nils-herrmann/clean_scirepeval huggingface dataset:
Two proofreading steps amplify the accuracy of genetic code translation
Venue: Proceedings of the National Academy of Sciences

We have discovered that two proofreading steps amplify the accuracy of genetic code reading, not one step, as hitherto believed. We have characterized the molecular basis of each one of these steps, paving the way for structural analysis in conjunction with structure based standard free energy computations. Our work highlights the essential role of elongation factor Tu for accurate genetic code translation in both initial codon selection and proofreading. Our results have implications for the evolution of efficient and accurate genetic code reading through multistep proofreading, which attenuates the otherwise harmful effects of the obligatory tradeoff between efficiency and accuracy in substrate selection by enzymes. Aminoacyl tRNAs (aa tRNAs) are selected by the messenger RNA programmed ribosome in ternary complex with elongation factor Tu (EF Tu) and GTP and then, again, in a proofreading step after GTP hydrolysis on EF Tu. We use tRNA mutants with different affinities for EF Tu to demonstrate that proofreading of aa tRNAs occurs in two consecutive steps. First, aa tRNAs in ternary complex with EF Tu*GDP are selected in a step where the accuracy increases linearly with increasing aa tRNA affinity to EF Tu. Then, following dissociation of EF Tu*GDP from the ribosome, the accuracy is further increased in a second and apparently EF Tu independent step. Our findings identify the molecular basis of proofreading in bacteria, highlight the pivotal role of EF Tu for fast and accurate protein synthesis, and illustrate the importance of multistep substrate selection in intracellular processing of genetic information.
A novel pilot scale stacked microbial fuel cell for efficient electricity generation and wastewater treatment.
Venue: Water research

A novel stacked microbial fuel cell (MFC) which had a total volume of 72 L with granular activated carbon (GAC) packed bed electrodes was constructed and verified to present remarkable power generation and COD removal performance due to its advantageous design of stack and electrode configuration. During the fed batch operation period, a power density of 50.9 1.7 W/m(3) and a COD removal efficiency of 97% were achieved within 48 h. Because of the differences among MFC modules in the stack, reversal current occurred in parallel circuit connection with high external resistances >100 O) This reversal current consequently reduced the electrochemical performance of some MFC modules and led to a lower power density in parallel circuit connection than that in independent circuit connection. While increasing the influent COD concentrations from 200 to 800 mg/L at hydraulic retention time of 1.25 h in continuous operation mode, the power density of stacked MFC increased from 25.6 2.5 to 42.1 1.2 W/m(3) and the COD removal rates increased from 1.3 to 5.2 kg COD/(m(3) d) This study demonstrated that this novel MFC stack configuration coupling with GAC packed bed electrode could be a feasible strategy to effectively scale up MFC systems.
Optimal Controls for a Large Insurance Under a CEV Model: Based on the Legendre Transform Dual Method

The purpose of this paper is to consider the optimal proportional reinsurance and investment strategies for an insurance company. The insurer's surplus process is approximated by a Brownian motion with drift. The insurance company can purchase proportional reinsurance and invest the surplus in a financial market which includes one risk free asset and one risky asset whose price is modeled by a CEV model. The primary problem is changed to the dual problem by implying Legendre transform. When the objective of the insurance company is to maximize the expected logarithmic utility from terminal wealth, the closed form expressions for the optimal reinsurance investment policy which is different to the Merton case to the primal optimal problem are obtained and numerical simulations are provided to demonstrate our results. Moreover, we find an interesting result that risk exposure is non monotonic in the cost of reinsurance.
Implicit Coordination in Crowded Multi Agent Navigation
Venue: AAAI

In crowded multi agent navigation environments, the motion of the agents is significantly constrained by the motion of the nearby agents. This makes planning paths very difficult and leads to inefficient global motion. To address this problem, we propose a new distributed approach to coordinate the motions of agents in crowded environments. With our approach, agents take into account the velocities and goals of their neighbors and optimize their motion accordingly and in real time. We experimentally validate our coordination approach in a variety of scenarios and show that its performance scales to scenarios with hundreds of agents.
Proxemic group behaviors using reciprocal multi agent navigation
Venue: 2016 IEEE International Conference on Robotics and Automation (ICRA)

