Miracle-dz/UniFAR-FTUs huggingface dataset:
A Provably Convergent Multifidelity Optimization Algorithm not Requiring High-Fidelity Derivatives

This paper presents a provably convergent multifidelity optimization algorithm for unconstrained problems that does not require high-fidelity gradients. The method uses a radial basis function interpolation to capture the error between a high-fidelity function and a low-fidelity function. The error interpolation is added to the low-fidelity function to create a surrogate model of the high-fidelity function in the neighborhood of a trust region. When appropriately distributed spatial calibration points are used, the low-fidelity function and radial basis function interpolation generate a fully linear model. This condition is sufficient to prove convergence in a trust region framework. In the case when there are multiple lower-fidelity models, the predictions of all calibrated lower-fidelity models can be combinedwith amaximum likelihood estimator constructed using kriging variance estimates from the radial basis function models. This procedure allows for flexibility in sampling lower-fidelity functions, does not alter the convergence proof of the optimization algorithm, and is shown to be robust to poor low-fidelity information. The algorithm is comparedwith a single-fidelity quasi-Newton algorithmand twofirst-order consistentmultifidelity trust region algorithms. For simple functions the quasi-Newton algorithm uses slightly fewer high-fidelity function evaluations; however, for more complex supersonic airfoil design problems it uses significantly more. In all cases tested, our radial basis function calibration approach uses fewer high-fidelity function evaluations when compared with first-order consistent trust region schemes.
Novel renewable ionic liquids as highly effective solvents for pretreatment of rice straw biomass by selective removal of lignin

Cholinium amino acids ionic liquids ([Ch][AA] ILs), a novel type of bio‐ILs that can easily be prepared from renewable biomaterials, were investigated for pretreatment of rice straw by selective extraction of lignin from this abundant lignocellulosic biomass material. Of the eight ILs examined, most were demonstrated to be excellent pretreatment solvents. Upon pretreatment using these ILs, the initial saccharification rates of rice straw residues were substantially improved as well as the extent to which polysaccharides could be digested (>90% for cellulose and >60% for xylan). Enzymatic hydrolysis of pretreated rice straw by Trichoderma reesei cellulase/xylanase furnished glucose and xylose with the yields in excess of 80% and 30%, respectively. Detailed spectroscopic characterization showed that the enhancement of polysaccharides degestibility derived mainly from delignification rather than changes in cellulose crystallinity. The yields of fermentable reducing sugars were significantly improved after individual optimization of pretreatment temperature and duration. With [Ch][Lys] as the solvent, the sugar yields of 84.0% for glucose and 42.1% for xylose were achieved after pretreatment at 90°C for 5 h. The IL [Ch][Lys] showed excellent reusability across five successive batches in pretreatment of rice straw. These bio‐ILs performed as well as or better than previously investigated non‐renewable ILs, and thus present a new and environmentally friendly way to pretreat lignocellulose for production of fermentable sugars and total utilization of the biomass. Biotechnol. Bioeng. 2012; 109: 2484–2493. © 2012 Wiley Periodicals, Inc.
Testosterone production, sexually dimorphic morphology, and digit ratio in the dark-eyed junco

The hormonal environment an individual experiences during development can have lasting effects on behavior, morphology, and physiology. However, measuring endogenous hormone exposure during early embryonic development and relating it to adult phenotype has proved to be challenging. The relative length of digit 2 to digit 4 (2D:4D) in adults is thought to reflect the relative concentration of androgens and estrogens during development and has been used as a morphological proxy of developmental hormone exposure, enabling the exploration of the relationships between individual differences in hormone exposure and phenotype. Here, we use this approach and ask whether 2D:4D relates to the responsiveness of the adult hypothalamic-pituitary-gonadal axis and to sexually dimorphic structures (wing, tail, and tarsus length) in a common songbird, the dark-eyed junco (Junco hyemalis). Among males, we found a negative relationship between 2D:4D and the ability to elevate testosterone in response to a physiological challenge, an injection of gonadotropin-releasing hormone. We also found age- and sex-specific relationships between 2D:4D and wing, tail, and tarsus length. We found a positive relationship between 2D:4D and body size measures in females, and second-year and older males, but a negative relationship in first-year males. We conclude that individual variation in exposure to developmental hormones, as reflected by 2D:4D, is correlated with adult hormone production ability and sexually dimorphic morphology in adulthood, suggesting that endogenous variation in steroid hormone exposure may have long-term consequences similar to those seen in experimental manipulations.
Negative and positive regulation by a short segment in the 5'-flanking region of the human cytomegalovirus major immediate-early gene

