Miracle-dz/UniFAR-FTUs huggingface dataset:
Strategy Revealing Phenotypic Differences among Synthetic Oscillator Designs

Considerable progress has been made in identifying and characterizing the component parts of genetic oscillators, which play central roles in all organisms. Nonlinear interaction among components is sufficiently complex that mathematical models are required to elucidate their elusive integrated behavior. Although natural and synthetic oscillators exhibit common architectures, there are numerous differences that are poorly understood. Utilizing synthetic biology to uncover basic principles of simpler circuits is a way to advance understanding of natural circadian clocks and rhythms. Following this strategy, we address the following questions: What are the implications of different architectures and molecular modes of transcriptional control for the phenotypic repertoire of genetic oscillators? Are there designs that are more realizable or robust? We compare synthetic oscillators involving one of three architectures and various combinations of the two modes of transcriptional control using a methodology that provides three innovations: a rigorous definition of phenotype, a procedure for deconstructing complex systems into qualitatively distinct phenotypes, and a graphical representation for illuminating the relationship between genotype, environment, and the qualitatively distinct phenotypes of a system. These methods provide a global perspective on the behavioral repertoire, facilitate comparisons of alternatives, and assist the rational design of synthetic gene circuitry. In particular, the results of their application here reveal distinctive phenotypes for several designs that have been studied experimentally as well as a best design among the alternatives that has yet to be constructed and tested.
Multicentric breast carcinomas: Clinical‐radiographic‐pathologic whole organ studies and 10‐year survival

Selection of breast cancer patients with microscopically limited disease but with excess mortality or women with regional disease and lessened mortality has remained an unsolved and critical challenge. The many usual histologic features such as tumor size, stage of disease or tumor differentiations were found reduced to lessened significant prognostic factors by the presence of multicentricity of tumors and multiplicity of histologic types of carcinoma. This observation was noted upon review of 161 clinical, radiographic and histopathologic whole breast studies on 156 patients with follow‐up from 11–15 years. Epidemiologic, clinical, and radiographic data had been compiled prospectively prior to diagnosis. Women with a single site and single type of carcinoma had a better prognosis (2.5% mortality per year) than those with multiple sites and multiple types (15% mortality per year) even though the stage of the disease may be similar. When the latter groups contained a scirrhous type duct carcinoma, the annual mortality rate appraoched 25%.
A new planar ultra wideband antenna for UWB applications

The recent allocation of the 3.1-10.6 GHz frequency spectrums for ultra-wideband (UWB) applications has presented many opportunities and challenges for antenna designers. Patch antennas are extensively used in wireless communications because of their light weight, low cost, and ease of fabrication. These features are desirable for both indoor and outdoor handheld UWB antenna applications. Ideally, UWB antennas should be non-dispersive or dispersive in a controlled fashion that is amenable to compensation. In this paper, to avoid the feeding problems and also costly fabrication, we modified the shape of the elliptical antenna by bending edges and cutting metal sections appropriately. The antenna structural parameters are then optimized to improve its performance. To avoid using the balun transformer and also to improve the antenna dispersion characteristics, the complement structure of the antenna was considered which results in a dragonfly shape antenna. The designed antenna was fabricated and the simulation results have been verified by comparing with measurements.
A Convex Positivstellensatz

We provide a specific representation of convex polynomials nonnegative on a convex (not necessarily compact) basic closed semi-algebraic set K ⊂ Rn. Namely, we prove that almost all of them belong to a specific subset of the quadratic module generated by the concave polynomials that define K. In particular, almost all nonnegative convex polynomials are sums of squares. Mathematics Subject Classification (2000). Primary 14P10; Secondary 11E25 12D15 90C25.
Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus

Systemic lupus erythematosus (SLE) is a complex, inflammatory autoimmune disease that affects multiple organ systems. We used global gene expression profiling of peripheral blood mononuclear cells to identify distinct patterns of gene expression that distinguish most SLE patients from healthy controls. Strikingly, about half of the patients studied showed dysregulated expression of genes in the IFN pathway. Furthermore, this IFN gene expression “signature” served as a marker for more severe disease involving the kidneys, hematopoetic cells, and/or the central nervous system. These results provide insights into the genetic pathways underlying SLE, and identify a subgroup of patients who may benefit from therapies targeting the IFN pathway.
Organization of the serotonergic innervation of the feeding (buccal) musculature during the maturation of the pond snail Lymnaea stagnalis: A morphological and biochemical study

