Miracle-dz/UniFAR-FTUs huggingface dataset:
Human Paraoxonase-3 Is an HDL-Associated Enzyme With Biological Activity Similar to Paraoxonase-1 Protein but Is Not Regulated by Oxidized Lipids

Abstract— Paraoxonase-1 (PON1) is a secreted protein associated primarily with high density lipoprotein (HDL) and participates in the prevention of low density lipoprotein (LDL) oxidation. Two other paraoxonase (PON) family members, namely, PON2 and PON3, have been identified. In this study, we report the cloning and characterization of the human PON3 gene from HepG2 cells. Tissue Northern analysis identifies an ≈1.3-kb transcript for PON3 primarily in the liver. PON3-specific peptide antibodies detect an ≈40-kDa protein associated with HDL and absent from LDL. Pretreatment of cultured human aortic endothelial cells with supernatants from HeLa Tet On cell lines overexpressing PON3 prevents the formation of mildly oxidized LDL and inactivates preformed mildly oxidized LDL. In contrast to PON1, PON3 is not active against the synthetic substrates paraoxon and phenylacetate. Furthermore, PON3 expression is not regulated in HepG2 cells by oxidized phospholipids and is not regulated in the livers of mice fed a high-fat atherogenic diet.
Non-Circadian Expression Masking Clock-Driven Weak Transcription Rhythms in U2OS Cells

U2OS cells harbor a circadian clock but express only a few rhythmic genes in constant conditions. We identified 3040 binding sites of the circadian regulators BMAL1, CLOCK and CRY1 in the U2OS genome. Most binding sites even in promoters do not correlate with detectable rhythmic transcript levels. Luciferase fusions reveal that the circadian clock supports robust but low amplitude transcription rhythms of representative promoters. However, rhythmic transcription of these potentially clock-controlled genes is masked by non-circadian transcription that overwrites the weaker contribution of the clock in constant conditions. Our data suggest that U2OS cells harbor an intrinsically rather weak circadian oscillator. The oscillator has the potential to regulate a large number of genes. The contribution of circadian versus non-circadian transcription is dependent on the metabolic state of the cell and may determine the apparent complexity of the circadian transcriptome.
[Outpatient prophylaxis and treatment of arterial hypertension with application of mobile telephone systems and Internet techniques].

AIM To compare clinical efficacy of standard outpatient follow-up of hypertensive patients with efficacy of such follow-up with application of internet techniques and mobile telephone systems (ITMTS). MATERIAL AND METHODS Two groups of hypertensive patients were examined: group 1 (n=97, 45% females, age 49 +/- 11 years) on one-year ITMTS follow-up; group 2 (n=102, 50% females, age 51 +/- 11 years) on standard one-year follow-up. Clinical efficacy was assessed by the rate of achievement and maintenance of target blood pressure, dynamics of modifiable risk factors (smoking, obesity) for a year. RESULTS Withdrawal in group 1 was 36%, target blood pressure was achieved in 77% patients vs. 12% in group 2 (p < 0.001). CONCLUSION Introduction of ITMTS technologies into outpatient clinics activity considerably raises efficacy of outpatient treatment of hypertensive patients.
CCAT: Combinatorial Code Analysis Tool for transcriptional regulation

Combinatorial interplay among transcription factors (TFs) is an important mechanism by which transcriptional regulatory specificity is achieved. However, despite the increasing number of TFs for which either binding specificities or genome-wide occupancy data are known, knowledge about cooperativity between TFs remains limited. To address this, we developed a computational framework for predicting genome-wide co-binding between TFs (CCAT, Combinatorial Code Analysis Tool), and applied it to Drosophila melanogaster to uncover cooperativity among TFs during embryo development. Using publicly available TF binding specificity data and DNaseI chromatin accessibility data, we first predicted genome-wide binding sites for 324 TFs across five stages of D. melanogaster embryo development. We then applied CCAT in each of these developmental stages, and identified from 19 to 58 pairs of TFs in each stage whose predicted binding sites are significantly co-localized. We found that nearby binding sites for pairs of TFs predicted to cooperate were enriched in regions bound in relevant ChIP experiments, and were more evolutionarily conserved than other pairs. Further, we found that TFs tend to be co-localized with other TFs in a dynamic manner across developmental stages. All generated data as well as source code for our front-to-end pipeline are available at http://cat.princeton. edu.
An Opportunity for Environmental Conservation: Evaluation of Test Material for Construction of Artificial Reefs Modules Trainers Made of Ecological Concrete

