Miracle-dz/UniFAR-FTUs huggingface dataset:
Medicago sativa cDNAs Encoding Chalcone Reductase

CHR is an enzyme that co-acts with CHS to produce a branch in the first step of the flavonoid pathway. CHS acting alone catalyzes the sequential coupling of three ma-lonyl-COA molecules with coumaroyl-COA to produce 4,2’,4’,6’-tetrahydroxychalcone (Heller and Hahlbrock, 1980). However, in the presence of CHR and NADPH the oxygen function of the polyketide intermediate, which would produce the 6’-hydroxyl of the chalcone, is reduced and then eliminated as water prior to cyclization, resulting in the formation of 4,2’,4’-trihydroxychalcone (6’-de-oxychalcone). This chalcone is the precursor of the 5-deoxy series of flavonoids and isoflavonoids (Harborne, 1988), which includes nodulation induction factors as well as pterocarpan phytoalexins of the Legu-minosae
Topological Data Analysis of Convolutional Neural Networks ’ Weights on Images

The topological properties of images have been studied for a variety of applications, such as classification, segmentation, and compression. For the application of image classification, high classification accuracy has been achieved by machine learning models, especially convolutional neural networks (CNNs), and we seek to understand the reasons behind their success. In our project, we apply topological data analysis to describe, visualize, and analyze topological properties of the weights learned from a CNN classifier trained on digit images from the MNIST data set.
2-D analysis and synthesis of dielectric lens antennas with boundary integral equations

At first, we study the electromagnetic performance of 2-D models of hemielliptic dielectric lens antennas (DLAs) with the aid of an advanced numerical algorithm. It is based on the Muller boundary integral equations (MBIE) discretized with the trigonometric Galerkin scheme. Then this solver, combined with an in-house genetic-type optimizer, is applied to the synthesis of the lens profile aimed at the improvement of the lens off-axis radiation properties. The results obtained highlight the interplay between the focusing and resonance mechanisms in the behaviour of compact dielectric lenses. Furthermore, it is demonstrated that the lens shaping enables one to improve the performance of switched-beam DLAs typically used in base stations for indoor communication systems.
Coherence brightened laser source for atmospheric remote sensing

We have studied coherent emission from ambient air and demonstrated efficient generation of laser-like beams directed both forward and backward with respect to a nanosecond ultraviolet pumping laser beam. The generated optical gain is a result of two-photon photolysis of atmospheric O2, followed by two-photon excitation of atomic oxygen. We have analyzed the temporal shapes of the emitted pulses and have observed very short duration intensity spikes as well as a large Rabi frequency that corresponds to the emitted field. Our results suggest that the emission process exhibits nonadiabatic atomic coherence, which is similar in nature to Dicke superradiance where atomic coherence is large and can be contrasted with ordinary lasing where atomic coherence is negligible. This atomic coherence in oxygen adds insight to the optical emission physics and holds promise for remote sensing techniques employing nonlinear spectroscopy.
An incremental refinement approach to a development of a flash-based file system in Event-B

Nowadays, many formal methods are used in the area of software development accompanied by a number of advanced theories and tools. However, more experiments are still required in order to provide significant evidence that will convince and encourage users to use, and gain more benefits from, those theories and tools. Event-B is a formalism used for specifying and reasoning about systems. Rodin is an open and extensible tool for Event-B specification, refinement and proof. The flash file system is a complex system. Such systems are a challenge to specify and verify at this moment in time. This system was chosen as a case study for our experiments, carried out using Event-B and the Rodin tool. The experiments were aimed at developing a rigorous model of flash-based file system; including implementation of the model, providing useful evidence and guidelines to developers and the software industry. We believe that these would convince users and make formal methods more accessible. An incremental refinement was chosen as a strategy in our development. The refinement was used for two different purposes: feature augmentation and structural refinement (covering event and machine decomposition). Several techniques and styles of modelling were investigated and compared; to produce some useful guidelines for modelling, refinement and proof. The model of the flash-based file system we have completed covers three main issues: fault-tolerance, concurrency and wear-levelling process. Our model can deal with concurrent read/write operations and other processes such as block relocation and block erasure. The model tolerates faults that may occur during reading/writing of files. We believe our development acts as an exemplar that other developers can learn from. We also provide systematic rules for translation of Event-B models into Java code. However, more work is required to make these rules more applicable and useful in the future.
Spatial cyberinfrastructures, ontologies, and the humanities