The serotonergic innervation of the buccal musculature responsible for feeding (radula protraction) was investigated during the maturation of the pond snail, Lymnaea stagnalis L. , applying light and electron microscopic immunohistochemistry and biochemical approaches. According to epifluorescence and laser confocal microscopy, the first 5‐HT‐like‐immunoreactive (5‐HTLIR) processes appeared on the surface of the musculature at the postmetamorphic E80% embryonic stage. Until hatching, the innervation continued to increase in density, showing axon arborizations with projections into the deeper muscle levels. An adult‐like pattern of 5‐HTLIR innervation appeared at P2–P3 juvenile stages. At the ultrastructural level, close (16–20 nm) but mostly unspecialized neuromuscular contacts were formed by both unlabeled and 5‐HTLIR axon profiles from the E80% embryonic stage. Labeled processes were also found located relatively far from the muscle cells. An HPLC assay showed a gradual increase of the 5‐HT level in the buccal mass during development. The buccal mass was characterized by a single‐component high‐affinity 5‐HT uptake system, and 5‐HT release could be evoked by 100 mM K+ and blocked in Ca2+‐free medium. It is suggested that 5‐HT plays a wide modulatory role in the peripheral feeding system and is also involved in the functional maturation of the muscle system. J. Comp. Neurol. 520:315–329, 2012. © 2011 Wiley Periodicals, Inc.
Improving the software testing skills of novices during onboarding through social transparency

Inexperienced software developers - for example, undergraduates entering the workforce - exhibit a lack of testing skills. They have trouble understanding and applying basic testing techniques. These inexperienced developers are hired by software companies, where this lack of testing skills has already been recognized. Companies allocate valuable resources and invest time and money in different onboarding strategies to introduce new hires to the organization’s testing practices. However, if the lack of testing skills is not addressed properly, the new hire is left to her own devices. This hinders her in becoming a high-quality engineer for the software company. This thesis proposes to improve the onboarding strategies with traits of social transparency in order to specifically address testing issues of inexperienced new hires. Social transparency has been shown to influence the testing behavior of development teams on a social coding site. An environment that is open for discussion helps newcomers to understand and adapt a team’s testing culture. Tailoring the onboarding process to better address testing skills of new hires makes it more effective and more efficient. This reduces the danger of carrying new hire’s testing deficits into commercial software development.
A Novel Rate Control Scheme for Constant Bit Rate Video Streaming

In this paper, a novel rate control mechanism is proposed for constant bit rate video streaming. The initial quantization parameter used for encoding a video sequence is determined using the average spatio-temporal complexity of the sequence, its resolution and the target bit rate. Simple linear estimation models are then used to predict the number of bits that would be necessary to encode a frame for a given complexity and quantization parameter. The experimental results demonstrate that our proposed rate control mechanism significantly outperforms the existing rate control scheme in the Joint Model (JM) reference software in terms of Peak Signal to Noise Ratio (PSNR) and consistent perceptual visual quality while achieving the target bit rate. Furthermore, the proposed scheme is validated through implementation on a miniature test-bed.
Combining MIMO Radar with OFDM Communications

MIMO radar systems have been proposed elsewhere which utilise OFDM waveforms as the scene illuminator. This suggests an opportunity exists to code the OFDM radar waveform in such a way as to provide a communication link to broadcast the radar data to remote users. The benefit of this would arise from the dual use of the microwave band, addressing the problem where demand for bandwidth is exceeding capacity. This paper explores the technical issues associated with this idea and outlines some of the key features of such a system. We describe how OFDM waveforms can be applied to MIMO radar; and what constraints must be placed on the waveform to ensure robust operation for both radar and communication functions. A candidate system design is presented, along with basic analysis of the expected performance of both radar and communications functionality
On the Lamb vector divergence in Navier–Stokes flows

The mathematical and physical properties of the Lamb vector divergence are explored. Toward this aim, the instantaneous and mean dynamics of the Lamb vector divergence are examined in several analytic and turbulent flow examples relative to its capacity to identify and characterize spatially localized motions having a distinct capacity to effect a time rate of change of momentum. In this context, the transport equation for the Lamb vector divergence is developed and shown to accurately describe the dynamical mechanisms by which adjacent high- and low-momentum fluid parcels interact to effect a time rate of change of momentum and generate forces such as drag. From this, a transport-equation-based framework is developed that captures the self-sustaining spatiotemporal interactions between coherent motions, e.g. ejections and sweeps in turbulent wall flows, as predicted by the binary source–sink distribution of the Lamb vector divergence. New insight into coherent motion development and evolution is found through the analysis of the Lamb vector divergence.
Volume-Stable Adipose Tissue Formation by Implantation of Human Adipose-Derived Stromal Cells Using Solid Free-Form Fabrication-Based Polymer Scaffolds