As a result of the degradation of coral reefs around the world and given that conservation efforts alone are not enough, artificial reefs have been proposed as a tool for the conservation of these ecosystems and recovery. As part of an initiative to develop modules forming artificial reefs made of concrete to promote the ecological conservation of the biodiversity of the Colombian Caribbean, this work constitutes a starting point. During eight months two trapezoidal plates were submerged in the waters surrounding the Bajo Grande (Isla Palma) archipelago de San Bernardo in the Colombian Caribbean; the plates were fabricated in concrete with Portland cement and waste ceramic. Seeking a more ecological product, aggregates were replaced entirely by ceramic waste. After making biological and physicochemical evaluations of the material exposed to the marine environment it was concluded that this is a favorable substrate for the development of coral reefs; and the plates were colonized on more than 30% of its surface by marine organisms, their structure was found internally stable and there were no adverse effects on marine biota near the test site.
Complex data integration into an active XML repository

Decision-making processes are becoming complex, particularly with the presence of huge amounts of distributed and heterogeneous data. Therefore, warehousing these complex data into a unified format has become an urgent necessity. In this paper, we focus on the integration phase and propose an architecture for integrating relevant complex data into a repository of Active XML (AXML) documents. AXML documents are XML documents with embedded calls to Web services. They have the advantage of not requiring to store all data explicitly, but AXML frequently updatable data can be loaded on the fly via calling Web services if necessary.
Predominant variable region gene usage by gamma/delta T cell receptor- bearing cells in the adult thymus

Previous studies have indicated that the diversity of gamma genes expressed by gamma/delta-bearing murine T cells is limited, but comparable information concerning the expressed diversity of delta genes is lacking. In this study, we have investigated the rearrangement and expression of delta and gamma genes in T cell hybridomas that express gamma/delta T cell receptors. Three productive delta chain cDNA clones were isolated (delta 7.3, delta 7.1, and delta 2.3) that encode new variable region sequences. Two of the delta cDNAs differ significantly from those observed in the V alpha repertoire. In addition, one cDNA expressed a new J delta region (J delta 2), which was localized between J delta 1 and C delta genes. Using these and other delta gene probes and gamma gene probes, we found that five independent hybridomas expressed four different V delta s and three different V gamma s. However, analysis of an enriched population of gamma/delta-expressing cells from the adult thymus suggests that only a few V delta genes and one V gamma gene are used by the majority of the cells. These results suggest that important components of receptor chain that contribute to specificity (i.e., the germline V gene sequences) are relatively nondiverse in the thymic gamma/delta population.
Prospective National Study of the Prevalence, Incidence, Management and Outcome of a Large Contemporary Cohort of Patients With Incident Non‐Valvular Atrial Fibrillation

Background There are few studies of atrial fibrillation (AF) outside of North America or Europe. The aim of the present study was to assess the prevalence, incidence, management and outcomes of patients with new atrial fibrillation, in a large contemporary cohort (2004–2012) of adult patients. Methods and Results The Clalit Health Services (CHS) computerized database of 2 420 000 adults, includes data of community clinic visits, hospital discharge records, medical diagnoses, medications, medical interventions, and laboratory test results. The prevalence of AF on January 1, 2004 was 71 644 (3%). Prevalence and incidence of AF increased with age and was higher in men versus women. During the study period (2004–2012) 98 811 patients developed new non‐valvular AF (mean age −72, 50% women, 46% with cardiovascular disease, 6% with prior stroke). The rate of persistent warfarin use (dispensed for >3 months in a calendar year) was low (25.7%) and it increased with increasing stroke risk score. Individual Time in Therapeutic Range (TTR) among warfarin users was 42%. The incidence rate of ischemic stroke and death increased with age. The rate of stroke increased from 2 per 1000 person years in patients with CHA2DS2_VASC SCORE of 0, to 58 per 1000 person years in those with a score of 9. Conclusions In the present study the prevalence and incidence of AF, stroke, and death were comparable to those reported in Europe and North America. The low use of anticoagulation calls for measures to increase adherence to current treatment recommendations in order to improve outcomes.
Visual attention based on long-short term memory model for image caption generation

