Miracle-dz/UniFAR-FTUs huggingface dataset:
Symbolic search-based testing

We present an algorithm for constructing fitness functions that improve the efficiency of search-based testing when trying to generate branch adequate test data. The algorithm combines symbolic information with dynamic analysis and has two key advantages: It does not require any change in the underlying test data generation technique and it avoids many problems traditionally associated with symbolic execution, in particular the presence of loops. We have evaluated the algorithm on industrial closed source and open source systems using both local and global search-based testing techniques, demonstrating that both are statistically significantly more efficient using our approach. The test for significance was done using a one-sided, paired Wilcoxon signed rank test. On average, the local search requires 23.41% and the global search 7.78% fewer fitness evaluations when using a symbolic execution based fitness function generated by the algorithm.
The Energetic Cost of Climbing in Primates

Primates are exceptional among mammals for their climbing abilities and arboreal lifestyles. Here we show that small primates (less than 0.5 kilogram) consume the same amount of mass-specific energy (COTTOT) whether climbing or walking a given distance. COTTOT decreases with increasing body size for walking but does not change for climbing. This divergence of COTTOT is likely due to fundamental differences in the biomechanical determinants of the costs of climbing versus walking. These results have important implications for understanding the origins of primates, suggesting that small early primates may have been able to move into a novel arboreal niche without increasing metabolic costs.
Cause-of-Death Analysis in Rodent Aging Studies

In research studies using rats or mice, the cause of death is often not evaluated or reported. An analysis of the causes of death is particularly valuable for aging and carcinogenesis studies. Comparing causes of death among the study groups is often an important adjunct to the biochemical, molecular, clinical, and histopathologic findings. The methods for evaluating causes of death, contributing causes of death, and comorbidities have been suggested in several publications. Surprisingly, in important mouse aging studies, causes of death are often not reported. Cause-of-death assignment in preclinical rodent model aging research suffers from a lack of a standardized approach and an understanding of the value that it can add to longevity and interventional studies. While assigning single cause of death may facilitate data analysis, defining and publishing data on contributing causes (comorbidities) provides more information on associated underlying chronic conditions and health span in mouse models. This article reviews factors that affect determination of cause of death and the methods for evaluating causes of death and comorbidities. The proposed systematic pathology analysis includes assigning cause of death and comorbidities to define total disease burden. The combination of pathology with in vivo data will fully characterize the effect of tested interventions on multiple chronic diseases and health span of aging mice with improved translation to human aging and age-associated lesions.
Virus Attenuation by Genome-Scale Changes in Codon Pair Bias

As a result of the redundancy of the genetic code, adjacent pairs of amino acids can be encoded by as many as 36 different pairs of synonymous codons. A species-specific “codon pair bias” provides that some synonymous codon pairs are used more or less frequently than statistically predicted. We synthesized de novo large DNA molecules using hundreds of over-or underrepresented synonymous codon pairs to encode the poliovirus capsid protein. Underrepresented codon pairs caused decreased rates of protein translation, and polioviruses containing such amino acid–independent changes were attenuated in mice. Polioviruses thus customized were used to immunize mice and provided protective immunity after challenge. This “death by a thousand cuts” strategy could be generally applicable to attenuating many kinds of viruses.
Epidermal Growth Factor Induces the Progeny of Subventricular Zone Type B Cells to Migrate and Differentiate into Oligodendrocytes