We present a decentralized algorithm for group based coherent and reciprocal multi agent navigation. In addition to generating collision free trajectories for each agent, our approach is able to simulate macroscopic group movements and proxemic behaviors that result in coherent navigation. Our approach is general, makes no assumptions about the size or shape of the group, and can generate smooth trajectories for the agents. Furthermore, it can dynamically adapt to obstacles or the behavior of other agents. The additional overhead of generating proxemic group behaviors is relatively small and our approach can simulate hundreds of agents in real time. We highlight its benefits on different benchmarks.
Decentralized Multi Agent Navigation Planning with Braids
Venue: WAFR

We present a novel planning framework for navigation in dynamic, multi agent environments with no explicit communication among agents, such as pedestrian scenes. Inspired by the collaborative nature of human navigation, our approach treats the problem as a coordination game, in which players coordinate to avoid each other as they move towards their destinations.We explicitly encode the concept of coordination into the agents' decision making process through a novel inference mechanism about future joint strategies of avoidance. We represent joint strategies as equivalence classes of topological trajectory patterns using the formalism of braids. This topological representation naturally generalizes to any number of agents and provides the advantage of adaptability to different environments, in contrast to the majority of existing approaches. At every round, the agents simultaneously decide on their next action that contributes collisionfree progress towards their destination but also towards a global joint strategy that appears to be in compliance with all agents' preferences, as inferred from their past behaviors. This policy leads to a smooth and rapid uncertainty decrease regarding the emerging joint strategy that is promising for real world scenarios. Simulation results highlight the importance of reasoning about joint strategies and demonstrate the efficacy of our approach.
Systematic review and meta analyses of the effect of lipid emulsion on microbial growth in parenteral nutrition.
Venue: The Journal of hospital infection

As lipid in parenteral nutrition (PN) purportedly enhances microbial growth, recommendations limit infusion of lipid PN (or lipid emulsion) from a single container to 24h (48h for lipid free PN) However, the associated evidence base is ambiguous.  To examine factors affecting microbial growth in PN.  A systematic review with meta analyses examined effects of nutrients on microbial growth in PN infusates over a 48 h period using the growth ratio {GR=log10[colony forming units (cfu)/mL at 48h/cfu/mL at time zero] FINDINGS Factors influencing GR in PN included glucose, microbial species, temperature, osmolarity, presence of vitamins, trace elements and lipid, and amino acid profile. Using unmatched datasets (N=306) a general linear model found that lipid inclusion in PN represented 3.3% of the variability, which was less than that due to glucose concentration (5.8% microbial species (35.3% and microbe infusate interaction (4.4% Using matched datasets (N=38 pairs) lipid inclusion in PN represented 5.4% of the variability (P=0.076) which was less than that due to glucose concentration (8.5% P=0.025) microbial species (75.5% P<0.001) and microbe infusate interaction (13.3% P=0.382) Using meta analyses of matched datasets, the presence of lipid in PN at fixed glucose concentrations did not significantly increase GR of Candida albicans, Escherichia coli or Staphylococcus epidermidis (P=0.352, P=0.025 and P=0.494, respectively; overall P=0.175) CONCLUSION Lipid inclusion in PN is only one of several factors that may influence microbial growth in PN. Any recommendations about the duration of PN infusion from a single container should account for all these factors, and should be weighted according to microbial species likely to contaminate PN.
Clinical study of midazolam sequential with dexmedetomidine for agitated patients undergoing weaning to implement light sedation in intensive care unit
Venue: Chinese journal of traumatology Zhonghua chuang shang za zhi