We report on research into building a cyberinfrastructure for Chinese biographical and geographic data. Our cyberinfrastructure contains (i) the McGill-Harvard-Yenching Library Ming Qing Women's Writings database (MQWW), the only online database on historical Chinese women's writings, (ii) the China Biographical Database, the authority for Chinese historical people, and (iii) the China Historical Geographical Information System, one of the first historical geographic information systems. Key to this integration is that linked databases retain separate identities as bases of knowledge, while they possess sufficient semantic interoperability to allow for multidatabase concepts and to support cross-database queries on an ad hoc basis. Computational ontologies create underlying semantics for database access. This paper focuses on the spatial component in a humanities cyberinfrastructure, which includes issues of conflicting data, heterogeneous data models, disambiguation, and geographic scale. First, we describe the methodology for integrating the databases. Then we detail the system architecture, which includes a tier of ontologies and schema. We describe the user interface and applications that allow for cross-database queries. For instance, users should be able to analyze the data, examine hypotheses on spatial and temporal relationships, and generate historical maps with datasets from MQWW for research, teaching, and publication on Chinese women writers, their familial relations, publishing venues, and the literary and social communities. Last, we discuss the social side of cyberinfrastructure development, as people are considered to be as critical as the technical components for its success.
Noninvasive Bioluminescence Imaging of Herpes Simplex Virus Type 1 Infection and Therapy in Living Mice

ABSTRACT Mouse models of herpes simplex virus type 1 (HSV-1) infection provide significant insights into viral and host genes that regulate disease pathogenesis, but conventional methods to determine the full extent of viral spread and replication typically require the sacrifice of infected animals. To develop a noninvasive method for detecting HSV-1 in living mice, we used a strain KOS HSV-1 recombinant that expresses firefly (Photinus pyralis) and Renilla (Renilla reniformis) luciferase reporter proteins and monitored infection with a cooled charge-coupled device camera. Viral infection in mouse footpads, peritoneal cavity, brain, and eyes could be detected by bioluminescence imaging of firefly luciferase. The activity of Renilla luciferase could be imaged after direct administration of substrate to infected eyes but not following the systemic delivery of substrate. The magnitude of bioluminescence from firefly luciferase measured in vivo correlated directly with input titers of recombinant virus used for infection. Treatment of infected mice with valacyclovir, a potent inhibitor of HSV-1 replication, produced dose-dependent decreases in firefly luciferase activity that correlated with changes in viral titers. These data demonstrate that bioluminescence imaging can be used for noninvasive, real-time monitoring of HSV-1 infection and therapy in living mice.
Improved emission tomography via multiscale sinogram analysis

In this paper, we extend a multiscale Bayesian approach to modeling and estimation of general Poisson processes previously developed in Timmermann and Nowak (1997), and apply it to the emission computed tomography (ECT) image reconstruction problem. We develop a practical prior model for the sinogram image, which we use to estimate the underlying sinogram intensity from the raw projection data prior reconstruction. This sinogram estimate is then used in conjunction with the standard filtered-backprojection algorithm to produce an improved image reconstruction. The impact of the new filtering approach on ECT imaging is illustrated with simulated and clinical data.
of the 23 rd Annual EMBS International Conference , October 25-28 , Istanbul , Turkey THE DESIGN OF A CARE MODEL AND ASSOCIATED PERIPHERALS TO ASSIST WITH NON-COMPLIANCE OF MEDICATION

