Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel roles for well-known players: from tobacco mosaic virus pests to enzymatically active assemblies

The rod-shaped nanoparticles of the widespread plant pathogen tobacco mosaic virus (TMV) have been a matter of intense debates and cutting-edge research for more than a hundred years. During the late 19th century, their behavior in filtration tests applied to the agent causing the 'plant mosaic disease' eventually led to the discrimination of viruses from bacteria. Thereafter, they promoted the development of biophysical cornerstone techniques such as electron microscopy and ultracentrifugation. Since the 1950s, the robust, helically arranged nucleoprotein complexes consisting of a single RNA and more than 2100 identical coat protein subunits have enabled molecular studies which have pioneered the understanding of viral replication and self-assembly, and elucidated major aspects of virus–host interplay, which can lead to agronomically relevant diseases. However, during the last decades, TMV has acquired a new reputation as a well-defined high-yield nanotemplate with multivalent protein surfaces, allowing for an ordered high-density presentation of multiple active molecules or synthetic compounds. Amino acid side chains exposed on the viral coat may be tailored genetically or biochemically to meet the demands for selective conjugation reactions, or to directly engineer novel functionality on TMV-derived nanosticks. The natural TMV size (length: 300 nm) in combination with functional ligands such as peptides, enzymes, dyes, drugs or inorganic materials is advantageous for applications ranging from biomedical imaging and therapy approaches over surface enlargement of battery electrodes to the immobilization of enzymes. TMV building blocks are also amenable to external control of in vitro assembly and re-organization into technically expedient new shapes or arrays, which bears a unique potential for the development of 'smart' functional 3D structures. Among those, materials designed for enzyme-based biodetection layouts, which are routinely applied, e.g., for monitoring blood sugar concentrations, might profit particularly from the presence of TMV rods: Their surfaces were recently shown to stabilize enzymatic activities upon repeated consecutive uses and over several weeks. This review gives the reader a ride through strikingly diverse achievements obtained with TMV-based particles, compares them to the progress with related viruses, and focuses on latest results revealing special advantages for enzyme-based biosensing formats, which might be of high interest for diagnostics employing 'systems-on-a-chip'.
A Dependable SRAM with 7T/14T Memory Cells

SUMMARY This paper proposes a novel dependable SRAM with 7T/14T memory cells, and introduces a new concept, “quality of a bit (QoB)” for it. The proposed SRAM has three modes: a normal mode, highspeed mode, and dependable mode, and dynamically scales its reliability, power and speed by combining two memory cells for one-bit information (i.e. 14 T/bit). By carrying out Monte Carlo simulation in a 65-nm process technology, the minimum voltages in read and write operations are improved by 0.21 V and 0.26 V, respectively, with a bit error rate of 10 −8 kept. In addition, we confirm that the dependable mode achieves a lower bit error rate than the error correction code (ECC) and multi module redundancy (MMR). Furthermore, we propose a new memory array structure to avoid the half-selection problem in a write operation. The respective cell area overheads in the normal mode are 26% and 11% in the cases where additional transistors are pMOSes and nMOSes, compared to the conventional 6T memory cell.
Energy Minimization of Contours Using Boundary Conditions

Reconstruction of objects from a scene may be viewed as a data fitting problem using energy minimizing splines as the basic shape. The process of obtaining the minimum to construct the "best" shape can sometimes be important. Some of the potential problems in the Euler-Lagrangian variational solution proposed by Kass et al. (1988), were brought to light by Amini et al. (1990), and a dynamic programming (DP) method was also suggested. In this paper we further develop the DP solution. We show that in certain cases, the discrete form of the solution presented by Amini et al., and adopted subsequently by others may also produce local minima, and develop a strategy to avoid this. We provide a stronger form of the conditions necessary to derive a solution when the energy depends on the second derivative, as in the case of "active contours".
The impact of the minimum wage on job separations and working hours among young people in Poland

