Miracle-dz/UniFAR-FTUs huggingface dataset:
MUTATIONAL MELTDOWNS IN SEXUAL POPULATIONS

Although it is widely acknowledged that the gradual accumulation of mildly deleterious mutations is an important source of extinction for asexual populations, it is generally assumed that this process is of little relevance to sexual species. Here we present results, based on computer simulations and supported by analytical approximations, that indicate that mutation accumulation in small, random‐mating monoecious populations can lead to mean extinction times less than a few hundred to a few thousand generations. Unlike the situation in obligate asexuals in which the mean time to extinction (t̄e) increases more slowly than linearly with the population carrying capacity (K), t̄e increases approximately exponentially with K in outcrossing sexual populations. The mean time to extinction for obligately selfing populations is shown to be equivalent to that for asexual populations of the same size, but with half the mutation rate and twice the mutational effect; this suggests that obligate selfing, like obligate asexuality, is inviable as a long‐term reproductive strategy. Under all mating systems, the mean time to extinction increases relatively slowly with the logarithm of fecundity, and mutations with intermediate effects (similar to those observed empirically) cause the greatest risk of extinction. Because our analyses ignore sources of demographic and environmental stochasticity, which have synergistic effects that exacerbate the accumulation of deleterious mutations, our results should yield liberal upper bounds to the mean time to extinction caused by mutational degradation. Thus, deleterious mutation accumulation cannot be ruled out generally as a significant source of extinction vulnerability in small sexual populations or as a selective force influencing mating‐system evolution.
AIDA: Automated analog IC design flow from circuit level to layout

This paper presents AIDA, an analog integrated circuit design automation environment, which implements a design flow from a circuit-level specification to a physical layout description. AIDA results from the integration of two in-house tools, namely, GENOM-POF and LAYGEN II. GENOM-POF performs fully automated circuit-level synthesis implemented with a multi-objective multi-constraint optimization approach, which addresses robust design requirements by considering Corners analysis together with an electrical simulator as the evaluation engine. LAYGEN II implements a DRC proved fully automated layout generation based on a sized circuit-level description and high level layout guidelines, described in a technology independent abstract layout template. The expert knowledge is used by LAYGEN II to guide the evolutionary optimization kernels during the automatic layout generation. Moreover, evolutionary computation techniques are extensively used, at both circuit-level and physical-level, as tool to solve design optimization problems. Finally, AIDA environment is demonstrated for the IC design of a classical circuit-level topology and state-of-the-art technology, and validated by industrial simulators and analysis tools, such as, HSPICE® and CALIBRE®.
Project Recommendation Using Heterogeneous Traits in Crowdfunding

Crowdfunding has gained widespread popularity in recent years. By funding entrepreneurs with creative minds, it is gradually taking over the role of venture capitalists who provide the much needed seed capital to jump start business ventures. Despite the huge success of the crowdfunding platforms, not every project is successful in reaching its funding goal. Therefore, in this paper, we intend to answer the following question "what set of features determine a project's success? ". We begin by studying the dynamics of Kickstarter, a popular reward-based crowdfunding platform, and the impact of social networks on this platform. Contrary to previous studies, our analysis is not restricted to project-based features alone; instead, we expand the features into four different categories: temporal traits, personal traits, geo-location traits, and network traits. Using a comprehensive dataset of 18K projects and 116K tweets, we provide several unique insights about these features and their effects on the success of Kickstarter projects. Based on these insights, we build a supervised learning framework to learn a model that can recommend a set of investors to Kickstarter projects. By utilizing features from the first three days of project duration alone, we show that our results are significantly better than the previous studies.
AutoFOCUS 3: Tooling Concepts for Seamless, Model-based Development of Embedded Systems