AbstractRegeneration of volume-stable adipose tissue is required for treatment of soft-tissue loss due to cancer, trauma, burns and for correctional cosmetic surgery. In this study, we hypothesized that transplantation of human adipose-derived stromal cells (hADSCs) using polycaprolactone (PCL) scaffolds fabricated with a solid free-form fabrication method would better maintain the volume of regenerated adipose tissues, as compared with the use of fibrin gel. Six weeks after implantation into the dorsal subcutaneous pockets of athymic mice, the volumes and adipose tissue areas of hADSC-PCL scaffold implants were significantly larger than those of hADSC-fibrin implants. In addition, the mRNA expression of adipogenic genes was more extensive in the hADSC-PCL scaffold implants.
Bound Ratio Minimization of Filter Bank Frames

This paper investigates and solves the problem of frame bound ratio minimization for oversampled perfect reconstruction (PR) filter banks (FBs). For a given analysis PRFB, a finite dimensional convex optimization algorithm is derived to redesign the subband gain of each channel. The redesign minimizes the frame bound ratio of the FB while maintaining its original properties and performance. The obtained solution is precise without involving frequency domain approximation and can be applied to many practical problems in signal processing. The optimal solution is applied to subband noise suppression and tree structured FB gain optimization, resulting in deeper insights and novel solutions to these two general classes of problems and considerable performance improvement. Effectiveness of the optimal solution is demonstrated by extensive numerical examples.
Sub‐Microsecond Molecular Thermometry Using Thermal Spin Flips

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Slant Discriminant Analysis for Image Feature Extraction

In this paper, a novel feature extraction algorithm,called Slant discriminant analysis (SDA), is proposed. SDA aims to use the relation of rows and columns of image samples to extract the directional feature of the image samples. The proposed algorithm is applied to image classification on Yale face Database.The experimental results demonstrate the effectiveness of the proposed algorithm.
Stereotactic Laser Ablation for Medically Intractable Epilepsy: The Next Generation of Minimally Invasive Epilepsy Surgery

Epilepsy is a common, disabling illness that is refractory to medical treatment in approximately one-third of patients, particularly among those with mesial temporal lobe epilepsy. While standard open mesial temporal resection is effective, achieving seizure freedom in most patients, efforts to develop safer, minimally invasive techniques have been underway for over half a century. Stereotactic ablative techniques, in particular, radiofrequency (RF) ablation, were first developed in the 1960s, with refinements in the 1990s with the advent of modern computed tomography and magnetic resonance-based imaging. In the past 5 years, the most recent techniques have used MRI-guided laser interstitial thermotherapy (LITT), the development of which began in the 1980s, saw refinements in MRI thermal imaging through the 1990s, and was initially used primarily for the treatment of intracranial and extracranial tumors. The present review describes the original stereotactic ablation trials, followed by modern imaging-guided RF ablation series for mesial temporal lobe epilepsy. The developments of LITT and MRI thermometry are then discussed. Finally, the two currently available MRI-guided LITT systems are reviewed for their role in the treatment of mesial temporal lobe and other medically refractory epilepsies.
Predictability of extreme events in a branching diffusion model

We propose a framework for studying predictability of extreme events in complex systems. Major conceptual elements — hierarchical structure, spatial dynamics, and external driving — are combined in a classical branching diffusion with immigration. New elements — observation space and observed events — are introduced in order to formulate a prediction problem patterned after the geophysical and environmental applications. The problem consists of estimating the likelihood of occurrence of an extreme event given the observations of smaller events while the complete internal dynamics of the system is unknown. We look for premonitory patterns that emerge as an extreme event approaches; those patterns are deviations from the long-term system’s averages. We have found a single control parameter that governs multiple spatio-temporal premonitory patterns. For that purpose, we derive i) complete analytic description of time- and space-dependent size distribution of particles generated by a single immigrant; ii) the steady-state moments that correspond to multiple immigrants; and iii) size- and space-based asymptotic for the particle size distribution. Our results suggest a mechanism for universal premonitory patterns
Towards semi-automatic extraction of lexical semantics relations for Polish