The aim of this paper is to investigate the impact of the minimum wage on the risk of job separation and changes in working hours among young people in Poland. To this end, we use longitudinal data from the Labour Force Survey 2003-2011 and a difference-in-differences matching estimator based on the changes in the individual position in the wage distribution. Specifically, we test the impact of the minimum wage by distinguishing between individuals who experienced a transition to the below-the-minimum-wage regime. Our results indicate that when the minimum wage was increased, employment levels, but not the number of hours of worked, declined among young people. We also found that the number of hours worked actually increased among those young people who remained employed after the minimum wage was raised. However, these effects of a hike in the minimum wage were found to have differed across various groups of workers, with men, students, and individuals who were working under a fixed-term contract being most likely to have either lost a job or increased their working longer hours.
Annual cycles in the interstellar scintillation time–scales of PKS B1519–273 and PKS B1622–253

We have used the University of Tasmania's 30-m radio telescope at Ceduna in South Australia to regularly monitor the flux density of a number of southern blazars. We report the detection of an annual cycle in the variability time-scale of the centimetre radio emission of PKSB1622−253. Observations of PKS B1519−273 over a period of nearly 2 yr confirm the presence of an annual cycle in the variability time-scale in that source. These observations prove that interstellar scintillation is the principal cause of inter-day variability at radio wavelengths in these sources. The best-fitting annual cycle model for both sources implies a high degree of anisotropy in the scattering screen and that it has a large velocity offset with respect to the local standard of rest. This is consistent with a greater screen distance for these 'slow' intra-day variability (IDV) sources than for rapid scintillators such as PKS B0405−385 or J1819+3845.
On a Cubic-Quintic Ginzburg-Landau Equation with Global Coupling

We study standing wave solutions in a Ginzburg-Landau equation which consists of a cubic-quintic equation stabilized by global coupling At = ΔA + μA + cA 3 - A 5 - kA (∫ Rn A 2 dx). We classify the existence and stability of all possible standing wave solutions.
Interval Diagram Techniques and Their Applications

Interval diagram techniques have been applied successfully to symbolic formal verification of process networks, Petri nets, a nd timed automata, outperforming conventional approaches and avoi ding some of their drawbacks. Our approach is based on a novel, efficient form of representation for multi-valued functions c alled interval decision diagram (IDD) and the corresponding image computation technique using interval mapping diagrams (IMDs). Besides formal verification, interval diagram techniques may be used to perform symbolic scheduling of heterogeneous embedded s ystems. IDDs and IMDs are presented, their properties are desc rib d, and the above applications are sketched.
A Fast Approach for Semantic Similar Short Texts Retrieval

Retrieving semantic similar short texts is a crucial issue to many applications, e.g., web search, ads matching, question-answer system, and so forth. Most of the traditional methods concentrate on how to improve the precision of the similarity measurement, while current real applications need to efﬁciently explore the top similar short texts semantically re-lated to the query one. We address the efﬁciency issue in this paper by investigating the similarity strategies and incorporating them into the FAST framework (efﬁcient F r A mework for semantic similar S hort T exts retrieval). We conduct comprehensive performance evaluation on real-life data which shows that our proposed method outperforms the state-of-the-art techniques.
Simulating the Random Dopant Effect: A New Three- Dimensional Monte Carlo Approach

In this work, we present a new three-dimensional Monte Carlo (MC) method which naturally recovers the realspace carrier-impurity Coulomb interaction by mesh-based resolution of Poisson’s equation. This method necessitates no additional modifications to the conventional MC simulator, thus simplifying the implementation process. The new method has been validated through the reproduction of the doping concentration dependent low-field electron and hole mobility in bulk Si. It is shown that our method can be an efficient alternative to the particle-particle-particle-mesh (P 3 M) approach, which is useful for the simulation of discrete random dopant fluctuation (RDF) effect. Keywords-random dopant fluctuation (RDF); Monte Carlo; Coulomb interation; impurity
Identification of Transduction Elements for Benzodiazepine Modulation of the GABAA Receptor: Three Residues Are Required for Allosteric Coupling