Image caption generation becomes a raising topic in computer vision and artificial intelligence. In order to solve the problem of stiff description, we intend to extract richer features using convolutional neural network (CNN). A neural and probabilistic framework has been proposed consequently which combines CNN with a special form of recurrent neural network (RNN) to produce an end-to-end image captioning. We use a model that takes advantage of word to vector to encode the variable length input into a fixed dimensional vector. Considering the description of the object in an image is not specific enough, we introduce an attention mechanism through visualization to show how the model is able to fix its gaze on salient objects. We validate our model on three benchmark datasets and get great performance by using standard evaluation metrics.
On the importance of evidence: a response to Halpern

Halperri argues for alternative non‐Bayesian approaches to uncertainty based on problems he perceives in the Bayesian approach. In particular, he argues for a distinction between degrees of belief and statistical statements (based on the concept of random sampling). In this response I show that there is no difference between these two concepts in the Bayesian framework, and that the replacement of variables by constants in probabilistic predicate calculus expressions is valid, despite Halpern's objections. The main reason for his rejection of the simpler approach is that he does not condition his belief statements on the evidence used to form these beliefs, and so gets into trouble when new evidence is received. This failure to properly take evidence into account invalidates most of his other criticisms. While I approve of his call for more formal rigor in representing Bayesian practice, his claim to have provided a semantics is misleading – what he has provided is not operational.
Hybrid adaptive impedance force controller using bang-bang and Particle Swarm Optimization approaches

Force control is one of the most challenging controls in robot manipulators. In this control scheme, the system dynamic does not only depend on actuator dynamic but also environment. Non-adaptive controller is not sufficient to efficiently regulate the plant when the environment such as manipulated object, contact point, etc. is changed. Adaptive controller is able to deal with this problem; however, its response in the learning (adaptation) period is often unsatisfactory. In some cases, this undesired response may damage the environment and actuator. To overcome this problem, our proposed technique applies Particle Swarm Optimization (PSO) to achieve the desired response. Hybrid structure is adopted to reduce the problem of unlearned response. The controller structure is based on the concept of impedance control which the controller regulates the system to act as the pre-specified impedance dynamics. Simulation results show that our proposed technique is applicable and superior to the conventional learning system.
Hybrid Seven-Level Cascaded Active Neutral-Point-Clamped-Based Multilevel Converter Under SHE-PWM

This paper presents the hybrid seven-level cascaded active neutral-point-clamped (ANPC)-based multilevel converter. The converter topology is the cascaded connection of a three-level ANPC converter and an H-bridge per phase. The voltage of the H-bridge is actively maintained to the required level through selection of the switching states of the converter. The topology is operated under selective harmonic elimination pulsewidth modulation (SHE-PWM), maintaining the switching frequency of the converter to a minimum. The operating principles, voltage balancing methods, and limitations of the converter are analyzed together with extensive simulation results of the topology. Experimental results from a low-power laboratory prototype are presented that verify the operation of the hybrid converter under SHE-PWM.
PrivateFS: a parallel oblivious file system

