Miracle-dz/UniFAR-FTUs huggingface dataset:
A microarray configuration to quantify expression levels and relative abundance of splice variants

Over the past decade, alternative RNA splicing has raised a great interest appearing to be of high importance in the generation of expression diversity. This regulatory process plays a critical role in the normal development and its impact on the initiation and development of human disorders as well as on the pharmacological properties of drugs is increasingly being recognized. Only few studies describe specific alternative splicing expression profiling. Microarray strategies have been conceived to address alternative splicing events but with very few experimental data related to their abilities to provide true quantification values. We have developed a specific microarray configuration relying on a few, well optimized probes per splice event. Basically, five probes of 24mer are used to fully characterize a splice event. These probes are of two types, exon probes and junction probes, and are either specific to a splice event or not. The performances of such a ‘splice array’ were validated on synthetic model systems and on complex biological materials. The results indicate that DNA chips based on this design combining exon and junction derived probes enable the detection and, absolute and relative quantification of splice variants. In addition, this strategy is compatible with all the microarrays that use oligonucleotide probes.
A High-Level Certification Language for Automatically Generated Code

Program verification using Hoare-style techniques requires many logical annotations. We have previously shown that a generic annotation inference algorithm can be used to weave in all annotations required to certify safety properties for automatically generated code. The algorithm is implemented as part of our AUTOCERT system. It uses patterns to capture generatorand property-specific code idioms and property-specific meta-program fragments to construct the annotations. It is customized by specifying the code patterns and integrating them with the meta-program fragments for annotation construction. However, the latter part has so far involved tedious and error-prone low-level term manipulations, which has made customization difficult. Here, we describe an annotation schema compiler that simplifies and largely automates this customization task. It takes a collection of high-level declarative annotation schemas tailored towards a specific code generator and safety property, and generates all glue code required for interfacing with the generic algorithm core, thus effectively creating a customized annotation inference algorithm. The compiler raises the level of abstraction and simplifies schema development and maintenance. It also takes care of some more routine aspects of formulating patterns and schemas, in particular handling of irrelevant program fragments and irrelevant variance in the program structure, which reduces the size, complexity, and number of different patterns and annotation schemas that are required. This paper further contributes to developing a declarative and generative approach to logical annotations. The improvements described here make it easier and faster to customize the system to a new safety property or a new generator. We have been able to show different properties for a variety of programs generated by our AUTOBAYES and AUTOFILTER generators. We have also applied AUTOCERT to code derived from MathWorks Real-Time Workshop, and show some initial results.
Embryonic gonadotropin-releasing hormone signaling is necessary for maturation of the male reproductive axis

Gonadotropin-releasing hormone (GnRH) signaling regulates reproductive physiology in mammals. GnRH is released by a subset of hypothalamic neurons and binds to GnRH receptor (GnRHR) on gonadotropes in the anterior pituitary gland to control production and secretion of gonadotropins that in turn regulate the activity of the gonads. Central control of reproduction is well understood in adult animals, but GnRH signaling has also been implicated in the development of the reproductive axis. To investigate the role of GnRH signaling during development, we selectively ablated GnRHR-expressing cells in mice. This genetic strategy permitted us to identify an essential stage in male reproductive axis development, which depends on embryonic GnRH signaling. Our experiments revealed a striking dichotomy in the gonadotrope population of the fetal anterior pituitary gland. We show that luteinizing hormone-expressing gonadotropes, but not follicle-stimulating hormone-expressing gonadotropes, express the GnRHR at embryonic day 16.75. Furthermore, we demonstrate that an embryonic increase in luteinizing hormone secretion is needed to promote development of follicle-stimulating hormone-expressing gonadotropes, which might be mediated by paracrine interactions within the pituitary. Moreover, migration of GnRH neurons into the hypothalamus appeared normal with appropriate axonal connections to the median eminence, providing genetic evidence against autocrine regulation of GnRH neurons. Surprisingly, genetic ablation of GnRHR expressing cells significantly increased the number of GnRH neurons in the anterior hypothalamus, suggesting an unexpected role of GnRH signaling in establishing the size of the GnRH neuronal population. Our experiments define a functional role of embryonic GnRH signaling.
Associating event logs with ontologies for semantic process mining and analysis