New neurons and oligodendrocytes are continuously produced in the subventricular zone (SVZ) of adult mammalian brains. Under normal conditions, the SVZ primary precursors (type B1 cells) generate type C cells, most of which differentiate into neurons, with a small subpopulation giving rise to oligodendrocytes. Epidermal growth factor (EGF) signaling induces dramatic proliferation and migration of SVZ progenitors, a process that could have therapeutic applications. However, the fate of cells derived from adult neural stem cells after EGF stimulation remains unknown. Here, we specifically labeled SVZ B1 cells and followed their progeny after a 7‐day intraventricular infusion of EGF. Cells derived from SVZ B1 cells invaded the parenchyma around the SVZ into the striatum, septum, corpus callosum, and fimbria‐fornix. Most of these B1‐derived cells gave rise to cells in the oligodendrocyte lineage, including local NG2+ progenitors, and premyelinating and myelinating oligodendrocytes. SVZ B1 cells also gave rise to a population of highly‐branched S100β+/glial fibrillary acidic protein (GFAP)+ cells in the striatum and septum, but no neuronal differentiation was observed. Interestingly, when demyelination was induced in the corpus callosum by a local injection of lysolecithin, an increased number of cells derived from SVZ B1 cells and stimulated to migrate and proliferate by EGF infusion differentiated into oligodendrocytes at the lesion site. This work indicates that EGF infusion can greatly expand the number of progenitors derived from the SVZ primary progenitors which migrate and differentiate into oligodendroglial cells. This expanded population could be used for the repair of white matter lesions. STEM CELLS 2009;27:2032–2043
H 3 N 2 Canine Influenza Virus Infection in a Dog

In 2015, H3N2 canine influenza emerged in dogs in the greater Chicago area. During this time, a 10-year-old German Shepherd dog presented to the referring veterinarian with lethargy and coughing that quickly progressed to death. This report describes the macroscopic and microscopic lesions and the molecular testing performed to identify the novel North American H3N2 strain of canine influenza. The larynx, pharynx, and trachea were covered by a fibrinonecrotic membrane. Bilaterally, the lungs had multifocal subpleural necrosis of the caudal lung lobes with hemorrhage, congestion, and pulmonary edema. Staphylococcus pseudointermedius was isolated from the lung. Mycoplasma cynos was identified by real-time polymerase chain reaction from nasal passages, oropharynx, larynx, trachea, and cranial lung lobes. The neuraminidase gene sequence from the influenza virus isolated obtained from this dog had 98% homology to the strain circulating in the Chicago area.
Consumer concern about food related health risks and their trust in experts

Theorists have claimed that we see an increased focus on risk in the society of today. Furthermore, the media has to an increasing degree focused on differences of opinion between various experts. It has been postulated that this may have led to a decline in the authority experts formerly possessed. With these theories as a point of departure, this paper presents results of a survey of consumer apprehension and valuations with regard to food‐related health risks. A survey of a representative sample of 1,050 Norwegian consumers above 15 years of age included questions pertaining to food safety, such as additives and contaminants, as well as nutritional aspects of the diet. Norwegian consumers were in general very much aware of the relationship between food and health, and also felt rather safe about these issues. A factor analysis of responses to different statements related to food and health identified two main factors, labelled “feeling of uncertainty” and “trust in experts. ” More respondents expressed “trust in experts” than “feeling of uncertainty. ” There were great variations between different consumer groups with regard to these factors, as well as their opinions on what aspects contribute to a healthy diet. Even though respondents expressed concern related to both the nutritional aspects of food and food safety issues, consumers felt a larger need for good and dependable information on the food safety issues.
Design of a UHF RFID tag baseband with the hummingbird cryptographic engine

Radio frequency identification (RFID) is a technology for automatic object identification. It has wide applications in many areas such as manufacturing, transportation, healthcare, and so on. However, many RFID systems are suffering from security issues. In this paper, we present an implementation of a secure UHF RFID tag baseband with a Hummingbird (HB) cryptographic engine using the SMIC 0. 13µm technology. An improvement of the Gen2 protocol based on our secure engine is proposed to enhance security. The implementation results show that the area of our baseband is 16,986 gate equivalents and the secure engine takes 23.6% of the entire die area. The overall power consumption of our baseband is 30. 67µW at a clock frequency of 1.28MHz and with 1.2V power supply, which is suitable for resource-constrained RFID tags.
Implementing A Star for Bicycle Route Finding System using OSM and GraphHopper: Case Study: Batu, Indonesia