Modulation of GABAA receptors by benzodiazepines (BZDs) is believed to involve two distinct steps: a recognition step in which BZDs bind and a conformational transition step in which the affinity of the receptor for GABA changes. Previously, using γ2/α1 chimeric subunits (χ), we demonstrated that although the N-terminal 167 γ2 amino acid residues confer high-affinity BZD binding, other γ2domains couple BZD binding to potentiation of the GABA-mediated Cl− current (IGABA). To determine which γ2 regions couple binding to potentiation, we generated χs with longer N-terminal γ2 segments for voltage-clamp experiments in Xenopus oocytes. Chimeras containing greater than the N-terminal 167 γ2 residues showed incremental gains in maximal potentiation for diazepam enhancement ofIGABA. Residues in γ2199–236, γ2224–236 (pre-M1), and particularly γ2257–297 (M2 and surrounding loops) are important for BZD potentiation. For several positive BZD modulators tested, the same regions restored potentiation of IGABA. In contrast, β-carboline inverse-agonism was unaltered in chimeric receptors, suggesting that structural determinants for positive and negative BZD allosteric modulation are different. Dissection of the γ2257–297 domain revealed that three residues in concert, γ2T281, γ2I282 (M2 channel vestibule), and γ2S291 (M2–M3 loop) are necessary to impart full BZD potentiation to chimeric receptors. Thus, these residues participate in coupling distant BZD-binding events to conformational changes in the GABAA receptor. The location of these novel residues provides insight into the mechanisms underlying allosteric coupling for other members of the ligand-gated ion channel superfamily.
Structure-function of proteins interacting with the α1 pore-forming subunit of high-voltage-activated calcium channels

Openings of high-voltage-activated (HVA) calcium channels lead to a transient increase in calcium concentration that in turn activate a plethora of cellular functions, including muscle contraction, secretion and gene transcription. To coordinate all these responses calcium channels form supramolecular assemblies containing effectors and regulatory proteins that couple calcium influx to the downstream signal cascades and to feedback elements. According to the original biochemical characterization of skeletal muscle Dihydropyridine receptors, HVA calcium channels are multi-subunit protein complexes consisting of a pore-forming subunit (α1) associated with four additional polypeptide chains β, α2, δ, and γ, often referred to as accessory subunits. Twenty-five years after the first purification of a high-voltage calcium channel, the concept of a flexible stoichiometry to expand the repertoire of mechanisms that regulate calcium channel influx has emerged. Several other proteins have been identified that associate directly with the α1-subunit, including calmodulin and multiple members of the small and large GTPase family. Some of these proteins only interact with a subset of α1-subunits and during specific stages of biogenesis. More strikingly, most of the α1-subunit interacting proteins, such as the β-subunit and small GTPases, regulate both gating and trafficking through a variety of mechanisms. Modulation of channel activity covers almost all biophysical properties of the channel. Likewise, regulation of the number of channels in the plasma membrane is performed by altering the release of the α1-subunit from the endoplasmic reticulum, by reducing its degradation or enhancing its recycling back to the cell surface. In this review, we discuss the structural basis, interplay and functional role of selected proteins that interact with the central pore-forming subunit of HVA calcium channels.
Distributed Sensor Selection using a Truncated Newton Method

We propose a new distributed algorithm for computing a truncated Newton method, where the main diagonal of the Hessian is computed using belief propagation. As a case study for this approach, we examine the sensor selection problem, a Boolean convex optimization problem. We form two distributed algorithms. The first algorithm is a distributed version of the interior point method by Joshi and Boyd, and the second algorithm is an order of magnitude faster approximation. As an example application we discuss distributed anomaly detection in networks. We demonstrate the applicability of our solution using both synthetic data and real traffic logs collected from the Abilene Internet backbone.
Friction law for dense granular flows: application to the motion of a mass down a rough inclined plane

The problem of the spreading of a granular mass released at the top of a rough inclined plane was investigated. The evolution of the avalanche was measured experimentally from the initiation up to the deposit using a Moiré image-processing technique. The results are quantitatively compared with the prediction of an hydrodynamic model based on depth-averaged equations. In the model, the interaction between the flowing layer and the rough bottom is described by a non-trivial friction force whose expression is derived from measurements on steady uniform flows. We show that the spreading of the mass is quantitatively predicted by the model when the mass is released on a plane free of particles. When an avalanche is triggered on an initially static layer, the model fails in quantitatively predicting the propagation but qualitatively captures the evolution.
Humanoid navigation and heavy load transportation in a cluttered environment