Process mining uses various forms of event logs to extract process-related information, in order to discover, analyze conformance, or to enhance (business) processes. The vast majority of process mining applications are based on event logs with flat, keyword-based activity and resource descriptions. Many human-designed processes, however, are based on explicit workflow or lifecycle models with associated product models, both of which can be described using taxonomies or more complicated ontologies. This additional information can be used to analyze and visualize the processes with better insight of and improved formal access to the data. In this paper, we introduce a generic approach for enriching process mining using events logs with associated ontology structures. The main contribution and benefit of this approach lies in the ability to analyze the models in different abstraction levels, which greatly helps understanding complicated processes. Our main application areas are related to engineering and documentation processes.
A CROSS-LINGUISTIC STUDY ON DISCOURSE AND SYNTACTIC BOUNDARY CUES IN SPONTANEOUS SPEECH : USING DURATION AS AN EXAMPLE

This study focuses on the acoustic-phonetic cues at discourse and syntactic boundaries in English, Guoyu, Putonghua, and Japanese. Speech was elicited by having talkers describe the events in The Pear Story film. Recorded data were transcribed and segmented into discourse and syntactic units. Acousticphonetic measurements of syllable duration and syllable onset intervals (SOIs) were taken on the digitized data. A comparison of discourse/syntax and acoustics was made in order to examine boundary cues in speech. Results showed that final lengthening of boundary syllables and SOIs is the most universal cue for signaling structural boundaries, and the degree of final SOI lengthening is reflective of disjuncture hierarchy. However, there are also language-specific cues. In English, in addition to final lengthening, initial pitch-accented syllables and SOIs are also lengthened. In Guoyu and Putonghua, the scope of final syllable lengthening is widened to include the penultimate syllable. English and Putonghua are similar to each other in that there is no reflection of hierarchy in the degree of final syllable lengthening, while Guoyu and Japanese are more alike in this regard since both languages show some reflection of hierarchy through the degree of boundary syllable lengthening. Bigger structural boundaries are signaled by a smaller degree of lengthening.
Spectral sparsification and restricted invertibility

In this thesis we prove the following two basic statements in linear algebra. Let B be an arbitrary n × m in matrix where m ≥ n and suppose 0 < e < 1 is given. (1) Spectral Sparsification . There is a diagonal matrix Sm×ms0 with at most c n/e2 c nonzero entries for which 1-e2BB TpBSBTp1+e 2BBT . Thus the spectral behavior of BBT is captured by a weighted subset of the columns of B, of size proportional to its rank n. (2) Restricted Invertibility. There is a diagonal matrix Sm×m with at least 1-e2 B2 FB 22 nonzero entries, all equal to 1, for which BSBTse2 B2F mI. Thus there is a large coordinate restriction of B (i.e., a submatrix of its columns, given by S), of size proportional to its numerical rank B 2FB 22 , which is well-invertible. This significantly improves a theorem of Bourgain and Tzafriri [14]. We give deterministic polynomial time algorithms for constructing the promised diagonal matrices S in time O(mn3/e 2) and O((1 – e)2 mn3), respectively. By applying (1) to the class of Laplacian matrices of graphs, we show that every graph on n vertices can be spectrally approximated by a weighted graph with O(n) edges, thus generalizing the concept of expander graphs, which are constant-degree approximations of the complete graph. We then present a second graph sparsification algorithm based on random sampling, which produces weaker sparsifiers with O(n log n) edges but runs in nearly-linear time. We also prove a refinement of (1) for the special case of B arising from John's decompositions of convex bodies, which allows us to show that every convex body can be approximated by one which has very few contact points with its minimum volume ellipsoid.
Learning for stochastic dynamic programming