Although many ailments both mental and physical are treated using orally administered drugs, patients frequently fail to comply with their medication regimens, the most typical failure being ‘under’ medication 111. This can be attributed to a number of factors, which include impaired manual dexterity, levels of cognition, poor packaging of medication, numbers of differing medications and failing vision. Various techniques have been investigated to reduce levels of non-compliance and although a number of automated systems have been developed to address this problem, not all individuals involved in the supply to intake chain for medication have been accommodated. It is therefore arguable that currently available systems are incomplete and improvements are possible if all stakeholders are catered for in the solution. It has been the aim of this study to indicate the requirements of an optimal compliance aid and to specify a suitable care model derived from the requirements of all stakeholders. It is intended that this care model should utilize the facilities offered by the Internet in terms of a dynamic adaptable communications infrastructure to include all persons involved in the supply to intake chain for orally administered medication and provide a holistic solution to the problem of noncompliance.
Forensic visualization of foreign matter in human tissue by near‐infrared spectral imaging: Methodology and data mining strategies

Rapidity of data acquisition, high image fidelity and large field of view are of tremendous value when looking for chemical contaminants or for the proverbial “needle in the haystack” – in this case foreign inclusions in histologic sections of biopsy or autopsy tissues. Near infrared chemical imaging is one of three chemical imaging techniques (NIR, MIR and Raman) based on vibrational spectroscopy, and provides distinct technical advantages for this application.
Characterization of the Unusual Insulin of Psammomys obesus, a Rodent With Nutrition-Induced NIDDM-Like Syndrome

Psammomys obesus fed a high-calorie diet develops a NIDDM-like syndrome. The use of reverse-phase highperformance liquid chromatography (HPLC) to study Psammomys insulin biosynthesis and release revealed a very delayed elution time for the Psammomys insulin peak appearing near the position of human proinsulin. This unusual peak was initially thought to represent partially processed insulin on the basis of its molecular size and susceptibility to trimming by carboxypeptidase B (CpB). However, the findings of an active carboxypeptidase E (CpE) enzyme and the normal amidated forms of gastrin and cholecystokinin octapeptide (CCK-8) in Psammomys tissues were inconsistent with CpE-related aberrant processing of insulin. Moreover, amino acid sequencing of the delayed peak of Psammomys insulin revealed fully processed insulin with amino acid sequence as predicted by the cDNA. The unique presence of a B-30 phenylalanine residue, resulting in an increased hydrophobicity of the insulin molecule, probably underlies the marked delay in elution time on HPLC. The unusual structure of Psammomys insulin does not appear to contribute to the proinsulinemia observed in diabetic Psammomys since the HPLC-purified molecule did not inhibit PCI and PC2 convertase activities in an in vitro assay.
User Perceptions of Decision Support System Restrictiveness: An Experiment

Abstract:We often think of decision support systems (dss) simply as expanding managerial information-processing capabilities. When a manager relies on the functional capabilities of a particular dss in solving a problem, however, he or she is actually restricted to some subset of the full range of possible decision-making processes. Dss builders may wish to use this “restrictiveness” characteristic as a design variable, deliberately choosing the ways in which a dss restricts its users. To do so effectively, builders need to know whether restrictiveness should be treated as an absolute or a relative attribute. A key research question, therefore, is whether all users will be restricted identically by a given dss.This paper reports on an experiment exploring if and how different users of the same dss differ in their perceptions of system restrictiveness. Subjects used three dss and ranked them from most to least restrictive. The results indicated that, while there was a significant similarity among rankings,.
Habitual physical activity and health-related physical fitness in fourth-grade children.