This paper presents tooling concepts in AUTOFOCUS 3 supporting the development of software-intensive embedded system design. AUTOFOCUS 3 is a highly integrated model-based tool covering the complete development process from requirements elicitation, deployment, the modelling of the hardware platform to code generation. This is achieved thanks to precise static and dynamic semantics based on the FOCUS theory [1]. Models are used for requirements, for the software architecture (SA), for the hardware platform and for relations between those different viewpoints: traces from requirements to the SA, refinements between SAs, and deployments of the SA to the platform. This holistic usage of models allows the provision of a wide range of analysis and synthesis techniques such as testing, model checking and deployment and scheduling generation. In this paper, we demonstrate how tooling concepts on different steps in the development process look like, based on these integrated models and implemented in AUTOFOCUS 3.
CHOOSING AN ATTACKER BY A LOCAL DERIVATION

Within the ! -limit set of a point, a uniform method is given for such problems as choosing for each point in its kernel a recurrent point that attacks it. In the light of recent counter-examples, the method appears to be optimal. It is inspired by a lemma of Kunugui and forms a local derivation.
Building Clinical Relationships With Teenagers Who Stutter

The purpose of this article is to describe some of the key principles for forming a strong clinical relationship with adolescents who stutter. Such a relationship provides the foundation for change. In the first section, a structure for understanding adolescence, along with some basic assumptions about the adolescent thought process, is provided. Following this, there are a number of suggestions for different skills to use when communicating with teenagers so as to (a) establish the clinician's credibility as a caring and competent adult and (b) gain insight into the adolescent as a person, and the meaning that he or she attaches to stuttering. The final portion of this article focuses on how the clinician can facilitate two important dimensions of stuttering management: changing cognition and building strong parent-teenager relationships.
Evaluating the performance of software cache coherence

In a shared-memory multiprocessor with private caches, cached copies of a data item must be kept consistent. This is called cache coherence. Both hardware and software coherence schemes have been proposed. Software techniques are attractive because they avoid hardware complexity and can be used with any processor-memory interconnection. This paper presents an analytical model of the performance of two software coherence schemes and, for comparison, snoopy-cache hardware. The model is validated against address traces from a bus-based multiprocessor. The behavior of the coherence schemes under various workloads is compared, and their sensitivity to variations in workload parameters is assessed. The analysis shows that the performance of software schemes is critically determined by certain parameters of the workload: the proportion of data accesses, the fraction of shared references, and the number of times a shared block is accessed before it is purged from the cache. Snoopy caches are more resilient to variations in these parameters. Thus when evaluating a software scheme as a design alternative, it is essential to consider the characteristics of the expected workload. The performance of the two software schemes with a multistage interconnection network is also evaluated, and it is determined that both scale well.
Valdecoxib is as effective as diclofenac in the management of rheumatoid arthritis with a lower incidence of gastroduodenal ulcers: results of a 26-week trial.

OBJECTIVE To compare the efficacy and upper gastrointestinal (GI) safety of valdecoxib 20 and 40 mg daily with those of diclofenac 75 mg slow release (SR) twice daily in treating rheumatoid arthritis (RA). METHODS Seven hundred and twenty-two patients with adult-onset RA were enrolled into this 26-week, randomized, multicentre, double-blind, parallel-group study (246 in the valdecoxib 20 mg daily arm, 237 in the valdecoxib 40 mg daily arm and 239 in the diclofenac 75 mg SR daily arm). Acetylsalicylic acid use (< or =325 mg per day) was similar across all groups: 5.4% in the diclofenac group, 5.7% in the valdecoxib 20 mg group and 5.9% in the valdecoxib 40 mg group. Efficacy was measured by the Patient's Assessment of Arthritis Pain [visual analogue scale (VAS)] and the modified Health Assessment Questionnaire (mHAQ) at baseline and at weeks 2, 6, 8, 12, 18 and 26 of treatment, or at early termination. Upper GI safety was evaluated by endoscopy at the end of treatment, which took place no more than 2 days after the last dose of study medication or at early termination. RESULTS Valdecoxib 20 and 40 mg daily were comparable to diclofenac 75 mg SR twice daily in treating the signs and symptoms of RA. No significant differences were observed between treatment groups with respect to mean changes from baseline in the Patient's Assessment of Arthritis Pain (VAS) or mHAQ. The incidence of gastroduodenal ulcers in patients receiving valdecoxib 20 mg daily (6%) and valdecoxib 40 mg daily (4%) was significantly lower (P < 0.001) than in patients receiving diclofenac 75 mg SR twice daily (16%). Valdecoxib 20 mg daily was also associated with significantly improved GI tolerability (P = 0.035) compared with diclofenac. CONCLUSIONS Single daily doses of valdecoxib 20 and 40 mg provided efficacy comparable to that of diclofenac, with a superior upper GI safety profile in the long-term treatment of RA patients.
An Analytical View on the Software Reuse