A recently started project on building the Polish wordnet (called plWordNet) is the background to the presented work. The goals of the project and the linguistic structure of plWordNet are described. The assumptions of the planned semi-automatic method of extending the initial core wordnet to its full size are presented. A multi-criteria algorithm of extraction of lexical semantic relations is presented. Several problems with application of the known methods of relation extraction to Polish – an inflectional and free word order language, are discussed. Experiments with the application of LSA to Polish news corpus and the extraction of noun similarity on the basis of co-occurrence of nouns and adjectives are presented. The experiments verify the assumed solutions to the problems of large number of Polish word forms, and the lack of sequential structure in Polish.
Variation of the mechanical properties of E-glass/epoxy composites subjected to hygrothermal aging

In this study, the effects of hygrothermal aging on the mechanical properties and impact behavior of glass-epoxy composites were investigated experimentally. The vacuum-assisted resin infusion molding was used to manufacture composites. In manufacturing of composites, unidirectional E-glass fabrics with areal density of 300 g/m2 and a resin system (Araldite LY 564/Aradur 3487 BD) were used. In order to determine mechanical properties such as modulus of elasticity, longitudinal and transverse strengths, shear strength, and Poisson’s ratio, the composite samples were prepared according to the ASTM standards. Then, the samples were conditioned at a constant temperature (95℃) and a constant humidity (70%) for different periods of times, ranging from 0 h to 1200 h. The conditioning temperature was chosen due to the glass transition temperature (Tg) of the intact composites which is determined as 78℃. It is noted that the most affected mechanical property via material degradation is modulus of elasticity in transverse direction (E2) while the least affected one is shear modulus (G12). The perforation threshold of the composite materials also decreases with increase of conditioning time.
State tying for context dependent phoneme models

In this paper several modi(cid:12)cations of two methods for parameter reduction of Hidden Markov Models by state tying are described. The two methods represent a data driven clustering triphone states with a bottom up algo-rithm [3, 9], and a top down method growing decision trees for triphone states [2, 10]. We investigate several aspects of state tying as the possible reduction of the word error rate by state tying, the consequences of di(cid:11)er-ent distance measures for the data driven approach and modi(cid:12)cations of the original decision tree approach such as node merging. The tests were performed on the test corpora for the 5000 word vocabulary of the WSJ November 92 task and on the evaluation corpora for the 3000 word VERBMOBIL ’95 task. The word error rate by state tying was reduced by 14% for the WSJ task and by 5% for the VERBMOBIL task.
Rate-distortion tradeoffs under Kernel-based distortion measures

Kernel methods have been used for turning linear learning algorithms into nonlinear ones. These nonlinear algorithms measure distances between data points by the distance in the kernel-induced feature space. In lossy data compression, the optimal tradeoff between the number of quantized points and the incurred distortion is characterized by the rate-distortion function. However, the rate-distortion functions associated with distortion measures involving kernel feature mapping have yet to be analyzed. We consider two reconstruction schemes, reconstruction in input space and reconstruction in feature space, and provide bounds to the rate-distortion functions for these schemes. Comparison of the derived bounds to the quantizer performance obtained by the kernel K-means method suggests that the rate-distortion bounds for input space and feature space reconstructions are informative at low and high distortion levels, respectively.
Changes in the potential distribution of humid tropical forests on a warmer planet

The future of tropical forests has become one of the iconic issues in climate-change science. A number of studies that have explored this subject have tended to focus on the output from one or a few climate models, which work at low spatial resolution, whereas society and conservation-relevant assessment of potential impacts requires a finer scale. This study focuses on the role of climate on the current and future distribution of humid tropical forests (HTFs). We first characterize their contemporary climatological niche using annual rainfall and maximum climatological water stress, which also adequately describe the current distribution of other biomes within the tropics. As a first-order approximation of the potential extent of HTFs in future climate regimes defined by global warming of 2°C and 4°C, we investigate changes in the niche through a combination of climate-change anomaly patterns and higher resolution (5 km) maps of current climatology. The climate anomalies are derived using data from 17 coupled Atmosphere–Ocean General Circulation Models (AOGCMs) used in the Fourth Assessment of the Intergovernmental Panel for Climate Change. Our results confirm some risk of forest retreat, especially in eastern Amazonia, Central America and parts of Africa, but also indicate a potential for expansion in other regions, for example around the Congo Basin. The finer spatial scale enabled the depiction of potential resilient and vulnerable zones with practically useful detail. We further refine these estimates by considering the impact of new environmental regimes on plant water demand using the UK Met Office land-surface scheme (of the HadCM3 AOGCM). The CO2-related reduction in plant water demand lowers the risk of die-back and can lead to possible niche expansion in many regions. The analysis presented here focuses primarily on hydrological determinants of HTF extent. We conclude by discussing the role of other factors, notably the physiological effects of higher temperature.