We present experimental results about learning function val- ues (i.e. Bellman values) in stochastic dynamic programming (SDP). All results come from openDP (opendp.sourceforge.net), a freely available source code, and therefore can be reproduced. The goal is an independent comparison of learning methods in the framework of SDP.
JQ1, a BET inhibitor, controls TLR4-induced IL-10 production in regulatory B cells by BRD4-NF-κB axis

Regulatory B cells, also well-known as IL-10-producing B cells, play a role in the suppression of inflammatory responses. However, the epigenetic modulation of regulatory B cells is largely unknown. Recent studies showed that the bromodomain and extra-terminal domain (BET) protein inhibitor JQ1 controls the expression of various genes involving cell proliferation and cell cycle. However, the role of BET proteins on development of regulatory B cells is not reported. In this study, JQ1 potently suppressed IL-10 expression and secretion in murine splenic and peritoneal B cells. While bromodomain-containing protein 4 (BRD4) was associated with NF-κB on IL-10 promoter region by LPS stimulation, JQ1 interfered the interaction of BRD4 with NF-κB on IL-10 promoter. In summary, BRD4 is essential for toll like receptor 4 (TLR4)-mediated IL-10 expression, suggesting JQ1 could be a potential candidate in regulating IL-10-producing regulatory B cells in cancer.
A Leakage-aware Bus Coding Algorithm

In this paper, we propose a low leakage bus coding algorithm which is suitable to both the address bus and the data bus. The proposed encoding scheme converts the input bits with low leakage state of a devised buffer. We characterize the bus and find optimal encoding scheme. It uses the staggered threshold voltage buffers. When it compared to the conventional bus, the proposed bus coding scheme reduces about 71% of total power and about 3 times leakage power.
Transition from linear to nonlinear viscoelasticity during deformation in a Zr-based glassy alloy

The transition behaviors from linear to nonlinear viscoelasticity during constant strain-rate deformations of a Zr-based glassy alloy near the glass transition temperature are investigated and a model calculation based on concept of a fictive stress is performed. The experimental results show that the viscoelastic behavior of the glassy alloy is characterized by a very narrow relaxation-time distribution due to its simple atomic structure. Hence, the transition between steady-state Newtonian and non-Newtonian flows can be analyzed by a stretched exponent relaxation-function of strain rate. And the condition at which the transition occurs in the Zr-based glassy alloy is investigated with a new model proposed on the basis of the hypothesis of stress-induced structural relaxation and a concept of fictive stress that expresses the structure of the material indirectly. Stress-strain curves calculated from the model agree quantitatively well with experimental results. The calculated curves of sufficiently higher strain-rates in the nonlinear viscoelastic regime show a stress- oscillation. This has been observed in many polymers, but has not been reported previously in glassy alloys. In the Zr-based glassy alloy, the oscillation is observed as predicted by the model.
Antimicrobial materials with medical applications

Abstract Despite intensive and considerable research achievements by material scientists and biologists, the problems of infections related to medical devices and implants remain knotty. The biofilm related infections are much harder to eradicate due to protection of extracellular polymeric substance secreted by the biofilms, hence shows a strong resistance to conventional antibiotics. Thus, there is a huge challenge for researchers to seek effective methods to combat device related bacterial infections ignited by biofilms to mitigate potential health risks and massive financial burdens to healthcare systems. Here we review the most recent progress and work on the applications of antibacterial biomaterials for the biomedical devices, concentrating on metals with antibacterial coatings/surfaces, antibacterial stainless steels and other commonly used antibacterial materials.
PSO based Neural Networks vs. traditional statistical models for seasonal time series forecasting