Cycling is an environmentally friendly alternative to transportation and sports. We provide a website-based navigation system for determining bicycle routes in Batu city named GoWes. GoWes is expected to assist in finding the best and fastest path for cycling. The public can find information about conducive cycling according to predetermined parameters. The parameters in this application are bicycle paths with minimum travel time, minimum travel distance, and minimum elevation. Some data are needed to classify the paths conducive for cycling, such as altitude data, road network maps, and data on public facilities in Batu City. The result of this research is a website that contains information on recommended cycling paths, which has been integrated with OpenStreetMap, GraphHopper routing engine, and SRTM as elevation data. The A-Star algorithm is applied in this study to identify the route with the shortest distance and lowest travel time. Tests were carried out using black box testing. With the help of this information, the system can suggest appropriate paths for each individual and estimate very accurate travel times.
EM Based Iterative Receiver for Joint Decoding and Channel Parameter Estimation in Space-Frequency Turbo Coded OFDM

Expectation-maximization (EM) based joint decoding and channel parameter estimation for multiple-input multiple-output (MIMO) orthogonal frequency division multiplexing (OFDM) system is considered. A new iterative receiver structure is proposed to operate together with space-frequency turbo coded modulation (SFTuCM) using decoder outputs to refine the channel parameter estimates. The proposed receiver performs well with low pilot overhead despite the fast changing channel state. The proposed receiver improves not only the error probability performance but remarkable improvement is achieved in the channel parameter estimation accuracy when compared to pilot based estimation with the same overhead
Serveur Académique Lausannois SERVAL serval.unil.ch

The inhalation of airborne pollutants, such as asbestos or silica, is linked to inflammation of the lung, fibrosis, and lung cancer. How the presence of pathogenic dust is recognized and how chronic inflammatory diseases are triggered are poorly understood. Here, we show that asbestos and silica are sensed by the Nalp3 inflammasome, whose subsequent activation leads to interleukin 1 β secretion. Inflammasome activation is triggered by reactive oxygen species, which are generated by a NADPH oxidase upon particle phagocytosis (NADPH is the reduced form of nicotinamide adenine dinucleotide phosphate). In a model of asbestos inhalation, Nalp3 − / − mice showed diminished recruitment of inflammatory cells to the lungs, paralleled by lower cytokine production. Our findings implicate the Nalp3 inflammasome in particulate matter–related pulmonary diseases and support its role as a major proinflammatory “danger” receptor.
Finite Scale of Spatial Representation in the Hippocampus

To determine how spatial scale is represented in the pyramidal cell population of the hippocampus, we recorded neural activity at multiple longitudinal levels of this brain area while rats ran back and forth on an 18-meter-long linear track. CA3 cells had well-defined place fields at all levels. The scale of representation increased almost linearly from <1 meter at the dorsal pole to ∼10 meters at the ventral pole. The results suggest that the place-cell map includes the entire hippocampus and that environments are represented in the hippocampus at a topographically graded but finite continuum of scales.
Brief Report: Impaired Cell Reprogramming in Nonhomologous End Joining Deficient Cells

Although there is an increasing interest in defining the role of DNA damage response mechanisms in cell reprogramming, the relevance of proteins participating in nonhomologous end joining (NHEJ), a major mechanism of DNA double‐strand breaks repair, in this process remains to be investigated. Herein, we present data related to the reprogramming of primary mouse embryonic fibroblasts (MEF) from severe combined immunodeficient (Scid) mice defective in DNA‐PKcs, a key protein for NHEJ. Reduced numbers of induced pluripotent stem cell (iPSC) colonies were generated from Scid cells using reprogramming lentiviral vectors (LV), being the reprogramming efficiency fourfold to sevenfold lower than that observed in wt cells. Moreover, these Scid iPSC‐like clones were prematurely lost or differentiated spontaneously. While the Scid mutation neither reduce the proliferation rate nor the transduction efficacy of fibroblasts transduced with reprogramming LV, both the expression of SA‐β‐Gal and of P16/INK4a senescence markers were highly increased in Scid versus wt MEFs during the reprogramming process, accounting for the reduced reprogramming efficacy of Scid MEFs. The use of improved Sleeping Beauty transposon/transposase systems allowed us, however, to isolate DNA‐PKcs‐deficient iPSCs which preserved their parental genotype and hypersensitivity to ionizing radiation. This new disease‐specific iPSC model would be useful to understand the physiological consequences of the DNA‐PKcs mutation during development and would help to improve current cell and gene therapy strategies for the disease. STEM Cells 2013;31:1726–1730
Challenges in Modeling Materials Properties Without Experimental Input