To analyze the significance of inducible DNase I-hypersensitive sites occurring in the 5'-flanking sequence of the major immediate-early gene of human cytomegalovirus (HCMV), various deleted portions of the HCMV immediate-early promoter regulatory region were attached to the chloramphenicol acetyltransferase (CAT) gene and assayed for activity in transiently transfected undifferentiated and differentiated human teratocarcinoma cells, Tera-2. Assays of progressive deletions in the promoter regulatory region indicated that removal of a 395-base-pair portion of this element (nucleotides -750 to -1145) containing two inducible DNase I sites which correlate with gene expression resulted in a 7.5-fold increase in CAT activity in undifferentiated cells. However, in permissive differentiated Tera-2, human foreskin fibroblast, and HeLa cells, removal of this regulatory region resulted in decreased activity. In addition, attachment of this HCMV upstream element to a homologous or heterologous promoter increased activity three- to fivefold in permissive cells. Therefore, a cis regulatory element exists 5' to the enhancer of the major immediate-early gene of HCMV. This element negative modulates expression in nonpermissive cells but positively influences expression in permissive cells.
Design and creation of a large-scale database of structural annotations

This paper describes the design and creation of an unprecedentedly large database of over 2400 structural annotations of nearly 1400 musical recordings. The database is intended to be a test set for algorithms that will be used to analyze a much larger corpus of hundreds of thousands of recordings, as part of the Structural Analysis of Large Amounts of Musical Information (SALAMI) project. This paper describes the design goals of the database and the practical issues that were encountered during its creation. In particular, we discuss the selection of the recordings, the development of an annotation format and procedure that adapts work by Peeters and Deruty [10], and the management and execution of the project. We also summarize some of the properties of the resulting corpus of annotations, including average inter-annotator agreement.
Joint Space Decomposition-and-Synthesis Approach and Achievable DoF Regions for $K$ -User MIMO Interference Channels

The paper proposes a new approach of joint space decomposition-and-synthesis (JSDS) for deriving achievable degree-of-freedom (DoF) region by interference alignment without symbol extension for K-user MIMO interference channel. Solving the interference alignment problem is to find the precoders that align desired signal and interference with disjoint subspaces at receivers. A related property of these precoders is that the solution range for each one of them is a union of linear spaces, termed transmit spaces. Based on this property, the JSDS approach is developed to derive transmit spaces that fulfill alignment conditions. From this approach, achievable DoF regions for 2 and 3-user interference channels are obtained. The region for the 2-user channel is shown to coincide with the existing result of the DoF capacity of the channel. For the K-user (K > 3) case, inner as well as outer bounds are given.
Statistical Image Reconstruction Methods for Simultaneous Emission/transmission Pet Scans

— Transmission scans are necessary for estimating the attenuation correction factors (ACFs) to yield quantitatively accurate PET emission images. To reduce the total scan time, post-injection transmission scans have been proposed in which one can simultaneously acquire emission and transmission data using rod sources and sinogram windowing. However, since the post-injection transmission scans are corrupted by emission coincidences, accurate correction for attenuation becomes more challenging. Conventional methods (emission subtraction) for ACF computation from post-injection scans are suboptimal and require relatively long scan times. We introduce statistical methods based on penalized-likelihood objectives to compute ACFs and then use them to reconstruct lower noise PET emission images from simultaneous trans-mission/emission scans. Simulations show the efficacy of the proposed methods. These methods improve image quality and SNR of the estimates as compared to conventional methods.
Reliability-Aware Runtime Power Management for Many-Core Systems in the Dark Silicon Era

