combination (DTFC) given twice daily in open-angle glaucoma and ocular hypertensive patients. Methods A double-masked, three-center, prospective, randomized, crossover comparison with two 8-week treatment periods following a 4-week medicine free washout period. Diurnal curve intraocular pressures (lOPs) were taken at 08:00 (trough) and 10:00 and 16:00 hours. Results A total of 35 patients were enrolled and 32 completed all evaluations. The diurnal untreated baseline intraocular pressures was 24.8 ± 2.4 mmHg. On the last day of treatment the mean diurnal intraocular pressures was 17.4 ± 2.9 for bimatoprost and 18.1 ± 2.8 mmHg for DTFC (p = 0.35). The individual time points for intraocular pressures were not statistically different between groups. Both groups statistically reduced the intraocular pressures from baseline for each time point and for the diurnal curve (p < 0.05). Regarding ocular safety and tolerability, there was more conjunctival hyperemia with bimatoprost (n = 15) than with DTFC (n = 7, p = 0.013) and more burning and stinging with DTFC (n = 12) than with bimatoprost (n = 0, p = 0.0005). Few systemic adverse events were recorded and there was no statistical difference between groups for any individual event (p > 0.05). Conclusions This study indicates that the intraocular pressures are lowered to a statistically similar amount with DTFC compared to bimatoprost in open-angle glaucoma and ocular hypertensive patients.
Revenue Sharing Based Resource Allocation for Dynamic Spectrum Access Networks

We propose a revenue sharing based resource allocation scheme for dynamic spectrum access (DSA) networks. In our scheme, based on a mutually agreed revenue sharing scheme, a primary network operator (PNO) actively shares its radio resource with a secondary network operator (SNO), which provides access service to secondary users (SUs) for its revenue maximization. To investigate the coupling effect between the revenue sharing and resource allocation, we formulate the interaction between PNO and SNO as a two-layered game, which includes a top layer game to model their revenue sharing and a bottom layer game to model their joint resource allocations. Specifically, in the top layer, based on their joint resource allocation decisions, the PNO and SNO form a Nash bargaining game to determine the revenue sharing scheme such that both of them can benefit from cooperation satisfactorily. Then, in the bottom layer, under the given revenue sharing scheme, the PNO and SNO form a Stackelberg game to determine their joint resource allocation decisions, which also influence their respective revenues. The two games work iteratively such that the PNO and SNO reach a final equilibrium state at which neither PNO nor SNO will change its decisions unilaterally in both layers. We propose efficient algorithms to solve both the top layer and bottom layer games and compute the final equilibrium of the two-layered game. Specifically, despite the non-convexity of joint resource allocation optimization problem in the bottom layer, we identify its hidden monotonic structure and propose an efficient algorithm, which is based on the polyblock approximation, to achieve the optimal solutions. Moreover, in the top layer, to tackle with the difficulty due to the lack of an analytical objective function for the revenue sharing problem, we explore its hidden unimodal property and propose a Brent's method based algorithm to achieve the optimal solution. Numerical results are presented to verify the performance of our algorithms and show that our revenue sharing based resource allocation scheme yields a win-win situation for the PNO and SNO.
C4-Dicarboxylate Transport in Bacillus subtilis Studied with 3-Fluoro-l-Erythro-Malate as a Substrate

Bacillus subtilis cells grown in yeast extract medium accumulated 3-fluoro-l-erythro-[1,2-14C2]malate more than 30-fold from the surrounding medium. No metabolic products derived from 3-fluoro-l-erythro-malate could be detected in these cells. l-Malate competitively inhibited transport of 3-fluoro-l-erythro-malate. This malate analogue was itself a competitive inhibitor of l-malate uptake. Cells that had been grown in yeast extract supplemented with 5 mM l-malate showed a 10-fold increased affinity towards 3-fluoro-l-erythro-malate relative to cells grown in yeast extract medium with no added malate. Our results suggest that two transport systems for l-malate can be induced in B. subtilis. The first of these systems seems to effect uptake of C4-dicarboxylates (l-malate, succinate, and fumarate) in yeast extract medium. The second transport system (or possibly a modification of the first transport system) seems to be induced by addition of l-malate to this medium and is also functioning in malate minimal medium.
On the Convergence of the Escalator Boxcar Train