PrivateFS is an oblivious file system that enables access to remote storage, while keeping both the file contents and client access patterns secret. PrivateFS is based on a new parallel Oblivious RAM mechanism (PD-ORAM)---instead of waiting for the completion of all ongoing client-server transactions, client threads can now engage a server in parallel without loss of privacy. This critical piece is missing from existing Oblivious RAMs (ORAM), which can not allow multiple clients threads to operate simultaneously without revealing intra- and inter-query correlations and thus incurring privacy leaks. And since ORAMs often require many communication rounds, this significantly and unnecessarily constrains throughput. The mechanisms introduced here eliminate this constraint, allowing overall throughput to be bound by server bandwidth only, and thus to increase by an order of magnitude. Further, new de-amortization techniques bring the worst case query cost in line with the average cost. Both of these results are shown to be fundamental to any ORAM. Extensions providing fork consistency against an actively malicious adversary are then presented. A high performance, fully functional PD-ORAM implementation was designed, built and analyzed. It performs multiple queries per second on a 1TB+ database across 50ms latency links, with unamortized, bound query latencies. Based on PD-ORAM, PrivateFS was built and deployed on Linux as a userspace file system.
Automagically Inferring the Source Words of Lexical Blends

Lexical blending is a highly productive and frequent process by which new words enter a language. A blend is formed when two or more source words are combined, with at least one them shortened, as in brunch(breakfast +lunch). We use linguistic and cognitive aspects of this process to motivate a computational treatment of neologisms formed by blending. We propose statistical features that can indicate the source words of a blend, and whether an unknown word was formed by blending. We present computational experiments that show the usefulness in these tasks of features tapping into the recognizability of the source words in the blend, in combination with their semantic properties.
Curious Continued Fractions, Nonlinear Recurrences, and Transcendental Numbers

We consider a family of integer sequences generated by nonlinear recurrences of the second order, which have the curious property that the terms of the sequence, and integer multiples of the ratios of successive terms (which are also integers), appear interlaced in the continued fraction expansion of the sum of the reciprocals of the terms. Using the rapid (double exponential) growth of the terms, for each sequence it is shown that the sum of the reciprocals is a transcendental number.
Adhesion analysis of two-level hierarchical morphology in natural attachment systems for 'smart adhesion'

The attachment ability of insects and lizards is well known. The Tokay gecko, in particular, has the most complex adhesion structures. The pads are covered by a large number of small hairs (setae) that contain many branches per seta with spatulae. Seta branch morphology is hierarchical. Hierarchical morphology of setae is responsible for adaptation of a large number of spatulae to rough surfaces. Van der Waals attraction between the large numbers of spatulae in contact with a rough surface is the primary mechanism for high adhesion. In order to investigate the effect of hierarchical structure, for the first time, the two-level hierarchical model has been developed. We consider one- and two-level hierarchically structured spring models for simulation of setae contacting with random rough surfaces and demonstrate the effect of the two-level hierarchical structure on the adhesion force, the number of contacts and the adhesion energy. Tip of spatula in a single contact was assumed as spherical. Rough surfaces with various roughness parameters which cover a common range of most of natural and artificial rough surfaces at the scale of gecko's pad were generated. It was found that significant adhesion enhancements are created with the two-level structure until a certain value of roughness which appears to be related to the maximum spring deformation. We conclude that the hierarchical morphology of a gecko seta is the necessary part for 'smart adhesion' of gecko, the ability to cling on and detach from different smooth, as well as rough surfaces.
Informative STR Markers for Marfan Syndrome in Birjand, Iran

Objective(s) Marfan syndrome (MFS) is a severe connective tissue disorder withan autosomal dominant inheritance pattern. Early diagnosis is critical in MFS. Because of the large size of fibrillin-1 gene (FBN1), the uniqueness of mutations, and the absence of genotype-to-phenotype correlations linkage analysis can be very helpful for early diagnosis of MFS. In this study, eight polymorphic markers were evaluated among families related to an affected pedigree. Materials and Methods An extended family in Birjand, Iran, with numerous cases of Marfan Syndrome in three consecutive generations, is being reported. From all consented members of these families, peripheral blood samples were collected in tubes containing EDTA. DNA extraction was performed by the conventional salting-out method. Eight STR markers were selected for linkage analysis, including four intragenic markers (MTS1, MTS2, MTS3, and MTS4) and another four flanking FBN1 markers (D15S119, D15S126, D15S1028, and D15S143). PCR-amplified fragments were evaluated on 15% polyacrylamide gel. Results MTS1, MTS2, and MTS3 were informative in the extended pedigree. D5S1028 was the only non-MTS marker which showed an informative diagnostic capability. Conclusion MTS markers were informative and useful in the molecular diagnosis of Marfan Syndrome in an extended pedigree. MTS1, MTS2, and MTS3 can be used as a prenatal or presymptomatic diagnosis for all members of the extended pedigree.
Split Queue Time Warp and a Flexible Distributed Simulation System

