Miracle-dz/UniFAR-FTUs huggingface dataset:
A set of endogenous control genes for use in quantitative real-time PCR experiments reveal that the wild-type formin Ldia2 is enriched in the early pond snail embryo

Although the pond snail Lymnaea stagnalis is an emerging model organism for molecular studies in a wide variety of fields including development, biomineralisation and neurophysiology, there are a limited number of verified endogenous control genes for use in quantitative real-time PCR (qRT-PCR). As part of larger study on snail chirality or left-right asymmetry, we wished to assay relative gene expression in pond snail embryos, so we evaluated six new candidate control genes, by comparing their expression in three tissues (ovotestis, foot, and embryo) and across three programs (geNorm, Normfinder and Bestkeeper). The specific utility of these control genes was then tested by investigating the relative expression of six experimental transcripts, including the formin Ldia2, a gene that has been associated with chirality in L. stagnalis. All six control genes were found to be suitable for use. Of the six experimental genes that were tested, it was found that all were relatively depleted in the early embryo compared with other tissues, except the formin gene Ldia2. Instead, transcripts of the wild type Ldia2dex were enriched in the embryo, whereas a non-functional frameshifted version Ldia2sin was severely depleted. These differences in Ldia2sin expression were less evident in the ovotestis and not evident in the foot tissue, suggesting that nonsense-mediated decay may be obscured in actively transcribing tissues. This work therefore provides a set of control genes that may be useful to the wider community, and shows how they may be used to assay differences in expression in the early embryo.
Feedback controllers in the cloud

Autonomic management of quality of service attributes by dynamic resource allocation is one of the requirements in cloud computing environments. In order to provide these requirements in a flexible way existing cloud providers expose static rule /threshold/heuristic based decision implementation frameworks to their consumers. These rule /threshold/heuristic based methods are relatively easy to design and develop. However, they suffer from lack of well-founded design process to decide important design parameters (e.g.: thresholds, the number of instances to add/remove, calm time) and difficulty of dynamically adjusting to different conditions. In addition, incorrect/non-adaptable rule settings could cause long term instabilities leading to service outages. The feedback control has been shown to be useful for performance management and resource allocation in many complex software systems. In this work, we investigate the advantages and limitations of applying feedback controllers in cloud platforms. In addition, we illustrate the suitability of standard feedback controllers depending on the consumer requirements/applications. Finally, we propose a novel platform as a service architecture to design, develop, integrate and runtime manage feedback controllers for the cloud consumer applications. KeywordsCloud, decision making, QoS management, feedback control, control theory
Measuring the Variability in K2 Optical Light Curves of the Binary Black Hole Candidate OJ 287 and Other Fermi Active Galactic Nuclei in 2014–2015

We characterize the variability in nearly continuous optical observations of nine active galactic nuclei (AGNs) detected with the Fermi Gamma Ray Space Telescope Large Area Telescope (Fermi-LAT), obtained during the K2 mission with the Kepler spacecraft with 1-minute or 30-minute cadences. The binary black hole candidate OJ 287, six other γ-ray blazars, the lobe-dominated radio quasar 3C 207, and the X-ray-bright quasar RBS 1273 were observed. The most dramatic variability was seen in PKS 1352−104, which varied by a factor of six in 4 days. OJ 287 varied by a factor of 2.8, six other blazars varied by factors of 1.14–2.23, and RBS 1273 varied by a factor of only 1.03. Power spectral densities (PSDs) were calculated for each object. Six of the nine AGNs were detected by the Fermi-LAT during the K2 observations. The slopes of the PSDs for these six contemporaneously detected AGNs were not significantly different from the slopes of the three contemporaneously undetected AGNs. The PSD slopes of the three BL Lac objects and the four flat-spectrum radio quasars were not significantly different, consistent with the relativistic jet acting as the dominant source of the emission in both subclasses of blazars. Overall, the slopes of most PSDs are consistent with turbulence in the relativistic jet, but the steepest PSDs require the addition of another mechanism that produces additional flux variations on timescales of several days during major flaring episodes.
Bit Error Rates of Information and Watermark Bits in Digital Watermarking Systems Based on SS Techniques

