Miracle-dz/UniFAR-FTUs huggingface dataset:
Accuracy of initial codon selection by aminoacyl-tRNAs on the mRNA-programmed bacterial ribosome

Significance The genetic code letters, codons, are in all life forms translated to protein building blocks, amino acids, on ribosomes with the help of tRNAs. For 15% of the total genetic code we have clarified how the rates of codon translation decrease as the accuracies of codon reading increase toward their maximal values. Our study is ground-breaking with respect to its large scope, its relevance for genetic code translation in living cells, and the precision of its error estimates. Our data suggest that the quality of the ensembles of proteins in cells is determined by “error hot spots” in code translation, where amino acid substitutions are frequent. Our study is essential for modeling of bacterial physiology and understanding genetic code evolution. We used a cell-free system with pure Escherichia coli components to study initial codon selection of aminoacyl-tRNAs in ternary complex with elongation factor Tu and GTP on messenger RNA-programmed ribosomes. We took advantage of the universal rate-accuracy trade-off for all enzymatic selections to determine how the efficiency of initial codon readings decreased linearly toward zero as the accuracy of discrimination against near-cognate and wobble codon readings increased toward the maximal asymptote, the d value. We report data on the rate-accuracy variation for 7 cognate, 7 wobble, and 56 near-cognate codon readings comprising about 15% of the genetic code. Their d values varied about 400-fold in the 200–80,000 range depending on type of mismatch, mismatch position in the codon, and tRNA isoacceptor type. We identified error hot spots (d = 200) for U:G misreading in second and U:U or G:A misreading in third codon position by His-tRNAHis and, as also seen in vivo, Glu-tRNAGlu. We suggest that the proofreading mechanism has evolved to attenuate error hot spots in initial selection such as those found here.
Detecting and mitigating the impact of wideband jammers in IEEE 802.11 WLANs

IEEE 802.11 Wireless LANs (WLANs) are highly sensitive to Denial of Service (DoS) attacks carried out with jamming devices. In this paper we focus on 2.4GHz wideband constant jammers. The interest in the wideband jammer lies in the fact that it beats all possible channels at the same time, leaving no possible escape following traditional channel-switching defenses. After studying and developing an effective detection mechanism, we propose the implementation of a load balancing technique based on cell breathing for mitigating the harmful effects of the jammer over an IEEE 802.11 WLAN. Cell breathing is achieved by dynamically tuning the transmission power to adjust the size of a WLAN cell.
Critical behaviour of the Rouse model for gelling polymers

It is shown that the traditionally accepted 'Rouse values' for the critical exponents at the gelation transition do not arise from the Rouse model for gelling polymers. The true critical behaviour of the Rouse model for gelling polymers is obtained from spectral properties of the connectivity matrix of the fractal clusters that are formed by the molecules. The required spectral properties are related to the return probability of a 'blind-ant' random walk on the critical percolating cluster. The resulting scaling relations express the critical exponents of the shear-stress-relaxation function, and hence those of the shear viscosity and of the first normal stress coefficient, in terms of the spectral dimension ds of the critical percolating cluster and the exponents σ and τ of the cluster-size distribution.
Discriminative learning in sequential pattern recognition