The Escalator Boxcar Train (EBT) is a numerical method that is widely used in theoretical biology to investigate the dynamics of physiologically structured population models, i.e., models in which individuals differ by size or other physiological characteristics. The method was developed more than two decades ago, but has so far resisted attempts to give a formal proof of convergence. Using a modern framework of measure-valued solutions, we investigate the EBT method and show that the sequence of approximating solution measures generated by the EBT method converges weakly to the true solution measure under weak conditions on the growth rate, birth rate, and mortality rate. In rigorously establishing the convergence of the EBT method, our results pave the way for wider acceptance of the EBT method beyond theoretical biology and constitutes an important step towards integration with established numerical schemes.
Handoff Management Schemes and Performance Analysis for IP/MPLS-Based Cellular Networks

One of the major challenges for the wireless networks is related to efficient mobility management issue. In this paper, we propose a new micro-mobility management scheme, called micro mobile MPLS, that supports both mobility and quality-of-service (QoS) management in cellular networks. Our proposal includes two protocol variants. In the first variant, called FC-micro mobile MPLS, the forwarding chain (FC) concept is provided to track efficiently the host mobility within a domain. This concept fits mobile nodes (MNs) with high mobility rate. The second protocol variant, called master forwarding chain (MFC)-micro mobile MPLS, aims to reduce the total signaling cost by controlling the number of registration updates with the root of the domain. In order to assess the efficiency of our proposals, all underlying protocols are compared through simulations using both two-dimensional (2-D) and one-dimensional (1-D) mobility models. Simulation results show that our proposed mechanisms can significantly reduce the registration updates cost and provide low handoff latency and packet loss rate under various scenarios
Anaesthetic drug administration as a potential contributor to healthcare-associated infections: a prospective simulation-based evaluation of aseptic techniques in the administration of anaesthetic drugs

Objective To evaluate the possibility that anaesthetists are administering potentially pathogenic micro-organisms to their patients. Design Prospective microbiological and observational study in a realistic simulated setting. Participants Ten anaesthetists supported by 10 anaesthetic technicians. Primary outcome measure The presence or absence of organisms cultured from sterile intravenous bags used to collect drugs injected during the simulated cases and from the needles and the contents of the syringes used. The authors also observed the aseptic techniques used. Results Organisms were isolated from five of 38 (13%) bags from five of 20 simulated cases anaesthetised by four of 10 anaesthetists, 10 of 197 (5%) syringes and six of 17 (35%) needles. None of the anaesthetists washed their hands prior to entry, used the hand gel provided, disinfected the phial septa before drawing up drugs or disinfected the intravenous ports on the intravenous administration set before use. One was seen to recap a needle left on a syringe for possible reuse. Three participants were observed to place equipment such as stethoscopes, drug charts and pens on top of their inuse drug trays. Conclusion The administration of intravenous drugs during anaesthesia may be an important factor in the genesis (or potentially the prevention) of healthcare-associated infection. These observations suggest room for improvement in the aseptic techniques of at least some anaesthetists when preparing and administering intravenous drugs. Confirmation of these findings in clinical settings is needed. Study registry number (for the VASER study) Australian New Zealand Clinical Trials Registry: Ref: ACTRN 12609000530224, https://www.anzctr. org.au/registry/trial_review. aspx? ID=308128; note that the work presented here is a subset of the registered trial and its outcomes were not included in this registration.
The Role of EUS-BD in the Management of Malignant Biliary Obstruction: The Indonesian Perspective

Aims To evaluate the success rate and related factors of endoscopic ultrasound guided-biliary drainage (EUS-BD). Material and Methods We conducted a retrospective study among 24 patients with malignant biliary obstruction who underwent EUS-BD after failed ERCP from January 2015 to December 2016 in a tertiary health center. The bilirubin levels before and after the procedure were used to define the clinical success rate, while the stent deployment was used to define the technical success rate. We placed either transluminal biliary stents or transpapillary biliary stents. Results Among 24 patients, choledochoduodenostomy technique was conducted in 23 patients (95.8%) and hepaticogastrostomy technique in 1 patient (4.2%). Transluminal stent placement was conducted in 23 patients, while transpapillary stent placement was conducted in 1 patient. The clinical success rate was 78.2% (18) in choledochoduodenostomy route and 100% (1) in hepaticogastrostomy route. EUS-BD was 2.37 times and 2.11 times more likely to be successful in reducing the bilirubin level in patients with tumor of the head of pancreas and periampullary tumor, respectively, but not in cholangiocarcinoma. Conclusions EUS-BD is an effective and efficient procedure to achieve biliary drainage among patients with malignant biliary obstruction after ERCP failure.