: High-quality software, delivered on time and budget, constitutes a critical part of most products and services. Today software engineers are faced with a demand for complex and powerful software systems. To be competitive in the market software engineers are forced to create software as quickly as possible. Software reuse or component-based development (CBD) is regarded as one of the most potent software technologies in order to reduce lead times, increase functionality, and reduce costs. In the region, CBD is still a process with lot of problems, not well defined either from theoretical or practical points of view. The lack of knowledge is probably the biggest problem. Our aim is to systemize the knowledge and understanding of CBD. This research is a literature review on the software reuse and the concepts behind it. It starts with an overview of software components and CBD, continues describing benefits and obstacles to software reuse. Nontechnical aspects like legal, economic and measurement issues are covered as well. Finally examples of successful software reuse and the state of practice are summarized.
An innovative three-dimensional user interface for exploring music collections enriched

We present a novel, innovative user interface to music repositories. Given an arbitrary collection of digital music files, our system creates a virtual landscape which allows the user to freely navigate in this collection. This is accomplished by automatically extracting features from the audio signal and training a Self-Organizing Map (SOM) on them to form clusters of similar sounding pieces of music. Subsequently, a Smoothed Data Histogram (SDH) is calculated on the SOM and interpreted as a three-dimensional height profile. This height profile is visualized as a three-dimensional island landscape containing the pieces of music. While moving through the terrain, the closest sounds with respect to the listener's current position can be heard. This is realized by anisotropic auralization using a 5.1 surround sound model. Additionally, we incorporate knowledge extracted automatically from the web to enrich the landscape with semantic information. More precisely, we display words and related images that describe the heard music on the landscape to support the exploration.
JSimil - A Java Bytecode Clone Detector

We present JSimil, a code clone detector that uses a novel algorithm to detect similarities in sets of Java programs at the bytecode level. The proposed technique emphasizes scalability and efficiency. It also supports customization through profiles that allow the user to specify matching rules, system behavior, pruning thresholds, and output details. Experimental results reveal that JSimil outperforms existing systems. It is even able to spot similarities when complex code obfuscation techniques have been applied.
A Novel FERM Domain Including Guanine Nucleotide Exchange Factor Is Involved in Rac Signaling and Regulates Neurite Remodeling

The Rho family of small GTPases, key regulators of the actin cytoskeleton in eukaryotic cells from yeast to human, is implicated in the control of neuronal morphology. Guanine nucleotide exchange factors (GEFs) are upstream positive regulators of Rho GTPases and integrate extracellular signaling for appropriate activation of Rho GTPases at specific subcellular regions. Here we describe the identification of a novel Dbl family GEF for Rho GTPases in Homo sapiens andMus musculus. It contains a tandem Dbl homology–pleckstrin homology domain and FERM domain, characteristic of the plasma membrane proteins linker. This gene, termed FERM domain including RhoGEF (FIR), was abundantly expressed in brain, lung, and testis, as well as embryonic hippocampal and cortical neurons. FIR was found to activate the biochemical pathway specific for Rac1 but not for RhoA or Cdc42. Ectopic expression of FIR in the cortical neurons resulted in significantly shortened neurites and excessive growth cones, presumably mediated by Rac1. These results suggest that FIR may regulate neurite remodeling by mediating the signaling pathways from membrane proteins to Rac.
Random Secretion of Growth Hormone in Humans.