Power management of networked many-core systems with runtime application mapping becomes more challenging in the dark silicon era. It necessitates considering network characteristics at runtime to achieve better performance while honoring the peak power upper bound. On the other hand, power management has a direct effect on chip temperature, which is the main driver of the aging effects. Therefore, alongside performance fulfillment, the controlling mechanism must also consider the current cores’ reliability in its actuator manipulation to enhance the overall system lifetime in the long term. In this paper, we propose a multiobjective dynamic power management technique that uses current power consumption and other network characteristics including the reliability of the cores as the feedback while utilizing fine-grained voltage and frequency scaling and per-core power gating as the actuators. In addition, disturbance rejecter and reliability balancer are designed to help the controller to better smooth power consumption in the short term and reliability in the long term, respectively. Simulations of dynamic workloads and mixed criticality application profiles show that our method not only is effective in honoring the power budget while considerably boosting the system throughput, but also increases the overall system lifetime by minimizing aging effects by means of power consumption balancing.
Social Stress Promotes and γ-Aminobutyric Acid Inhibits Tumor Growth in Mouse Models of Non–Small Cell Lung Cancer

Psychologic distress is associated with increased lung cancer incidence and mortality. We have shown that non–small cell lung cancer (NSCLC) cells in vitro are stimulated by the cyclic AMP (cAMP)-dependent activation of cAMP-responsive element binding protein (CREB) and extracellular signal–regulated kinase (ERK) downstream of β-adrenergic receptors and that this pathway is inhibited by the neurotransmitter γ-aminobutyric acid (GABA). Because the stress neurotransmitters noradrenalin and adrenalin are β-adrenergic agonists, the current study has tested the hypothesis that social stress stimulates NSCLC growth in vivo and that GABA inhibits this effect. Social stress was induced in mice carrying xenografts from two NSCLC cell lines in the presence and absence of treatment with GABA. Xenograft sizes were measured after 30 days. Noradrenalin, adrenalin, cortisol, GABA, and cAMP were measured in blood and tumor tissues by immunoassays. Expression of nicotinic receptors in the xenografts was assessed by real-time PCR and Western blotting. Protein expression of phospho (p)-CREB, CREB, phospho (p)-ERK, ERK, and glutamate decarboxylase (GAD) 65 and 67 were determined by Western blotting. Xenograft sizes in stress-exposed mice were significantly increased. Nicotinic acetylcholine receptor (nAChR) subunits α3, α4, α5, and α7 in xenograft tissues showed posttranscriptional induction. Noradrenalin, adrenalin, and cortisol were elevated in serum and xenograft tissue whereas GABA was suppressed. Levels of cAMP, p-CREB, and p-ERK were increased whereas GAD65 and GAD67 were suppressed in tumor tissue. Treatment with GABA reversed the effects of stress. Our findings suggest that social stress stimulates NSCLC by increasing nAChR-mediated stress neurotransmitter signaling and that GABA is a promising novel agent for NSCLC intervention. Cancer Prev Res; 5(2); 189–96. ©2011 AACR.
A Tool for Easing the Cognitive Analysis of Design Prototypes of Aircraft Cockpit Instruments: The Human Efficiency Evaluator