OBJECTIVE To examine the relationship between habitual physical activity and components of health-related physical fitness in children. DESIGN Cross-sectional survey with correlational analysis. SETTING Seven public elementary schools in a suburban southern California city. PARTICIPANTS Five hundred twenty-eight healthy fourth-grade children (274 boys and 254 girls), 85% of whom were non-Hispanic whites. Ninety-eight percent of eligible students participated. INTERVENTIONS None. MEASUREMENTS/MAIN RESULTS Results of six measures of physical activity in children (monitoring by accelerometer, parent report, and child self-reports of weekday activity, weekend activity, and summer involvement in activity classes and youth sports) were combined in a physical activity index. This index of habitual physical activity was examined in relation to measures of five components of health-related fitness: the mile run, skin-fold tests, pull-ups, sit-ups, and the sit-and-reach test. The physical activity index was significantly associated with all five fitness components. The canonical correlation was . 29. CONCLUSION Active children appear to engage in a sufficient variety of activities to enhance multiple components of health-related fitness.
Actualisation and Re-enactment: Two Categories in Understanding the Old Testament

Exegesis has been an integral part of Professor Jurie le Roux's life. Throughout his scholarly career, he has continually worked to realise the 'actualisation' and 're-enactment' of Old Testament stories and ideas. As a modest tribute to Professor le Roux, this contribution seeks to demonstrate that both concepts also play a central role within the process of composing Old and New Testament texts. This will be illustrated with reflections on how Old and New Testament texts speak about the Sabbath. Firstly, the Sabbath commandment in the books of Exodus and Deuteronomy will be dealt with. Secondly, a brief survey will present how the Sabbath commandment has been understood during the Second Temple period. Finally, it will be argued that the New Testament authors sought to forge a link with the original tenor of the Sabbath commandment by presenting Jesus as the one who 'actualises' and 're-enacts' the Sabbath commandment that often became rigid over time.
Antibody Array-Generated Profiles of Cytokine Release from THP-1 Leukemic Monocytes Exposed to Different Amphotericin B Formulations

ABSTRACT Cytokine antibody arrays were used to establish the profiles of cytokine release from THP-1 monocytes exposed to different amphotericin B (AMB) drug delivery systems. Fungizone (FZ) and Amphotec (ABCD) caused the release of significantly more inflammatory molecules and the release of inflammatory molecules at higher levels than either AmBisome (L-AMB) or Abelcet (ABLC) after 6 h of treatment. Specifically, tumor necrosis factor alpha (TNF-α), interleukin-8 (IL-8), GRO-(αβγ), monocyte chemoattractant protein-1 (MCP-1), RANTES, IL-10, and IL-6 were detected and semiquantified with a chemiluminscence imaging system. TNF-α, IL-8, and MCP-1 were the most predominant; however, little if any TNF-α was present in ABLC- or L-AMB-treated cultures. The TNF- α and IL-8 levels determined by quantitative enzyme-linked immunosorbent assay correlated with the relative cytokine levels measured by using the antibody arrays. Although the viabilities of THP-l monocytes in all AMB-treated cultures were similar by trypan blue exclusion, the amount of lactic dehydrogenase released was significantly larger in FZ- and ABCD-treated cultures than in L-AMB- and ABLC-treated cultures, indicating more membrane perturbations with those formulations. Membrane cation channel formation was also measured in model cholesterol-containing large unilamellar vesicles to directly assess the ion channel formation ability of the system. Only FZ and ABCD induced significant ion currents at concentrations less than 1.5 × 10−5 M. These results may help provide rationales for the immediate cytokine-mediated side effects observed with FZ and ABCD and the reduced side effects observed with L-AMB and ABLC.
Surgical Correction of the Fat Neck

This is an tip-to-date review of the state of the art in the treatment of the fat neck at the University of Miami School of Medicine, based on twenty-five years of experience including several thousand cases. The combination of submental lipectomy, platysma myectomy, facelift, submandibular lipectomy, platysma myotomy, and posterior muscle traction with suture fixation has consistently produced marked improvement in the fat neck. Under this regimen, when the patient returns in five to ten years for a second lift, it is rare that the neck requires more than the skin tightening that comes with a simple facelift.
Detection and Classification of Multiple Power-Quality Disturbances With Wavelet Multiclass SVM