In spread spectrum (SS)-based digital watermark- ing systems, watermark information is spread by a pseudo- random code and added to the original information signal. On the other hand, we have proposed another watermarking system having one watermark channel and several image transmission channels. Information data is modulated by SS codes with variable code length according to its significance. This paper inspects bit error rate of such a watermarking system for both watermark channel and image transmission channels. †
Evaluation of a Team Project Based Learning Module for Developing Employability Skills

This paper presents a case study, in which a new module, aimed at enhancing students’ employ-ability skills, is evaluated. Employability skills for graduates from higher education are regarded as essential outcomes from their degree programmes, but it can be difficult to provide appropriate opportunities to develop these skills in the context of their studies. This paper describes a new module, called Live Projects, designed to provide project based learning on campus, but involv-ing local businesses and organisations, to provide the projects and become clients for a team of students. Evaluation of the first year of running the module was through a student questionnaire, client sur-veys and assessment by the tutors. Results showed satisfaction from students and clients with the outcomes. Students reported a positive experience, and recognised that they had developed em-ployability skills, such as team working, project management and professional skills. Clients re-ported a good level of satisfaction with the outputs from the projects, and were enthusiastic in supporting the venture, seeing the benefits employers might gain from employing students who have developed these skills. The partnership between the university and local organisations is also an important form of engagement with the local community.
TTSS'11 - 5th International Workshop on Harnessing Theories for Tool Support in Software

Model checking has a long stigmatized history of being slow and not scalable to large real life systems. In this talk we report on our experiences of using model checking at the core of our C/C++ source code analysis tool Goanna. We present our underlying abstractions, refinement models and auxiliary techniques to obtain a solution that is fast, scalable, and sufficiently precise. Moreover, we report on our experience from routinely uncovering security vulnerabilities and mission critical bugs in real life systems, and the challenges in moving our Goanna software from an academic project to widely used commercial product. Bio Dr. Ralf Huuck is a senior researcher with NICTA, Australia’s national center of excellence for computer science research, a senior lecturer with the Univeristy of New South Wales, Sydney, and the CTO and co-Founder of Red Lizard Software, an enterprise delivering software source code analysis solutions. Ralf obtained his PhD in formal methods from the University of Kiel, Germany, and was holding visiting appointments in France, Hong Kong, Australia and Japan.
Importance of measuring endolysosome, cytosolic, and extracellular pH in understanding the pathogenesis of and possible treatments for glioblastoma multiforme

Glioblastoma multiforme (GBM) is a very aggressive form of brain cancer that carries with it a tragically poor prognosis. As with many other forms of cancer, the extracellular environment near GBM tumors is acidified and is relevant to the pathogenesis of GBM because decreased pH promotes tumor cell invasion, increases angiogenesis, decreases immune surveillance, and increases resistance to possible treatments. Recently, vacuolar ATPase (v‐ATPase), a proton pump that helps maintain the acidic environment in endosomes and lysosomes (hereafter referred to endolysosomes) as well as proton gradients across the plasma membrane, was identified as a novel therapeutic target for GBM. However, information is lacking about cancer cell and tissue pH of endolysosomes, cytosol, and extracellular fluid.
Biomedical Literature Mining for Biological Databases Annotation

Margherita Berardi 1,5, Donato Malerba1 , Roberta Piredda2, Marcella Attimonelli2, Gaetano Scioscia3,4 and Pietro Leo3,4 1Dipartimento di Informatica – Universita degli Studi di Bari 2Dipartimento di Biochimica e Biologia Molecolare “E.Quagliariello" – Universita degli Studi di Bari 3IBM Italia S.p.A. Molecular Biodiversity Laboratory 4IBM Italia S.p.A. GBS Innovation Centre 5Exhicon S.r. l. , Bari Italy
Essential gene networks in acute myeloid leukemia identified using a microRNA-knockout CRISPR library screen