In this article, we studied the objective functions of MMI, MCE, and MPE/MWE for discriminative learning in sequential pattern recognition. We presented an approach that unifies the objective functions of MMI, MCE, and MPE/MWE in a common rational-function form of (25). The exact structure of the rational-function form for each discriminative criterion was derived and studied. While the rational-function form of MMI has been known in the past, we provided the theoretical proof that the similar rational-function form exists for the objective functions of MCE and MPE/MWE. Moreover, we showed that the rational function forms for objective functions of MMI, MCE, and MPE/MWE differ in the constant weighting factors CDT (s1 . . . sR) and these weighting factors depend only on the labeled sequence s1 . sR, and are independent of the parameter set - to be optimized. The derived rational-function form for MMI, MCE, and MPE/MWE allows the GT/EBW-based parameter optimization framework to be applied directly in discriminative learning. In the past, lack of the appropriate rational-function form was a difficulty for MCE and MPE/MWE, because without this form, the GT/EBW-based parameter optimization framework cannot be directly applied. Based on the unified rational-function form, in a tutorial style, we derived the GT/EBW-based parameter optimization formulas for both discrete HMMs and CDHMMs in discriminative learning using MMI, MCE, and MPE/MWE criteria. The unifying review provided in this article has been based upon a large number of earlier contributions that have been cited and discussed throughout the article. Here we provide a brief summary of such background work. Extension to large-scale speech recognition tasks was accomplished in the work of [59] and [60]. The dissertation of [47] further improved the MMI criterion to that of MPE/MWE. In a parallel vein, the work of [20] provided an alternative approach to that of [41], with an attempt to more rigorously provide a CDHMM model re-estimation formula that gives positive growth of the MMI objective function. A crucial error of this attempt was corrected in [2] for establishing an existence proof of such positive growth. The main goal of this article is to provide an underlying foundation for MMI, MCE, and MPE/MWE at the objective function level to facilitate the development of new parameter optimization techniques and to incorporate other pattern recognition concepts, e.g., discriminative margins [66], into the current discriminative learning paradigm.
A viscoplastic-fatigue-creep damage model for tin-based solder alloy

During the past decade the demand for high performance automotive electronics is steadily increasing. An efficient development of such products requires the use of durability assessment techniques throughout the whole design optimization process. Since typical components comprise a large number of different materials and complex geometrical structures, Finite Element (FE) analysis is preferably used for durability evaluation and continuously replaces analytical calculations. However, a direct lifetime calculation by means of FE-techniques is still not achieved, partly due to the lack of material models capable of mapping the intrinsic material degradation under the relevant thermo-mechanical loads. Here, we propose a material model for a tin-based solder alloy which describes the non-linear mechanical behavior at the beginning of deformation as well as during continuous cyclic aging. We investigated the evolution of the mechanical properties and microstructure of the solder alloy Sn96:5Ag3:5 by cyclic strain-rate controlled fatigue- and creep-tests on as-casted standardized specimens. Material modeling is focused on the description of the complex interplay between viscoplastic, fatigue and creep processes observed in the experiment. Finally, a very good agreement is obtained between the measurements and the numerical model, which can offer new opportunities for lifetime simulations of lead-free solder joints.
Anaphora – Clause Annotation and Alignment Tool.

The paper presents Anaphora ‐ an OS and language independent tool for clause annotation and alignment, developed at the Department of Computational Linguistics, Institute for Bulgarian Language, Bulgarian Academy of Sciences. The tool supports automated sentence splitting and alignment and modes for manual monolingual annotation and multilingual alignment of sentences and clauses. Anaphora has been successfully applied for the annotation and the alignment of the Bulgarian-English Sentence- and ClauseAligned Corpus (Koeva et al. 2012a) and a number of other languages including French and Spanish.
Unanimous Voting using Support Vector Machines

This paper proposes a new approach to classification reliability. The key idea is to maintain version spaces containing (close approximations of) the target classifiers. In this way the unanimous-voting rule applied on these version spaces outputs reliable instance classifications. Version spaces are defined in a hypothesis space of oriented hyperplanes. The unanimous-voting rule is implemented by testing whether version spaces are empty. Testing is done by support vector machines. Hence, the approach is called version space support vector machines. Experiments with the approach show a 100% accuracy on the classified instances at the cost of not classifying all instances.
Stability analysis of grid-connected voltage source inverters with LCL-filters using partial state feedback