To evaluate midazolam sequential with dexmedetomidine for agitated patients undergoing weaning to implement light sedation in ICU.  This randomized, prospective study was conducted in Tianjin Third Central Hospital, China. Using a sealed envelope method, the patients were randomly divided into 2 groups (40 patients per group) Each patient of group A received an initial loading dose of midazolam at 0.3 3 mg/kg*h 24 h before extubation, followed by an infusion of dexmedetomidine at a rate of 0.2 1 mg/kg*h until extubation. Each patient of group B received midazolam at a dose of 0.3 3 mg/kg*h until extubation. The dose of sedation was regulated according to RASS sedative scores maintaining in the range of 2 1. All patients were continuously monitored for 60 min after extubation. During the course, heart rate (HR) mean artery pressure (MAP) extubation time, adverse reactions, ICU stay, and hospital stay were observed and recorded continuously at the following time points: 24 h before extubation (T1) 12 h before extubation (T2) extubation (T3) 30 min after extubation (T4) 60 min after extubation (T5) Results Both groups reached the goal of sedation needed for ICU patients. Dexmedetomidine was associated with a significant increase in extubation quality compared with midazolam, reflected in the prevalence of delirium after extubation (20% (8/40) vs 45% (18/40) respectively (p 0.017) There were no clinically significant decreases in HR and MAP after infusing dexmedetomidine or midazolam. In the group A, HR was not significantly increased after extubation; however, in the group B, HR was significantly increased compared with the preextubation values (p 0.05) HR was significantly higher in the group B compared with the group A at 30 and 60 min after extubation (both, p 0.05) Compared with preextubation values, MAP was significantly increased at extubation in the group B (p 0.05) and MAP was significantly higher at T3, T4, T5 in the group B than group A (p 0.05) There was a significant difference in extubation time (3.0 1.5) d vs (4.3 2.2) d, p 0.05) ICU stay (5.4 2.1) d vs (8.0 1.4) d, p 0.05) hospital stay (10.1 3.0) d vs (15.3 2.6) d, p 0.05) between group A and B.  Midazolam sequential with dexmedetomidine can reach the goal of sedation for ICU agitated patients, meanwhile it can maintain the respiratory and circulation parameters and reduce adverse reactions.
High performance parametric design optimization of RF devices
Venue: 2016 IEEE International Vacuum Electronics Conference (IVEC)

We present an integrated environment for large scale multi parameter design optimization of RF devices based on AFRL's Galaxy Simulation Builder productivity tool for distributed high performance computing, Sandia National Lab's DAKOTA optimization library, and a suite of highly efficient GPU based Electromagnetic codes developed at NRL in collaboration with Leidos, Inc. The environment allows for an end to end optimization cycle of an RF device to be set up, deployed, carried out, monitored and analyzed in a quick, user friendly, robust, and flexible fashion using a diverse variety of high end parallel computing resources.
Design of vibratory energy harvesters under stochastic parametric uncertainty: a new optimization philosophy

Vibratory energy harvesters as potential replacements for conventional batteries are not as robust as batteries. Their performance can drastically deteriorate in the presence of uncertainty in their parameters. Parametric uncertainty is inevitable with any physical device mainly due to manufacturing tolerances, defects, and environmental effects such as temperature and humidity. Hence, uncertainty propagation analysis and optimization under uncertainty seem indispensable with any energy harvester design. Here we propose a new modeling philosophy for optimization under uncertainty; optimization for the worst case scenario (minimum power) rather than for the ensemble expectation of the power. The proposed optimization philosophy is practically very useful when there is a minimum requirement on the harvested power. We formulate the problems of uncertainty propagation and optimization under uncertainty in a generic and architecture independent fashion, and then apply them to a single degree of freedom linear piezoelectric energy harvester with uncertainty in its different parameters. The simulation results show that there is a significant improvement in the worst case power of the designed harvester compared to that of a naively optimized (deterministically optimized) harvester. For instance, for a 10% uncertainty in the natural frequency of the harvester (in terms of its standard deviation) this improvement is about 570%
Virulence factors of Candida species isolated from patients with urinary tract infection and obstructive uropathy
Venue: Pakistan journal of medical sciences