Seasonality is a distinctive characteristic which is often observed in many practical time series. Artificial Neural Networks (ANNs) are a class of promising models for efficiently recognizing and forecasting seasonal patterns. In this paper, the Particle Swarm Optimization (PSO) approach is used to enhance the forecasting strengths of feedforward ANN (FANN) as well as Elman ANN (EANN) models for seasonal data. Three widely popular versions of the basic PSO algorithm, viz. Trelea-I, Trelea-II and Clerc-Type1 are considered here. The empirical analysis is conducted on three real-world seasonal time series. Results clearly show that each version of the PSO algorithm achieves notably better forecasting accuracies than the standard Backpropagation (BP) training method for both FANN and EANN models. The neural network forecasting results are also compared with those from the three traditional statistical models, viz. Seasonal Autoregressive Integrated Moving Average (SARIMA), Holt-Winters (HW) and Support Vector Machine (SVM). The comparison demonstrates that both PSO and BP based neural networks outperform SARIMA, HW and SVM models for all three time series datasets. The forecasting performances of ANNs are further improved through combining the outputs from the three PSO based models.
PHOTOSYSTEM II PROTEIN 33 , a Protein Conserved in the Plastid Lineage , Is Associated with the Chloroplast Thylakoid Membrane and Provides Stability to Photosystem II Supercomplexes in Arabidopsis 1 [ OPEN ]

Department of Chemistry and Biochemistry (R.F., C.E.B.-H., S.S.M.) and Institute for Genomics and Proteomics (S.S.M.), University of California, Los Angeles, California 90095; Department of Biological and Environmental Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden (A.H., B.L.); Department of Chemistry, Ångström Laboratory, Uppsala University, 751 20 Uppsala, Sweden (F.M.); and Department of Biochemistry and Molecular Biology and Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (R.L.L., B.L.)
Analysis of Lead-Free Piezoceramic-Based Power Ultrasonic Transducers for Wire Bonding

Since the 1950s, lead zirconate-titanate (PZT) has been the dominant transduction material utilized in power ultrasonics, while lead-free piezoceramics have been largely neglected due to their relatively poor piezoelectric and electromechanical properties. However, the implementation of environmental directives that regulate and control the use of hazardous materials, such as lead, triggered a search for new high-performance lead-free piezoceramics. Recent advances have led to lead-free piezoceramics exhibiting properties similar to PZT, but despite this, reports utilizing these novel piezoceramics in practice are limited. This research employs a modified variant of bismuth sodium titanate (BNT) in a power ultrasonic transducer used for metal welding during the manufacture of semiconductors. The important factors for transducer reliability and performance are investigated, such as piezoceramic aging and stack preload level. It is reported that BNT-based transducers exhibit good stability, and can withstand a stack preload level of 90 MPa without depoling. Although the BNT-based transducers exhibited larger dissipative losses compared to identical PZT8-based transducers, the tool displacement gain was larger under constant current conditions. Semiconductor wire bonds which satisfied the commercial quality control requirements were also formed by this BNT-based transducer.
Frequency of proteinuria in type 2 diabetes mellitus seen at a diabetes centre in southern India

The frequency of proteinuria was assessed in a cohort of 1848 diabetic patients attending a diabetes centre in south India. A total of 127 (6.9%) patients had evidence of macroproteinuria and 49 (2.5%) patients had microproteinuria. Thus overall 9.4% of patients had diabetes related proteinuria. In addition, 70 patients (3.8%) had evidence of proteinuria with no evidence of retinopathy. The frequency of both microproteinuria and macroproteinuria increased linearly with duration of diabetes. Multiple logistic regression analysis showed that duration of diabetes, serum creatinine, and glycated haemoglobin were risk factors for macroproteinuria.
Mechanisms of immune activation of human immunodeficiency virus in monocytes/macrophages