Development and evaluation of dynamic and complex systems require new techniques and tools to evaluate the risks of Human and Systems Error, especially for safety critical systems. Established techniques like the cognitive workload analysis that can be used to assess the individual perceived operator workload for sets of tasks these are not widely used in industrial development. That is, because cognitive analysis of dynamic systems depends on complex architectures and simulations to evaluate workload over time, and is still driven by proprietary notations for cognitive models that require in-depth cognitive modeling skills and is currently only accessible to experts. In this paper we present an extension to CogTool, the Human Efficiency Evaluator (HEE) to ease the analysis of the impact of new instruments and new display designs with respect to human operator workload and task execution times. The tool is designed to make these cognitive analysis techniques available to non-experts, such as system analysts and engineers. We explain the cognitive modeling and analysis process supported by the HEE referring to an aeronautics scenario presented earlier by Hutchins. The cognitive analysis compares the task performance and workload of three generations of cockpit instrument designs to support pilots' with the slats/flaps settings during an aircraft approach with the current support in modern aircrafts and was performed by using the HEE.
Extending iTaSC to support inequality constraints and non-instantaneous task specification

In [1], we presented our constraint-based programming approach, iTaSC1, that formulates instantaneous sensor-based robot tasks as constraint sets, and subsequently solves a corresponding least-squares problem to obtain control set points, such as desired joint velocities or joint torques. This paper further extends this approach, (i) by explicitly supporting the inclusion of inequality constraints in the task and (ii) by supporting a broader class of objective functions for translating the task constraints into robot motion. These extensions are made while retaining a tractable mathematical problem structure (a convex program). Furthermore, first results on extending the approach to non-instantaneous tasks are presented. As illustrated in the paper, the power of the approach lies (i) at its versatility to specify a wide range of robot behaviors and the ease of making task adjustments, and (ii) at its generic nature, that permits using systematic procedures to derive the underlying control equations.
Evaluation of the SPF10-INNO LiPA Human Papillomavirus (HPV) Genotyping Test and the Roche Linear Array HPV Genotyping Test

ABSTRACT The need for accurate genotyping of human papillomavirus (HPV) infections is becoming increasingly important, since (i) the oncogenic potential among the high-risk HPV genotypes varies in the pathogenesis of cervical cancer, (ii) monitoring multivalent HPV vaccines is essential to investigate the efficiency of the vaccines, and (iii) genotyping is crucial in epidemiologic studies evaluating HPV infections worldwide. Various genotyping assays have been developed to meet this demand. Comparison of different studies that use various HPV genotyping tests is possible only after a performance assessment of the different assays. In the present study, the SPF10 LiPA version 1 and the recently launched Roche Linear Array HPV genotyping assays are compared. A total of 573 liquid-based cytology samples were tested for the presence of HPV by a DNA enzyme immunoassay; 210 were found to be positive for HPV DNA and were evaluated using both genotyping assays (163 with normal cytology, 22 with atypical squamous cells of undetermined significance, 20 with mild/moderate dysplasia, and 5 with severe dysplasia). Comparison analysis was limited to the HPV genotype probes common to both assays. Of the 160 samples used for comparison analysis, 129 (80.6%) showed absolute agreement between the assays (concordant), 18 (11.2%) showed correspondence for some but not all genotypes detected on both strips (compatible), and the remaining 13 (8.2%) samples did not show any similarity between the tests (discordant). The overall intertest comparison agreement for all individually detectable genotypes was considered very good (κ value, 0.79). The genotyping assays were therefore highly comparable and reproducible.
Bayesian Optimal Data Detector for mmWave OFDM System With Low-Resolution ADC