This paper addresses the stability of discrete controlled grid connected voltage source inverters with LCL-filter usually found in wind power generation systems. First a theorem that relates the controllability of the discrete dynamic equation with the LCL-filter parameters and the sampling frequency is derived. Then, a robust partial state feedback design on the linear matrix inequalities framework guarantee the stability damping the LCL-filter resonance for a large set of grid conditions without requiring tuning procedures. Finally, an internal model controller is added to ensure asymptotic reference tracking and disturbance rejection, therefore reducing significantly the impact of grid background voltage distortion on the line currents. Simulation and experimental results are presented to support the theoretical analysis carried out and to demonstrate the system performance.
Preconditioning for active set and projected gradient methods assemi-smooth Newton methods for PDE-constrained optimization with control constraints

Optimal control problems with partial differential equations play an important role in many applications. The inclusion of bound constraints for the control poses a significant additional challenge for optimization methods. In this paper we propose preconditioners for the saddle point problems that arise when a primal-dual active set method is used. We also show for this method that the same saddle point system can be derived when the method is considered as a semi-smooth Newton method. In addition, the projected gradient method can be employed to solve optimization problems with simple bounds and we discuss the efficient solution of the linear systems in question. In the case when an acceleration technique is employed for the projected gradient method, this again yields a semi-smooth Newton method that is equivalent to the primal-dual active set method. Numerical results illustrate the competitiveness of this approach.
Story Comprehension through Argumentation 1

This paper presents a novel application of argumentation for automated Story Comprehension (SC). It uses argumentation to develop a c mputational approach for SC as this is understood and studied in psychology . Argumentation provides uniform solutions to various representational an d reasoning problems required for SC such as the frame, ramification, and qualification pr blems, as well as the problem of contrapositive reasoning with default inf ormation. The grounded semantics of argumentation provides a suitable basis for the c onstruction and revision of comprehension models, through the synthesis of the e xplicit information from the narrative in the text with the implicit (in the reader ’s mind) common sense world knowledge pertaining to the topic(s) of the story give n in the text. We report on the empirical evaluation of the approach through a pro totype system and its ability to capture both the majority and the variability o f understanding of stories by human readers. This application of argumentation can p rovide an important test-bed for the more general development of computational arg umentation.
Invariant generation for linearizability proofs

Linearizability is a widely recognised correctness criterion for concurrent objects. A number of proof methods for verifying linearizability exist. In this paper, we simplify one such method with a systematic approach for invariant generation. Although this existing refinement-based method is itself systematic and fully tool-supported, it requires the verifier to provide a specific invariant over the implementation. While a chosen invariant may suffice for some proof obligations of the method, it may not for others resulting in a new, stronger invariant to be chosen and the previously completed proof steps to be redone. Our approach avoids such wasted proof effort by generating an invariant which is guaranteed to be sufficient for all proof obligations.
A Quantitative Approach to Analyzing Genome Reductive Evolution Using Protein–Protein Interaction Networks: A Case Study of Mycobacterium leprae

The advance in high-throughput sequencing technologies has yielded complete genome sequences of several organisms, including complete bacterial genomes. The growing number of these available sequenced genomes has enabled analyses of their dynamics, as well as the molecular and evolutionary processes which these organisms are under. Comparative genomics of different bacterial genomes have highlighted their genome size and gene content in association with lifestyles and adaptation to various environments and have contributed to enhancing our understanding of the mechanisms of their evolution. Protein–protein functional interactions mediate many essential processes for maintaining the stability of the biological systems under changing environmental conditions. Thus, these interactions play crucial roles in the evolutionary processes of different organisms, especially for obligate intracellular bacteria, proven to generally have reduced genome sizes compared to their nearest free-living relatives. In this study, we used the approach based on the Renormalization Group (RG) analysis technique and the Maximum-Excluded-Mass-Burning (MEMB) model to investigate the evolutionary process of genome reduction in relation to the organization of functional networks of two organisms. Using a Mycobacterium leprae (MLP) network in comparison with a Mycobacterium tuberculosis (MTB) network as a case study, we show that reductive evolution in MLP was as a result of removal of important proteins from neighbors of corresponding orthologous MTB proteins. While each orthologous MTB protein had an increase in number of interacting partners in most instances, the corresponding MLP protein had lost some of them. This work provides a quantitative model for mapping reductive evolution and protein–protein functional interaction network organization in terms of roles played by different proteins in the network structure.
Different types of offenders with schizophrenia : the antisocial and the non-antisocial