Simulations of materials behavior are an important component of materials science research, partly because measurements are indirect, requiring theoretical interpretation, and partly because often the ideal experiment simply cannot be performed (due to technological limitations). Empirical physical models used in this context often rely on parameters drawn from experiments on simpler systems, and so introduce various inaccuracies. In contrast, a quantum mechanical model can potentially offer an independent source of data more closely attuned to the complexities of the system at hand. This Perspective reviews current quantum mechanics–based materials modeling approaches and their successes and limitations, and offers a view to the future.
Trustingness & trustworthiness: A pair of complementary trust measures in a social network

The increase in analysis of real life social networks has led to a better understanding of the ways humans socialize in a group. Since trust is an important part of any social interaction, researchers use such networks to understand the nuances of trust relationships. One of the major requirements in trust applications is identifying the trustworthy actors in these networks. This paper proposes a pair of complementary measures that can be used to measure trust scores of actors in a social network using involvement of social networks. Based on the proposed measures, an iterative matrix convergence algorithm is developed that calculates the trustingness and the trustworthiness of each actor in the network. Trustingness of an actor is defined as the propensity of an actor to trust his neighbors in the network. Trustworthiness, on the other hand, is defined as the willingness of the network to trust an individual actor. The algorithm is proposed based on the idea that a person having higher trustingness score contributes to the trustworthiness of its neighbors to a lower degree. Conversely, a higher trustworthiness score is a result of lots of neighbors linked to the actor having low trustingness scores. The algorithm runs in O(k × |E|) time where k denotes the number of iterations and |E| denotes the number of edges in the network. Moreover, the paper shows that the algorithm converges to a finite value quickly. Finally the proposed scores for trust prediction is implemented for various social networks and is shown that the proposed algorithm performs better (average 5%) than the state of the art trust scoring algorithms. The full version of the paper along with the coding implementation can be found at [3].
Structural and Biochemical Characterization of AidC, a Quorum‐Quenching Lactonase With Atypical Selectivity

Quorum‐quenching catalysts are of interest for potential application as biochemical tools for interrogating interbacterial communication pathways, as antibiofouling agents, and as anti‐infective agents in plants and animals. Herein, the structure and function of AidC, an N‐acyl‐l‐homoserine lactone (AHL) lactonase from Chryseobacterium, is characterized. Steady‐state kinetics show that zinc‐supplemented AidC is the most efficient wild‐type quorum‐quenching enzymes characterized to date, with a kcat/KM value of approximately 2 × 106 M−1 s−1 for N‐heptanoyl‐l‐homoserine lactone. The enzyme has stricter substrate selectivity and significantly lower KM values (ca. 50 μM for preferred substrates) compared to those of typical AHL lactonases (ca. >1 mM). X‐ray crystal structures of AidC alone and with the product N‐hexanoyl‐l‐homoserine were determined at resolutions of 1.09 and 1.67 Å, respectively. Each structure displays as a dimer, and dimeric oligiomerization was also observed in solution by size‐exclusion chromatography coupled with multiangle light scattering. The structures reveal two atypical features as compared to previously characterized AHL lactonases: a “kinked” α‐helix that forms part of a closed binding pocket that provides affinity and enforces selectivity for AHL substrates and an active‐site His substitution that is usually found in a homologous family of phosphodiesterases. Mutations on this His substitution are being studied along with other suspected catalytic residues. Implications of the catalytic mechanism of AHL lactonases will be discussed based on these data and prior knowledge of other AHL lactonases.
The Structure of Mercury's Magnetic Field from MESSENGER's First Flyby