Orthogonal frequency division multiplexing (OFDM) has been widely used in communication systems operating in the millimeter wave (mmWave) band to combat frequency-selective fading and achieve multi-Gbps transmissions, such as the IEEE 802.15. 3c and the IEEE 802.11ad. For mmWave systems with ultra high sampling rate requirements, the use of low-resolution analog-to-digital converters (ADCs) (i.e., 1–3 bits) ensures an acceptable level of power consumption and system costs. However, orthogonality among subchannels in the OFDM system cannot be maintained because of the severe nonlinearity caused by low-resolution ADC, which renders the design of data detector challenging. In this paper, we develop an efficient algorithm for optimal data detection in the mmWave OFDM system with low-resolution ADCs. The analytical performance of the proposed detector is derived and verified to achieve the fundamental limit of the Bayesian optimal design. On the basis of the derived analytical expression, we further propose a power allocation (PA) scheme that seeks to minimize the average symbol error rate. In addition to the optimal data detector, we also develop a feasible channel estimation method, which can provide high-quality channel state information without significant pilot overhead. Simulation results confirm the accuracy of our analysis and illustrate that the performance of the proposed detector in conjunction with the proposed PA scheme is close to the optimal performance of the OFDM system with infinite-resolution ADC.
A Pathologic Cascade Leading to Synaptic Dysfunction in α-Synuclein-Induced Neurodegeneration

Several neurodegenerative diseases are typified by intraneuronal α-synuclein deposits, synaptic dysfunction, and dementia. While even modest α-synuclein elevations can be pathologic, the precise cascade of events induced by excessive α-synuclein and eventually culminating in synaptotoxicity is unclear. To elucidate this, we developed a quantitative model system to evaluate evolving α-synuclein-induced pathologic events with high spatial and temporal resolution, using cultured neurons from brains of transgenic mice overexpressing fluorescent-human-α-synuclein. Transgenic α-synuclein was pathologically altered over time and overexpressing neurons showed striking neurotransmitter release deficits and enlarged synaptic vesicles; a phenotype reminiscent of previous animal models lacking critical presynaptic proteins. Indeed, several endogenous presynaptic proteins involved in exocytosis and endocytosis were undetectable in a subset of transgenic boutons (“vacant synapses”) with diminished levels in the remainder, suggesting that such diminutions were triggering the overall synaptic pathology. Similar synaptic protein alterations were also retrospectively seen in human pathologic brains, highlighting potential relevance to human disease. Collectively the data suggest a previously unknown cascade of events where pathologic α-synuclein leads to a loss of a number of critical presynaptic proteins, thereby inducing functional synaptic deficits.
Controlled Mobility Sensor Networks for Target Tracking Using Ant Colony Optimization

In mobile sensor networks, it is important to manage the mobility of the nodes in order to improve the performances of the network. This paper addresses the problem of single target tracking in controlled mobility sensor networks. The proposed method consists of estimating the current position of a single target. Estimated positions are then used to predict the following location of the target. Once an area of interest is defined, the proposed approach consists of moving the mobile nodes in order to cover it in an optimal way. It thus defines a strategy for choosing the set of new sensors locations. Each node is then assigned one position within the set in the way to minimize the total traveled distance by the nodes. While the estimation and the prediction phases are performed using the interval theory, relocating nodes employs the ant colony optimization algorithm. Simulations results corroborate the efficiency of the proposed method compared to the target tracking methods considered for networks with static nodes.
Human Cytomegalovirus Enhances A. actinomycetemcomitans Adherence to Cells

Adherence of Actinobacillus actinomycetemcomitans to epithelial cells is an important step in periodontal disease pathogenesis. Recent publications describe the subgingival presence of a wide array of viruses [e.g., human cytomegalo-virus (hCMV)]. Since viruses can increase cellular susceptibility for bacterial adherence, we investigated whether hCMV renders epithelial cells more prone to adherence by Actinobacillus actinomycetemcomitans. Cultivated HeLa and primary epithelial cells were shown to be semi-permissive for hCMV infection, which resulted in increased bacterial adherence. This increase correlated with viral concentrations, was evident in all Actinobacillus actinomycetemcomitans strains examined, and increased during the first 24 hrs, followed by a slight decrease. Immediate early antigen expression was not correlated with the increased adherence of Actinobacillus actinomycetemcomitans. The results confirmed our hypothesis that the adherence of Actinobacillus actinomycetemcomitans is influenced by hCMV in vitro.