Fungal urinary tract infections due to Candida have increased significantly in recent years. Our research objective was to study Candida species in urine samples of patients with urinary tract infections (UTIs) associated with obstructive uropathy and to investigate the virulence factors of the isolated Candida.  Patients were divided into two groups: Group I (cases) 50 patients with UTIs and obstructive uropathy. Group II (control) 50 patients with UTIs but with no functional or anatomical obstruction of their urinary tract. Clinical histories and physical examinations, together with laboratory investigations of urine samples were carried out in all patients in this study. Mid stream urine samples were examined microscopically and by fungal cell culture. The isolated Candida species were identified by analytical profile index (API) Candida Virulence factors were determined for the isolated Candida. The susceptibility to fluconazole was evaluated.  This study revealed an overall isolation rate of 27% of Candida species among all patient groups. The rate was 36% in cases, and 18% in controls, a difference found to be statistically significant (P<0.05) By API, C.albicans was detected in 44% of Candida species in cases, and in 33% in controls. While C.glabrata was detected in 28% of Candida species in cases, and in 22% in controls. C.tropicalis was detected in 17% of Candida species in cases, and in 22% in controls. Both C.krusei and C.kyfr were detected in 5.5% of Candida species in cases, and in 11% in controls. In terms of virulence factors the study showed that 11 out of 27 (40.5% of Candida isolates were biofilm positive by tube adherence. Phospholipase activity was demonstrated in 12 out of 27 (44.5% of Candida isolates. Secretory aspartic proteinase activity was demonstrated in 13 out of 27 (48% of the Candida isolates.  Candida is an important cause of UTIs and obstructive uropathy is a major predisposing factor.
Genotypes and virulence factors of Candida species isolated from oralcavities of patients with type 2 diabetes mellitus.
Venue: Turkish journal of medical sciences

This study compared the genotypes and virulence factors of Candida species isolated from oral cavities of healthy individuals and patients with diabetes mellitus (DM)  A total of 142 healthy individuals and 73 diabetic patients participated in this study. Study populations were classified into 4 groups as follows: Group I Healthy, without caries; Group II Healthy, with caries; Group III DM, with caries; Group IV DM, without caries. Diabetic patients' blood glucose and hemoglobin A1c concentrations were determined. Identification of Candida species was performed with conventional methods. Biofilm production, proteinase, phospholipase, and esterase were analyzed. The genetic diversity of Candida species was established using rep PCR.  The most isolated species was Candida albicans. There were statistical differences in terms of isolated Candida frequency between healthy subjects and diabetic patients. There was no statistical difference between the virulence factors of groups. Twelve genotypes were determined. While there were statistical differences in aerobe biofilm production, proteinase, and phospholipase activity between genotypes, there were no statistical differences in anaerobe biofilm production and esterase activity between genotypes.  Diabetes has no effect on the activities of virulence factors of Candida species. Different genotypes of Candida albicans exhibited different virulence activities.
Evaluation of Virulence Factors of Candida Species Isolated from Superficial Versus Systemic Candidiasis

Various virulence factors are contributing to the colonization and pathogenicity of Candida during both superficial and systemic infections  The current study was conducted to investigate production of extracellular hydrolytic enzymes, hemolysis and biofilm formation among Candida species isolated from superficial versus systemic candidiasis and to compare the production of these virulence factors among albicans and non albicans Candida species, in addition to comparing hemolysis and hydrolytic enzymes production under aerobic and anaerobic conditions.  A total of 51 Candida strains isolated from vulvovaginal candidiasis and 44 strains isolated from systemic candidiasis were included in the study. Germ tube test and Hi Crom Candida Differential Agar medium were used for species identification of the isolates. The Candida isolates were tested for expression of hemolytic activity, phospholipase, proteinase and esterase production under aerobic and anaerobic conditions, in addition to their ability of biofilm formation.  In both groups, 55 isolates were identified as Candida albicans (C. albicans) while 44 isolates were identified as non albicans species. Hemolytic activity and biofilm formation were significantly higher among the systemic Candida isolates than superficial isolates, while expression of proteinase activity was significantly higher among superficial isolates. Expression of phospholipase and esterase was significantly higher among C. albicans isolates than non albicans isolates. Expression of proteinase and esterase activities was significantly better under aerobic conditions than under anaerobic conditions.  Hemolytic activity and bioflm formation were more evident among the systemic isolates while proteinase production appears to be more evident among the vaginal isolates. Phospholipase production is almost an exclusive characteristic feature of C. albicans, while C. albicans is the leading species in terms of esterase production. Aerobic conditions favor expression of proteinase and esterase activities.
The replenishment policy of agri products with stochastic demand in integrated agricultural supply chains
Venue: Expert Syst. Appl.