Although in recent years several studies aimed at the navigation of robots in cluttered environments, just a few have addressed the problem of robots navigating while moving a large or heavy object. This is especially useful when transporting loads with variable weights and shapes without having to change the robot hardware. On one hand, a major advantage of using a humanoid robot to move an object is that it has arms to firmly grasp it and control it. On the other hand, humanoid robots tend to have higher drift than their wheeled counterparts as well as having significant lateral swing while walking, which propagates to anything they carry. In this work, we present algorithms for a humanoid robot navigating in a cluttered environment while pushing a cart-like object. In addition, the algorithms make use of the hands and arms to articulate the cart when executing tight turns using whole body control scheme to reduce the lateral swing effect on the load and ensure a safe transport. Experiments conducted on a real Nao robot assessed the proposed approach and algorithms, they show that the payload of a humanoid robot can be significantly increased without changing the humanoid robot's hardware, and therefore enact the capacity of humanoid robots in real-life situations.
Oxidative addition of the ethane CC bond to Pd. An ab initio benchmark and DFT validation study

We have computed a state‐of‐the‐art benchmark potential energy surface (PES) for the archetypal oxidative addition of the ethane CC bond to the palladium atom and have used this to evaluate the performance of 24 popular density functionals, covering LDA, GGA, meta‐GGA, and hybrid density functionals, for describing this reaction. The ab initio benchmark is obtained by exploring the PES using a hierarchical series of ab initio methods [HF, MP2, CCSD, CCSD(T)] in combination with a hierarchical series of five Gaussian‐type basis sets, up to g polarization. Relativistic effects are taken into account either through a relativistic effective core potential for palladium or through a full four‐component all‐electron approach. Our best estimate of kinetic and thermodynamic parameters is −10.8 (−11.3) kcal/mol for the formation of the reactant complex, 19.4 (17.1) kcal/mol for the activation energy relative to the separate reactants, and −4.5 (−6.8) kcal/mol for the reaction energy (zero‐point vibrational energy‐corrected values in parentheses). Our work highlights the importance of sufficient higher angular momentum polarization functions for correctly describing metal‐d‐electron correlation. Best overall agreement with our ab initio benchmark is obtained by functionals from all three categories, GGA, meta‐GGA, and hybrid DFT, with mean absolute errors of 1.5 to 2.5 kcal/mol and errors in activation energies ranging from −0.2 to −3.2 kcal/mol. Interestingly, the well‐known BLYP functional compares very reasonably with a slight underestimation of the overall barrier by −0.9 kcal/mol. For comparison, with B3LYP we arrive at an overestimation of the overall barrier by 5.8 kcal/mol. On the other hand, B3LYP performs excellently for the central barrier (i.e., relative to the reactant complex) which it underestimates by only −0.1 kcal/mol. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1006–1020, 2005
Risk Alleles for Systemic Lupus Erythematosus in a Large Case-Control Collection and Associations with Clinical Subphenotypes