Monocytes/macrophages (M/M) are the major host of human immunodeficiency virus (HIV) in solid tissues. However, blood monocytes are nonpermissive for HIV infection, indicating that M/M activation or differentiation is necessary for HIV replication. Since M/M are activated during immune responses, we investigated the effect of T-cell activation on HIV expression in M/M derived from peripheral blood of HIV-infected individuals. Previously, we reported that coculture of monocytes from HIV-infected donors with T cells and mitogens resulted in M/M differentiation and HIV expression. Production of HIV by M/M from infected donors required direct contact between monocytes and T cells (for the first 24 h), and the response to alloantigens, but not mitogens, was restricted to HLA-DR. In this study, we found that HIV was more readily recovered from M/M of asymptomatic HIV seropositive donors (69%) than from M/M of symptomatic donors (57%). Viral antigens (e.g., inactivated herpes simplex virus) could initiate the immune response and HIV expression. The ability of noninfected T cells to activate HIV expression in M/M and observations that treatments of M/M with antibodies to deplete T cells did not reduce HIV expression suggested that the monocytes were endogenously infected. To define the aspects of immune activation specifically involved in initiating HIV expression in M/M, interactions of M/M and T cells and participation of cytokines were investigated. The T cell which activated M/M was CD4+ CD8-. Fixed allogeneic cells are known to induce T-cell activation but were not able to serve as antigen for M/M differentiation, suggesting that M/M may need to function as antigen-presenting cells to receive the signal to differentiate and express HIV. Blocking of M/M-T-cell interaction with antibodies directed against LFA-1 or interleukin-1 prevented HIV expression. However, inhibition of later stages of T-cell activation, such as blocking of interleukin-2 receptors, did not diminish HIV expression in M/M. Consistent with the requirement for cell-cell contact between M/M and T cells, a variety of cytokines were unable to initiate HIV replication in M/M. The ability of T cells to induce cellular differentiation and HIV replication in M/M in vitro suggests that initiation of an immune response to an antigen, such as an opportunistic pathogen, could be a mechanism by which HIV disseminates to tissues in vivo.
Maturation feeding and reproductive development in adult pine weevil, Hylobius abietis (Coleoptera: Curculionidae)

Abstract Maturation feeding on conifer bark by newly emerged Hylobius abietis(Linnaeus) is essential for reproductive development. When feeding occurs on young conifer transplants, this weevil causes significant economic damage. Between emergence and oviposition however, weevils feed on bark from different sources but of unknown nutritional ‘quality’. The factors influencing the rate of feeding by males and females and female reproductive development were determined in laboratory bioassays using two contrasting food sources – the bark on different species of seedling conifer and on logs of mature trees. The nutritional ‘quality’ of bark was characterized by the concentration of nitrogen, total sugars, total polyphenols and resin. Regression models were used to show that overall, the rate of feeding on the bark of both seedlings and logs increased with weevil size and was negatively related to nitrogen concentration. The nitrogen concentration in seedling bark (mean 1.1%) was about three times higher than that of logs (mean 0.4%). The rate of reproductive development increased with nitrogen intake during feeding and the preoviposition period for weevils feeding on seedlings and logs was ~ 13 days and 46 days, respectively. Analysis of weevil mortality and of the weight gain of surviving weevils suggests that a nitrogen content of around 0.3% may be limiting for H. abietis. The possibility that nutritionally adequate food resources may be limiting for H. abietis is briefly discussed.
Application of STATCOM for Transient Stability Improvement and Performance Enhancement for a Wind Turbine based Induction Generator

Voltage stability is a key issue to achieve the uninterrupted operation of wind farms equipped with squirrel cage induction generators (SCIG) during grid faults. A Static Synchronous Compensator (STATCOM) is applied to a power network which includes a SCIG driven by a wind turbine, for steady state voltage regulation and transient voltage stability support. The STATCOM is controlled by using PQ controller technique with voltage regulation as basic scenario. The system is implemented using MATLAB/ SIMULINK. Results illustrate that the STATCOM improves the transient voltage stability and therefore helps the wind turbine generator system to remain in service during grid faults. The time to reach steady state torque and speed without using vector control or direct torque control can also be achieved by using this STATCOM control technique.