We study EOQ/EPQ models considering stochastic demand of agri products.We build system dynamic model for replenishment policies.We report the optimal replenishment policies of the supply chain. Market demand of agri products is influenced by uncertain factors, such as weather, temperature, and customer preferences. In integrated agricultural supply chains, traditional inventory models are useless because of the stochastic demand and deteriorative characteristic of agri products. This paper provides a method to determine the optimal replenishment policy of integrated agricultural supply chains with stochastic demand. In these EOQ/EPQ models, shortages are allowed and are backlogged if market demand is stochastic. The objective function is to minimize the total cost of the supply chain in the planning horizon. The total cost includes the ordering cost, the holding cost, the shortage cost and the purchasing cost. Thinking of the nonlinear relationship and dynamic forces in models, a system dynamic (SD) simulation model is constructed to find the optimal lot size and replenishment interval. Finally, an example is given to make a sensitivity analysis of the simulation model. Compared to traditional methods (such as equalize stochastic demand) the total cost decreases by 16.27% if the supply chains adopt the new replenishment policy. The results illustrated that the new replenishment policy (with intelligent method) is beneficial to help supply chain make decision scientifically. Moreover, the intelligent method can simulate stochastic demand perfectly, and it is effectively for solving the complicated and mathematically intractable replenishment problem.
Stochastic Dynamic Programming for Three Echelon Inventory System of Limited Shelf Life Products

Coordination of inventory decisions within the supply chain is one of the major determinants of its competitiveness in the global market. Products with limited shelf life impose additional challenges in managing the inventory across the supply chain because of the additional wastage costs incurred in case of being stored beyond product's useful life. This paper presents a stochastic dynamic programming model for inventory replenishment in a serial multi echelon distribution supply chain. The model considers uncertain stationary discrete demand at the retailer and zero lead time. The objective is to minimize expected total costs across the supply chain echelons, while maintaining a preset service level. The results illustrate that a cost saving of around 17% is achievable due to coordinating inventory decisions across the supply chain.
Respiratory and gastrointestinal dysfunctions associated with auriculo condylar syndrome and a homozygous PLCB4 loss of function mutation
Venue: American journal of medical genetics. Part A

Condylar Syndrome (ACS) is a craniofacial malformation syndrome characterized by external ear anomalies, hypoplasia of the mandibular condyle, temporomandibular joint abnormalities, micrognathia, and microstomia. Glossoptosis, masticatory abnormalities, orthodontic problems, and malocclusion occur in a majority of affected subjects. The clinical diagnosis is usually suggested by the pathognomonic ear appearance "question mark ear" consisting of a variable degree of clefting between the helix and earlobe. The genetic mechanisms underlying ACS have recently been identified. Both autosomal dominant and recessive inheritance of mutations in phospholipase C, beta 4 (PLCB4) and endothelin 1 (EDN1) have been reported along with autosomal dominant mutations in guanine nucleotide binding protein (G protein) a inhibiting activity polypeptide 3 (GNAI3) We report 6 years of follow up of a child with a clinical phenotype consistent with ACS due to a homozygous frameshift mutation in PLCB4. The baby presented feeding difficulties associated with failure to thrive and a complex sleep related respiratory disorder, characterized by central and obstructive apnoeas. Our observations of this case further delineate the phenotype of ACS associated with autosomal recessive PLCB4 loss of function mutations, underscoring gastrointestinal dysfunction and severe sleep related breathing abnormalities as additional features when compared to patients with heterozygous mutations with a presumed dominant negative effect.