Simulation belongs to the oldest computer applications: using a model for quasi-empirical studies is a cost-effecive and sometimes unique way of analysing a real sytem and getting a basis for decisions. A more recent purpose is to build virtual environments for training or entertainment. There is a variety of modeling approaches and computational techniques. Discrete event simulation, which is our subject here, considers the dynamics of the object system as a sequence of instantaneous state transformations called events. (Queueing systems are a classic example, with events like a job entering or leaving a queue.) In this abstraction, nothing happens between event times, so that the simulation skips the intervals. Computation time and simulated time thus become independent concepts: the computer dedicates its time and efforts to the events – which, in reality, have no duration at all. This orthogonality has two important consequences. First, a computer simulation can be orders of magnitude faster or slower than the real thing; this depends on the frequency of events and their computational cost. Second, to make simulated time go on, there must always be a future event to continue with. Event processing therefore has the additional obligation to deduce subsequent events from the current state of affairs. (In a queueing example, the event of a job entering service may imply leaving it some definite time later.) Such future events are then managed in the event list (calendar, agenda, . . . ), a priority queue of what-when pairs ordered by time-stamps, where the foremost entry defines the current event and the current time.
Optics at the nanometer scale : imaging and storing with photonic near fields

Preface. Theory and Basic Principles. Theory of Imaging in Near-Field Microscopy J.J. Greffet, R. Carminati. Light Scattering by Tips in Front of Surfaces A. Madrazo, et al. A Numerical Study of a Model Near-Field Optical Microscope A.A. Maradudin, et al. Short and Long Range Interactions in Near Field Optics O. Keller. Modelling Optical Resonators Probed by Subwavelength Sized Optical Detectors A. Castiaux, et al. Experiments: Fundamentals and Applications. Instrumentation in Near Field Optics D. Courjon, et al. Effect of the Coherence in Near Field Microscopy F. de Fornel, et al. Scanning Interferometric Apertureless Microscopy at Ten Angstrom Resolution H.K. Wickramasinghe, et al. Primary Imaging Modes in Near-Field Microscopy M. Vaez-Iravani. Local Excitation of Surface Plasmons by TNOM B. Hecht, et al. Weak Localization of Surface Plasmon Polaritons: Direct Observation with Photon Scanning Tunneling Microscope S.I. Bozhevolnyi, et al. STM-Induced Photon Emission from Au (110) R. Berndt. Writing of Nanolines on a Ferroelectric Surface with a Scanning Near-Field Optical Microscope J. Massanell, et al. Near Field Optics with High-Q Whispering Gallery Modes N. Dubreuil, et al. Fluorescence Microscopy and Spectroscopy by Scanning Near- Field Optical/Atomic Force Microscope (SNOM-AFM) M. Fujihira. Fluorescence Lifetime Contrast Combined with Probe Microscopy O.H. Willemsen, et al. Towards SNIM: Scanning Near-Field Microscopy in the Infrared F. Keilmann. 6 NM Lateral Resolution in Scanning Near Field Optical Microscopy with the Tetrahedral Tip J. Koglin, et al. An Aperture-Type Reflection-Mode SNOM C. Durkan, I.V. Shvets. Surface Modifications Via Photo-Chemistry in a Reflection Scanning Near-Field Optical Microscope S. Madsen, et al. Near-Field Diffraction Microscopy with a Coherent Low-Energy e-Beam: Fresnel Projection Microscope V.T. Binh, et al. Author Index. Subject Index.