MicroRNAs (miRNA) are small RNAs that function as key modulators of gene expression. Due to their promiscuity of binding, a single miRNA may regulate several genes and hence, multiple pathways simultaneously. In addition, the 3’-UTR of mRNA can be recognized by several miRNA for suppression or degradation. We built a microRNA-only Knock-out (miRKo) CRISPR/Cas-9 library to identify essential miRNA in Acute Myeloid Leukemia (AML) using OCI-AML2, OCI-AML3 and U937 cell lines as in vitro models. 10 miRNA were identified to be essential in our screen among all three cell lines: miR-19b-1, -19b-2, 29b-2, -302a, -3678, -3713, -3910-1, -4447, -4718 and -6795. By using weighted degrees of association, we identified pathway hubs that uniquely affect all 3 cell lines by integrating miRNA:mRNA networks using mirDIP and pathway analysis using pathDIP. Through the miRKo screen, network membership analyses and biological anticorrelation scoring through patient data analysis, we identified RRP2CA, RPS6KB-1, CREB1, RPM1A, MAPK10, MAP3K2, ITCH, FBX-W7, NR3C1 and XIAP as likely targets of the essential miRNA in AML; and signal transduction, apoptosis, TGF-beta signalling and MAPK signalling as candidate essential pathways in AML.
Function approximation, "neural" networks, and adaptive nonlinear control

The resurgence of interest in flexible computational methods loosely inspired by biological signal processing mechanisms has produced a variety of possible new algorithms for adaptively controlling partially known nonlinear systems. However, for such methods to be useful in practice, the exact factors which govern successful applications must be identified and quantified; ad hoc, trial and error approaches must be supplanted by rigorous theoretical foundations and practical, constructive algorithms. Recent developments in this direction have provided just such a framework, by combining into a single methodology elements of constructive approximation theory, nonlinear stability theory, and robust nonlinear adaptation and control techniques. This paper presents an overview of this methodology and illustrates it by reviewing the structure of "neural" adaptive robot controllers with guaranteed stability and convergence properties. <<ETX>>
Vital role for Plasmodium berghei Kinesin8B in axoneme assembly during male gamete formation and mosquito transmission

Summary Sexual development is an essential phase in the Plasmodium life cycle, where male gametogenesis is an unusual and extraordinarily rapid process. It produces 8 haploid motile microgametes, from a microgametocyte within 15 minutes. Its unique achievement lies in linking the assembly of 8 axonemes in the cytoplasm to the three rounds of intranuclear genome replication, forming motile microgametes, which are expelled in a process called exflagellation. Surprisingly little is known about the actors involved in these processes. We are interested in kinesins, molecular motors that could play potential roles in male gametogenesis. We have undertaken a functional characterization in Plasmodium berghei of kinesin-8B (PbKIN8B) expressed specifically in male gametocytes and gametes. By generating Pbkin8B-gfp parasites, we show that PbKIN8B is specifically expressed during male gametogenesis and is associated with the axoneme. We created a ΔPbkin8B knockout cell line and analysed the consequences of the absence of PbKIN8B on male gametogenesis. We show that the ability to produce sexually differentiated gametocytes is not affected in ΔPbkin8B parasites and that the 3 rounds of genome replication occur normally. Nevertheless, the development to free motile microgametes is halted and the life cycle is interrupted in vivo. Ultrastructural analysis revealed that intranuclear mitoses is unaffected whereas cytoplasmic microtubules, although assembled in doublets and elongated, fail to assemble in the normal axonemal “9+2” structure and become motile. Absence of a functional axoneme prevented microgamete assembly and release from the microgametocyte, severely reducing infection of the mosquito vector. This is the first functional study of a kinesin involved in male gametogenesis. These results reveal a previously unknown role for PbKIN8B in male gametogenesis, providing new insights into Plasmodium flagellar formation.
Quantifying perennial ryegrass (Lolium perenne L.) and white clover (Trifolium repens L.) seed germination responses to water potential and temperature with a hydrothermal time model