This paper presents an integrated model for recognizing power-quality disturbances (PQD) using a novel wavelet multiclass support vector machine (WMSVM). The so-called support vector machine (SVM) is an effective classification tool. It is deemed to process binary classification problems. This paper combined linear SVM and the disturbances-versus-normal approach to form the multiclass SVM which is capable of processing multiple classification problems. Various disturbance events were tested for WMSVM and the wavelet-based multilayer-perceptron neural network was used for comparison. A simplified network architecture and shortened processing time can be seen for WMSVM.
Oncogenes and Tumor Suppressors Therapeutic Ef fi cacy of p 53 Restoration in Mdm 2-Overexpressing Tumors

The p53 (TP53) tumor suppressor is the most frequently mutated gene in human cancers. Restoring expression of wild-type p53 has led to tumor growth suppression in a variety of tumor models that are p53 deficient. Other mechanisms, for example, upregulation of Mdm2, exist in tumors to inactivate the p53 pathway. Mdm2, an E3 ubiquitin ligase that targets p53 for proteasomal degradation, is present at high levels inmany tumorswithwild-type p53. In this study, the effects of restoring p53 activity were probed in Mdm2-overexpressing tumors genetically using animal models. Here, it was demonstrated that elevated levels of Mdm2 and decreased levels of p53 act additively to dampen p53 activity inDNAdamage response and tumor development.Our data further indicate that restoration of wild-type p53 expression in Mdm2-overexpressing angiosarcomas results in tumor stasis and regression in some cases. Finally, it was determined that restored p53 suppressed cell proliferation but did not elicit apoptosis in the Mdm2-overexpressing angiosarcomas. Implications: Restoration of wild-type p53 expression in Mdm2-overexpressing tumors suppresses tumor growth, which represents a potential clinical strategy to treat tumors with high levels of Mdm2. Visual Overview: http://mcr.aacrjournals. org/content/12/6/901/F1.large. jpg. Mol Cancer Res; 12(6); 901–11. 2014 AACR.
Image Latent Semantic Analysis for Face Recognition

In this paper, we propose a novel and effective image descriptor— Image Latent Semantic Analysis (ILSA) for extracting latent semantic features of face image. The features are obtained from a feature-image matrix, which obtains a wealth of information than the conventional image semantic and has a stronger expression and classification than the low-level features. The unique feature extraction by the ILSA can be better overcome the impact of some negative factors, such as the image quality fuzzy, illumination changes effect. The experiment results on the ORL and large-scale FERET databases show that proposed algorithms significantly outperforms other well-known algorithms in terms of recognition of recognition rate.
Design for Casting - A New Paradigm for Preventing Potential Problems

Design revisions are expensive and time consuming. Yet, these are inevitable because product designers have limited knowledge about casting processes and have no means to evaluate the influence of design features on castability (costs, quality and productivity). Problems appear much later, at the tooling or manufacturing stage, when it is much more expensive to incorporate changes than at the design stage. Progressive engineering companies therefore rely on design review committees, which include tooling and casting engineers, to suggest early modifications to a product design for ease of manufacture. This paper presents an intelligent design environment to assist product engineers in assessing a part design for castability. The software simulates the way casting engineers decide the casting process, parting line, cores, mold box, feeders, gating system and mold layout, and analyzes each decision to suggest how the design could be modified to improve quality as well as reduce tooling and manufacturing costs. The software also facilitates electronic exchange of information between product, tooling and casting engineers, thus improving the level of communication between them and helping compress the total lead time to complete a project.
Clustered class-dependant training method for digit recognition classifiers

This paper presents a convolutional neural network clustering approach for handwritten digits recognition. Neural networks were trained individually, using the same training set and combined into clusters, depending on the training method used. These clusters formed a layered architecture, where each layer attempted to recognize the given digit, when the previous layers were not able to do so with sufficient certainty. We examine various ways of combining such clusters and training their constituent networks.