Individuals with schizophrenia are at an increased nsk to commit non-violent and violent crimes, compared to persons with no mental illness. The present study examined 27 male offenders with schizophrenia, 17 with persistent antisocial behaviour since childhood and 10 with no histoiy of antisocial behaviour pnor to the onset of schizophrenia. Compansons ofthe men with and without a stable pattem of antisocial behaviour revealed no differences in the course or symtomology ofschizophrenia. However, men with antisocial behaviour since childhood were younger at first conviction, were convicted ofthe first crime pnor to the first psychiatric admission, had accumulated more convictions, and committed more non-violent offences. The nonantisocial men, however, commifled proportionately more violent offences. The findings have implications for treatment and intervention programs.
MODELING VEGETATION AS A DYNAMIC COMPONENT IN SOIL‐VEGETATION‐ATMOSPHERE TRANSFER SCHEMES AND HYDROLOGICAL MODELS

Vegetation affects the climate by modifying the energy, momentum, and hydrologic balance of the land surface. Soil‐vegetation‐atmosphere transfer (SVAT) schemes explicitly consider the role of vegetation in affecting water and energy balance by taking into account its physiological properties, in particular, leaf area index (LAI) and stomatal conductance. These two physiological properties are also the basis of evapotranspiration parameterizations in physically based hydrological models. However, most current SVAT schemes and hydrological models do not parameterize vegetation as a dynamic component. The seasonal evolution of LAI is prescribed, and monthly LAI values are kept constant year after year. The effect of CO2 on the structure and physiological properties of vegetation is also neglected, which is likely to be important in transient climate simulations with increasing CO2 concentration and for hydrological models that are used to study climate change impact. The net carbon uptake by vegetation, which is the difference between photosynthesis and respiration, is allocated to leaves, stems, and roots. Carbon allocation to leaves determines their biomass and LAI. The timing of bud burst, leaf senescence, and leaf abscission (i.e., the phenology) determines the length of the growing season. Together, photosynthesis, respiration, allocation, and phenology, which are all strongly dependent on environmental conditions, make vegetation a dynamic component. This paper (1) familiarizes the reader with the basic physical processes associated with the functioning of the terrestrial biosphere using simple nonbiogeochemical terminology, (2) summarizes the range of parameterizations used to model these processes in the current generation of process‐based vegetation and plant growth models and discusses their suitability for inclusion in SVAT schemes and hydrological models, and (3) illustrates the manner in which the coupling of vegetation models and SVAT schemes/hydrological models may be accomplished.
Analyzing the Effectiveness of Privacy Related Add-Ons Employed to Thwart Web Based Tracking

With the rise in popularity of using websites to distribute content to users, content creators needed to gain revenue from page views. To achieve this, they use third-party networks to distribute advertisements and perform analytics on users to customize their advertisements. These networks build up a profile of their users (e.g., navigation patterns, visit frequency, personal interest), which poses a significant privacy risk as this information can be sold to others or used in targeted advertising. In order for users to protect themselves, they need to install add-ons for their web browser which removes third-party content. This paper surveys some of the existing add-ons to block third-party content, and determine which add-ons are required to provide adequate protection. Further analytics are conducted to evaluate the effectiveness of those add-ons through the experiments.
Positive Portrayals of Old Age Do Not Always Have Positive Consequences.