During its first flyby of Mercury, the MESSENGER spacecraft measured the planet's near-equatorial magnetic field. The field strength is consistent to within an estimated uncertainty of 10% with that observed near the equator by Mariner 10. Centered dipole solutions yield a southward planetary moment of 230 to 290 nanotesla RM3 (where RM is Mercury's mean radius) tilted between 5° and 12° from the rotation axis. Multipole solutions yield non-dipolar contributions of 22% to 52% of the dipole field magnitude. Magnetopause and tail currents account for part of the high-order field, and plasma pressure effects may explain the remainder, so that a pure centered dipole cannot be ruled out.
12-Step Participation and Attitudes Toward 12-Step Meetings in Dual Diagnosis Patients

Abstract This study examined participation in 12-step programs and attitudes toward 12-step meetings in an outpatient sample of 81 severely mentally ill patients with comorbid substance use disorders. The study found that dual diagnosis patients attended 12-step programs at rates comparable to those reported for patients in primary addiction treatment settings. Diagnosis and attitudes toward 12-step meetings each had independent effects on 12-step participation. The difficulties that some dual diagnosis patients report experiencing at 12-step meetings may need to be addressed to maximize 12-step attendance and potential to benefit from 12-step programs.
Broadband Circularly Polarized Metasurface Antenna Based on Characteristic Mode Analysis

A broadband circularly polarized (CP) metasurface antenna based on characteristic mode analysis (CMA) is proposed. The antenna consists of a truncated corner square driver patch loaded with L-shaped branches, sandwiched between a $4\times 4$ metasurface and a ground plane. The CP wave is generated by exciting the driving patch, and the CP wave excites the surface wave propagating on the metasurface, resulting in a wide impedance bandwidth and Axial ratio (AR) bandwidth. The overall size of the antenna is $36\text{mm}\times 36\text{mm}\times 4.5\text{mm}\ (0.72\ \lambda_{0}\times 0.72 \lambda_{0}\times 0.09\ \lambda_{0})$. The simulation results show that the bandwidth of $\vert \mathrm{S}_{11}\vert < -10\ \text{dB}$ is 4.04-8.83 GHz (74.44%), the 3dB AR bandwidth is 4.65-6.92 GHz (39.24%), and the peak gain is 6.83 dBic. In addition, the antenna has good left-handed CP radiation performance within the operating bandwidth, which is suitable for C-band satellite communication applications.
High Rates of Oxygen Reduction over a Vapor Phase–Polymerized PEDOT Electrode

The air electrode, which reduces oxygen (O2), is a critical component in energy generation and storage applications such as fuel cells and metal/air batteries. The highest current densities are achieved with platinum (Pt), but in addition to its cost and scarcity, Pt particles in composite electrodes tend to be inactivated by contact with carbon monoxide (CO) or by agglomeration. We describe an air electrode based on a porous material coated with poly(3,4-ethylenedioxythiophene) (PEDOT), which acts as an O2 reduction catalyst. Continuous operation for 1500 hours was demonstrated without material degradation or deterioration in performance. O2 conversion rates were comparable with those of Pt-catalyzed electrodes of the same geometry, and the electrode was not sensitive to CO. Operation was demonstrated as an air electrode and as a dissolved O2 electrode in aqueous solution.
MESSENGER Observations of the Composition of Mercury's Ionized Exosphere and Plasma Environment

The region around Mercury is filled with ions that originate from interactions of the solar wind with Mercury's space environment and through ionization of its exosphere. The MESSENGER spacecraft's observations of Mercury's ionized exosphere during its first flyby yielded Na+, O+, and K+ abundances, consistent with expectations from observations of neutral species. There are increases in ions at a mass per charge (m/q) = 32 to 35, which we interpret to be S+ and H2S+, with (S+ + H2S+)/(Na+ + Mg+) = 0.67 ± 0.06, and from water-group ions around m/q = 18, at an abundance of 0.20 ± 0.03 relative to Na+ plus Mg+. The fluxes of Na+, O+, and heavier ions are largest near the planet, but these Mercury-derived ions fill the magnetosphere. Doubly ionized ions originating from Mercury imply that electrons with energies less than 1 kiloelectron volt are substantially energized in Mercury's magnetosphere.