Systemic lupus erythematosus (SLE) is a genetically complex disease with heterogeneous clinical manifestations. Recent studies have greatly expanded the number of established SLE risk alleles, but the distribution of multiple risk alleles in cases versus controls and their relationship to subphenotypes have not been studied. We studied 22 SLE susceptibility polymorphisms with previous genome-wide evidence of association (p<5×10−8) in 1919 SLE cases from 9 independent Caucasian SLE case series and 4813 independent controls. The mean number of risk alleles in cases was 15.1 (SD 3.1) while the mean in controls was 13.1 (SD 2.8), with trend p = 4×10−128. We defined a genetic risk score (GRS) for SLE as the number of risk alleles with each weighted by the SLE risk odds ratio (OR). The OR for high-low GRS tertiles, adjusted for intra-European ancestry, sex, and parent study, was 4.4 (95% CI 3.8–5.1). We studied associations of individual SNPs and the GRS with clinical manifestations for the cases: age at diagnosis, the 11 American College of Rheumatology classification criteria, and double-stranded DNA antibody (anti-dsDNA) production. Six subphenotypes were significantly associated with the GRS, most notably anti-dsDNA (ORhigh-low = 2.36, p = 9e−9), the immunologic criterion (ORhigh-low = 2.23, p = 3e−7), and age at diagnosis (ORhigh-low = 1.45, p = 0.0060). Finally, we developed a subphenotype-specific GRS (sub-GRS) for each phenotype with more power to detect cumulative genetic associations. The sub-GRS was more strongly associated than any single SNP effect for 5 subphenotypes (the above plus hematologic disorder and oral ulcers), while single loci are more significantly associated with renal disease (HLA-DRB1, OR = 1.37, 95% CI 1.14–1.64) and arthritis (ITGAM, OR = 0.72, 95% CI 0.59–0.88). We did not observe significant associations for other subphenotypes, for individual loci or the sub-GRS. Thus our analysis categorizes SLE subphenotypes into three groups: those having cumulative, single, and no known genetic association with respect to the currently established SLE risk loci.
Using Decision Diagrams to Design ULMs for FPGAs

Many modern field programmable logic arrays (FPGAs) use lookup table (LUT) logic blocks which can be programmed to realize any function of a fixed number of inputs. It is possible to employ logic blocks that realize only a subset of all functions, while the rest can be obtained by permuting and negating the inputs such blocks, known as Universal Logic Modules (ULMs), have already been considered for application in FPGAs; we propose a new class of ULMs which is more useful in the FPGA environment. Methodology for systematic development of such blocks is presented, based on the BDD description of logic functions. We give an explicit construction of a three-input LUT replacement that requires only five programming bits, which is the optimum for such ULMs. A realistic size four-input LUT replacement is obtained which uses 13 programming bits.
ret2dir: Deconstructing Kernel Isolation

Return-to-user (ret2usr) attacks redirect corrupted kernel pointers to data residing in user space. In response, several kernel-hardening approaches have been proposed to enforce a more strict address space separation, by preventing arbitrary control flow transfers and dereferences from kernel to user space. Intel and ARM also recently introduced hardware support for this purpose in the form of the SMEP, SMAP, and PXN processor features. Unfortunately, although mechanisms like the above prevent the explicit sharing of the virtual address space among user processes and the kernel, conditions of implicit sharing still exist due to fundamental design choices that trade stronger isolation for performance. In this work, we demonstrate how implicit page frame sharing can be leveraged for the complete circumvention of software and hardware kernel isolation protections. We introduce a new kernel exploitation technique, called return-to-direct-mapped memory (ret2dir), which bypasses all existing ret2usr defenses, namely SMEP, SMAP, PXN, KERNEXEC, UDEREF, and kGuard. We also discuss techniques for constructing reliable ret2dir exploits against x86, x86-64, AArch32, and AArch64 Linux targets. Finally, to defend against ret2dir attacks, we present the design and implementation of an exclusive page frame ownership scheme for the Linux kernel that prevents the implicit sharing of physical memory pages with minimal runtime overhead.
Inter-Domain QoS Routing Algorithms

Quality-of-Service routing satisfies performance requirements of applications and maximizes utilization of network resources by selecting paths based on the resource needs of application sessions and link load. QoS routing can significantly increase the number of reserved bandwidth sessions that a network can carry, while meeting application QoS requirements. Most research on QoS routing to date, has focussed on routing within a single domain. We argue that since the peering links joining different network domains are often congestion points for network traffic, it is even more important to apply QoS routing concepts to inter-domain routing. BGP, the de facto standard for inter-domain routing provides no support for QoS routing, and indeed it facilitates the use of localized routing polices that can lead to poor end-to-end performance. This paper proposes a new approach to inter-domain routing for sessions requiring reserved resources. We introduce two specific routing algorithms based on this approach and evaluate their performance using simulation.