ABSTRACT In New Zealand, a commonly sown pasture combination is perennial ryegrass with white clover. The hydrothermal time model (HTT) was used to quantify germination under different temperature (T) and water potential (WP) conditions for white clover ‘Nomad’ and perennial ryegrass ‘Stellar AR1’. Seeds were germinated in vitro under a range of T × WP combinations, and HTT models were fitted to germination time course data. Rapid germination of white clover under optimum T and WP was reflected by a much lower value for its HTT constant compared with perennial ryegrass (10.8 vs 80.7 MPa °C d). However, the lower base water potential for perennial ryegrass (−1.29 vs −0.495 MPa) and a higher threshold temperature for thermoinhibition (21.8 vs 18.3°C), meant that predicted perennial ryegrass germination was more resilient in warm dry conditions. HTT models can be used to assist decisions about the timing of perennial ryegrass and white clover sowing.
Full-thickness resection of neuroendocrine tumors in the rectum

Abstract Background Rectal neuroendocrine tumors (NETs) are subepithelial tumors with potential for malignancy. Depending on tumor characteristics, endoscopic or surgical resection is recommended. However, the optimal endoscopic approach is not defined. This is the first larger study evaluating endoscopic full-thickness resection (EFTR) of rectal NETs. Methods For resection, the full-thickness resection device (FTRD) was used. A registry was created as part of post-market clinical follow-up. All cases of rectal NETs in the registry were analyzed retrospectively. Results 31 German centers entered data of 501 FTRD procedures and 40 cases of rectal NETs were identified. The median lesion size was 8 mm. All lesions could be resected using FTRD. The median procedure time was 18.5 minutes. Resection was macroscopically and histologically complete in all cases. Full-thickness resection was achieved in 95 %. No major adverse events occurred. Endoscopic follow-up showed no evidence of residual or recurrent tumor. Conclusion EFTR is safe and effective for resection of smaller rectal NETs. Prospective comparative trials are needed to define the role of EFTR of rectal NETs.
Disentangled Feature Learning for Noise-Invariant Speech Enhancement

Most of the recently proposed deep learning-based speech enhancement techniques have focused on designing the neural network architectures as a black box. However, it is often beneficial to understand what kinds of hidden representations the model has learned. Since the real-world speech data are drawn from a generative process involving multiple entangled factors, disentangling the speech factor can encourage the trained model to result in better performance for speech enhancement. With the recent success in learning disentangled representation using neural networks, we explore a framework for disentangling speech and noise, which has not been exploited in the conventional speech enhancement algorithms. In this work, we propose a novel noise-invariant speech enhancement method which manipulates the latent features to distinguish between the speech and noise features in the intermediate layers using adversarial training scheme. To compare the performance of the proposed method with other conventional algorithms, we conducted experiments in both the matched and mismatched noise conditions using TIMIT and TSPspeech datasets. Experimental results show that our model successfully disentangles the speech and noise latent features. Consequently, the proposed model not only achieves better enhancement performance but also offers more robust noise-invariant property than the conventional speech enhancement techniques.
How Not to Locate Earthquake Epicenters

Thanks to the many readers who have sent their comments and suggestions to me over the past year. I plan to use your suggestions when I return to those topics in future columns. This issue's column features a rapid return to the subject of earthquake location, which generated an unusual level of correspondence. Here, I mention two contributions. First, Prof. Jose Pujol (University of Memphis) has created graphics related to the classic geometric techniques of earthquake location, and links to his figures can be found via the EduQuakes Web page. Second, Prof. Cinna Lomnitz (UNAM) has provided a guest column that further discusses the problems of hypocenter determination. Here is the quite engaging column from Cinna Lomnitz. Earthquake location is not just one of the most basic and important activities in seismology, it is still an unsolved problem. Ruff (“EduQuakes”, SRL 72 , p. 197, 2001) lifts the lid off an ancient bucket …
Gold nanoparticles as cancer theranostic agents