In normal humans, growth hormone (GH) is secreted from a gland located adjacent to the brain(pituitary) into the blood in distinct pulses, but in patients bearing a tumor within the pituitary(acromegaly) GH is excessively secreted in an irregular manner. It has been hypothesized that GHsecretion in the diseased state becomes random. This hypothesis is supported by demonstrating thatGH secretion in patients with acromegaly can not be distinguished from a variety of linear stochasticprocesses based on the predictability of the ﬂuctuations of GH concentration in the bloodstream. [S0031-9007(96)00996-9]
Chandra Observations of Ultraluminous Infrared Galaxies: Extended Hot Gaseous Halos in Merging Galaxies

We study the properties of hot gaseous halos in 10 nearby ultraluminous IRAS galaxies observed with the ACIS instrument on board Chandra. For all sample galaxies, diffuse soft X-ray emissions are found within ~10 kpc of the central region; their spectra are well fitted by a MEKAL model plus emission lines from α-elements and other ions. The temperature of the hot gas is about 0.7 keV and metallicity is about 1 Z☉. Outside the central region, extended hot gaseous halos are found for 9 out of the 10 ultraluminous infrared galaxies (ULIRGs). Most spectra of these extended halos can be fitted with a MEKAL model with a temperature of about 0.6 keV and a low metallicity (Z ~ 0.1 Z☉). We discuss the implications of our results on the origin of X-ray halos in elliptical galaxies and the feedback processes associated with starbursts.
Rigidity of Graph Joins and Hendrickson's Conjecture

Whiteley \cite{wh} gives a complete characterization of the infinitesimal flexes of complete bipartite frameworks. Our work generalizes a specific infinitesimal flex to include joined graphs, a family of graphs that contain the complete bipartite graphs. We use this characterization to identify new families of counterexamples, including infinite families, in $\R^5$ and above to Hendrickson's conjecture on generic global rigidity.
Morphological, hydrological, biogeochemical and ecological changes and challenges in river restoration – the Thur River case study

River restoration can enhance river dynamics, environmental heterogeneity and biodiversity, but the underlying processes governing the dynamic changes need to be understood to ensure that restoration projects meet their goals, and adverse effects are prevented. In particular, we need to comprehend how hydromorphological variability quantitatively relates to ecosystem functioning and services, biodiversity as well as ground- and surface water quality in restored river corridors. This involves (i) physical processes and structural properties, determining erosion and sedimentation, as well as solute and heat transport behavior in surface water and within the subsurface; (ii) biogeochemical processes and characteristics, including the turnover of nutrients and natural water constituents; and (iii) ecological processes and indicators related to biodiversity and ecological functioning. All these aspects are interlinked, requiring an interdisciplinary investigation approach. Here, we present an overview of the recently completed RECORD (REstored CORridor Dynamics) project in which we combined physical, chemical, and biological observations with modeling at a restored river corridor of the perialpine Thur River in Switzerland. Our results show that river restoration, beyond inducing morphologic changes that reshape the river bed and banks, triggered complex spatial patterns of bank infiltration, and affected habitat type, biotic communities and biogeochemical processes. We adopted an interdisciplinary approach of monitoring the continuing changes due to restoration measures to address the following questions: How stable is the morphological variability established by restoration? Does morphological variability guarantee an improvement in biodiversity? How does morphological variability affect biogeochemical transformations in the river corridor? What are some potential adverse effects of river restoration? How is river restoration influenced by catchment-scale hydraulics and which feedbacks exist on the large scale? Beyond summarizing the major results of individual studies within the project, we show that these overarching questions could only be addressed in an interdisciplinary framework.
Single-Ended Speech Quality Measurement Using Machine Learning Methods