OBJECTIVES The literature on "image of aging" suggests that exposure to positive portrayals of old age has positive downstream consequences for older adults. This study examined whether these positive consequences might have limits, such that they occurred for portrayals of old age that were positive, but not those that were extremely positive. METHOD Younger and older adults were allowed to selectively view (Study 1) or were experimentally exposed to (Studies 2 and 3) portrayals of old age of different levels of positivity. Their attention (Study 1) and physiological responses (Study 2) toward the portrayals, as well as perception of personal aging (Study 1) and memory performance (Study 3) after the exposure, were assessed. RESULTS Findings from 3 studies suggested that older adults have a less negative perception of personal aging (Study 1) and a stronger calming physiological response (Study 2) when being exposed to portrayals of old age that were positive, but not extremely positive. Moreover, extremely positive portrayals lowered downstream memory performance (Study 3) and attracted less attention from older adults when they found these portrayals unrealistic (Study 1). DISCUSSION These findings pinpoint the conditions under which positive portrayals of old age may benefit older adults.
Capturing a Surface Light Field Under Virtual Illumination

Surface light fields can be used to render the complex reflectance properties of a physical object. One limitation is that they can only represent the fixed lighting conditions of the environment where the model was captured. If a specific lighting condition is desired, then there are two options: either use a combination of physical lights as an approximation, or capture a full 6D surface reflectance field and only use the portion that corresponds to the desired lighting. In this paper we present a method for capturing a surface light field using the virtual illumination from an environment map. We use a simple setup consisting of a projector, a camera, a pan-tilt unit, and tracking fiducials to recreate the desired lighting environment. To decrease noise and improve the quality of the capture under low- and highdynamic range environment maps, we use an extended version of the multiplexed illumination algorithm. We show results from objects captured under different lighting environments.
Generation of a Library of Non‐Toxic Quantum Dots for Cellular Imaging and siRNA Delivery

The development of non-toxic quantum dots and further investigation of their composition-dependent cytotoxicity in a high-throughput manner have been critical challenges for biomedical imaging and gene delivery. Herein, we report a rapid sonochemical synthetic methodology for generating a library of highly biocompatible ZnS-AgInS(2) (ZAIS) quantum dots for cellular imaging and siRNA delivery.
Vascular b -adrenergic receptor system is dysfunctional after myocardial infarction

Goldman. Vascular b -adrenergic receptor system is dysfunctional after myocardial infarction. Am J Physiol Heart Circ Physiol 280: H1129–H1135, 2001. —We identiﬁed abnormalities in the vascular b -adrenergic receptor ( b -AR) signaling pathway in heart failure after myocardial infarction (MI). To examine these abnormalities, we measured b -AR-mediated hemodynamics, vascular reactiv-ity, and the vascular b -AR molecular signaling components in rats with heart failure after MI. Six weeks after MI, these rats had an increased left ventricular (LV) end-diastolic pressure, decreased LV systolic pressure, and decreased rate of LV pressure change (dP/d t ). LV dP/d t responses to isoproterenol were shifted downward, although the responses for systemic vascular resistance were shifted upward in heart failure rats ( P , 0.05). Isoproterenol- and IBMX-induced vasorelaxations were blunted in heart failure rats ( P , 0.05) with no change in the forskolin-mediated vasorelaxation. These changes were associated with the following alterations in b -AR signaling ( P , 0.05): decreases in b -AR density (aorta: 58.7 6 6.0 vs. 35.7 6 1.9 fmol/mg membrane protein; carotid: 29.6 6 5.6 vs. 18.0 6 3.9 fmol/mg membrane protein, n 5 5), increases in G protein-coupled receptor kinase activity levels (relative phosphorimage counts of 191 6 39 vs. 259 6 26 in the aorta and 115 6 30 vs. 202 6 7 in the carotid artery, n 5 5), and decreases in cGMP and cAMP in the carotid artery (0.85 6 0.10 vs. 0.31 6 0.06 pmol/mg protein and 2.3 6 0.3 vs. 1.2 6 0.1 pmol/mg protein, n 5 5) with no change in G a s or G a i in the aorta. Thus in heart failure there are abnormalities in the vascular b -AR system that are similar to those seen in the myocardium. This suggests a common neurohormonal mechanism and raises the possibility that treatment in heart failure focused on the myocardium may also affect the vasculature.