The application of nanotechnology in medicine involves using nanomaterials to develop novel therapeutic and diagnostic modalities. Given the unique physiochemical and optical properties of gold nanoparticle (GNP) such as good biocompatibility, nontoxic nature, surface properties and comparative stability, it has been widely studied in medicine, especially as a cancer theranostic agent. This review focuses on recent progresses in the field of gold nanostructures in cancer treatment and diagnosis. As far as cancer detection is concerned, several studies have indicated that GNPs can be used for X-ray, MR and optical imaging. With regard to cancer treatment, most studies have investigated the effect of GNPs in different treatment modalities like photothermal therapy, photodynamic therapy, sonodynamic therapy, drug delivery, and radiotherapy. In this paper, we have focused on reviewing the role of GNPs in improving radiotherapy efficiency as radiosensitizers. For optimization of parameters influencing the radiosensitization of GNPs, several studies have been undertaken in different scientific routes. We categorize these studies into three categories; Monte Carlo simulation, cellular studies and animal studies. Finally, according to findings reported by different researchers, the physical and biological mechanism of GNPs in generating radiosensitizing effect is discussed.
Clarification Question Generation for Speech Recognition Error Recovery Using Monolingual SMT

Clarification dialogue is an efficient and direct way of handling speech recognition errors in speech interface applications. In this paper we present a new approach to Clarification Question (CQ) generation. Monolingual phrase-based SMT (PB-SMT) framework is introduced to generate robust and flexible CQs. A parallel corpus from simulated error to manually annotated CQ is established and used for training the model. A new type of generalized phrase pair is expanded from conventional translation phrase table. Combining both generalized and conventional phrase pairs, a two-step decoding process is carried out to generate CQs. Both manually and automatic metrics are used to evaluate the quality of generated CQs. Experimental results show that our method can effectively generate reasonable CQs form miss-recognized utterances, and generated CQs can be used to prompt a clarification dialogue for error handling.
Algorithmic software fault localization

Debugging tools offer a rich set of breakpoint and displaying facilities. Those do not involve, however, a means for automatic identification of potentially faulty parts of the programs being debugged. Although that goal might be unrealistic in general, even partial solution to the problem, for a restricted classes of faults, might be useful. Towards that goal the authors present a novel fault localization algorithm that is capable of identifying a restricted class of programming faults for Pascal-like languages. The algorithm uses the following principle for fault localization: if a program component produces an incorrect result, while its input is correct, then the program component is faulty. The algorithm uses the computation trajectory-based influence relations to formulate hypotheses about the nature of the fault. User input is needed to assess correctness of intermediate situations on the trajectory. The set of potentially faulty statements generated by the algorithm is closely related to the concept of dynamic slice (B. Korel et al., 1988). The algorithm has been implemented in the System for Testing and Debugging (B. Korel et al., 1988). Early experiments indicate that the approach can be quite useful, particularly for inexperienced programmers. <<ETX>>
Lecture Notes for a course on System Identification, v2012

System identification in a narrow sense is concerned with tasks of parameter estimation based on observations originating from a dynamical system. System identification in a broad sense deals with many subtleties coming up when designing, conducting and interpreting results from such an experiment. The purpose of this text is to survey the collection of ideas, insights, theorems, intuitions, language and practical experiences which constitute the art of system identification. In this course we will guide you along the basic methods and concepts, as well as show you the many connections to related fields of applied science.
Study of cogging torque in permanent magnet machines

Cogging torque is produced in a permanent magnet machine by the magnetic attraction between the rotor mounted permanent magnets and the stator. It is an undesired effect that contributes to the machines output ripple, vibration, and noise. This paper analyzes various cogging torque minimization techniques as applied to a permanent magnet machine used in an electric power steering system. A six pole, eighteen slot, surface mounted, rare earth type, brushless permanent magnet machine is analyzed. The resultant cogging torque values are computed using a two dimensional finite element analysis package.