We describe a novel single-ended algorithm constructed from models of speech signals, including clean and degraded speech, and speech corrupted by multiplicative noise and temporal discontinuities. Machine learning methods are used to design the models, including Gaussian mixture models, support vector machines, and random forest classifiers. Estimates of the subjective mean opinion score (MOS) generated by the models are combined using hard or soft decisions generated by a classifier which has learned to match the input signal with the models. Test results show the algorithm outperforming ITU-T P.563, the current "state-of-art" standard single-ended algorithm. Employed in a distributed double-ended measurement configuration, the proposed algorithm is found to be more effective than P.563 in assessing the quality of noise reduction systems and can provide a functionality not available with P.862 PESQ, the current double-ended standard algorithm
The Diguanylate Cyclase HsbD Intersects with the HptB Regulatory Cascade to Control Pseudomonas aeruginosa Biofilm and Motility

The molecular basis of second messenger signaling relies on an array of proteins that synthesize, degrade or bind the molecule to produce coherent functional outputs. Cyclic di-GMP (c-di-GMP) has emerged as a eubacterial nucleotide second messenger regulating a plethora of key behaviors, like the transition from planktonic cells to biofilm communities. The striking multiplicity of c-di-GMP control modules and regulated cellular functions raised the question of signaling specificity. Are c-di-GMP signaling routes exclusively dependent on a central hub or can they be locally administrated? In this study, we show an example of how c-di-GMP signaling gains output specificity in Pseudomonas aeruginosa. We observed the occurrence in P. aeruginosa of a c-di-GMP synthase gene, hsbD, in the proximity of the hptB and flagellar genes cluster. We show that the HptB pathway controls biofilm formation and motility by involving both HsbD and the anti-anti-sigma factor HsbA. The rewiring of c-di-GMP signaling into the HptB cascade relies on the original interaction between HsbD and HsbA and on the control of HsbD dynamic localization at the cell poles.
Benchmarking the performance of hadoop triple replication and erasure coding on a nation-wide distributed cloud

Large Scale distributed storage systems play a vital role in maintaining data across storage locations globally. These systems use replication as the default mechanism for providing fault-tolerance. Recently, erasure codes are being used as a viable alternative to replication, since they provide the same fault-tolerance for reduced storage overhead. However, their performance is unclear in a geographically diverse distributed storage system. This paper compares the performance of triple replication with the erasure coding (Reed-Solomon codes) used in Apache Hadoop's implementation of a distributed file system, on a cluster distributed across Australia that runs on the NeCTAR research cloud. Our results show that using erasure coding does not degrade the read performance in such a setting. We also compare the Hadoop's code with a local reconstruction code, implemented in the XORBAS version of Hadoop. These codes perform well in our clusters but the performance gain observed in our results does not conform to the results reported. Hence, we need new codes that perform better, addressing the geographical diversity issue. We believe that our framework is readily usable to test a range of novel erasure codes that are being introduced in the literature.
Self Adaptive Trust Model for Secure Geographic Routing in Wireless Sensor Networks

The presence of malicious nodes in the ad hoc and sensor networks poses serious security attacks during routing which affects the network performance. To address such attacks, numerous researchers have proposed defense techniques using a human behavior pattern called trust. Among existing solutions, direct observations based trust models have gained significant attention in the research community. In this paper, the authors propose a Self Adaptive Trust Model (SATM) of secure geographic routing in wireless sensor networks (WSNs). Unlike conventional weight based trust models, SATM intelligently assigns the weights associated with the network activities. These weights are applied to compute the final trust value. SATM considers direct observations to restrict the reputation based attacks. Due to the flexible and intelligent weight computation, SATM dynamically detects the malicious nodes and direct the traffic towards trustworthy nodes. SATM has been incorporated into Greedy Perimeter Stateless Routing (GPSR) protocol. Simulation results using the network simulator NS-2 have shown that GPSR with SATM is robust against detecting malicious nodes.