Miracle-dz/UniFAR-FTUs huggingface dataset:
A Density-Genetic Algorithm Method for Computing Electronic Structures of Doped and Undoped Polythiophene Oligomers: A Modified Su–Schrieffer–Heeger Hamiltonian-Based Study

We propose a genetic algorithm (GA)-driven density matrix method for calculating the equilibrium geometry and charge storage configurations of hole(bipolaron)-doped Polythiophene (PT) oligomers. A modified version of the Su–Schrieffer–Heeger Hamiltonian is used to describe the PT chain. A population of geometry strings are used to generate the corresponding PT-Hamiltonians which act as generators of corresponding unitary transformations which transform a single trial one-electron density matrix into a population of density matrices for different geometries. As the geometry strings evolve under the action of GA operators, the density matrices also evolve on the fitness landscape. Once the fitness reaches maximum, the optimum geometry string, the corresponding Hamiltonian, and the density matrix lead to equilibrium geometry, energy, charge distribution, band gap, Fermi energy, etc. The bipolaronic defect–induced conducting state is predicted to have a symmetric lattice-like admixture of “aromatic” and “quininoid” regions and is characterized by nonzero density of states at Fermi energy and low band gaps.
Osteoblasts produce soluble factors that induce a gene expression pattern in non‐metastatic prostate cancer cells, similar to that found in bone metastatic prostate cancer cells

Progressive prostate cancer typically metastasizes to bone where prostate cancer cells gain an osteoblast‐like phenotype and induce osteoblastic metastases through unknown mechanisms. To investigate the biology of prostate cancer skeletal metastases, we compared gene expression between the non‐metastatic LNCaP cell line and its derivative cell line C4‐2B that metastasizes to bone.
A sequential approach for multi-class discriminant analysis with kernels

Linear discriminant analysis (LDA) is a standard statistical tool for data analysis. Recently, a method called generalized discriminant analysis (GDA) has been developed to deal with nonlinear discriminant analysis using kernel functions. Difficulties for the GDA method can arise in the form of both computational complexity and storage requirements. We present a sequential algorithm for GDA avoiding these problems when one deals with large numbers of datapoints.
Air separation with cryogenic energy storage: Optimal scheduling considering electric energy and reserve markets

The concept of cryogenic energy storage (CES) is to store energy in the form of liquid gas and vaporize it when needed to drive a turbine. Although CES on an industrial scale is a relatively new approach, the technology is well known and essentially part of any air separation unit that utilizes cryogenic separation. In this work, the operational benefits of adding CES to an existing air separation plant are assessed. Three new potential opportunities are investigated: (1) increasing the plant's flexibility for load shifting, (2) storing purchased energy and selling it back to the market during higher-price periods, and (3) creating additional revenue by providing operating reserve capacity. A mixed-integer linear programming scheduling model is developed and a robust optimization approach is applied to model the uncertainty in reserve demand. The proposed model is applied to an industrial case study, which shows significant potential economic benefits. © 2015 American Institute of Chemical Engineers AIChE J, 61: 1547–1558, 2015
Modelling, Verification and Synthesis of Two-Tier Hierarchical Fixed-Priority Preemptive Scheduling

Hierarchical scheduling has major benefits when it comes to integrating hard real-time applications. One of those benefits is that it gives a clear runtime separation of applications in the time domain. This in turn gives a protection against timing error propagation in between applications. However, these benefits rely on the assumption that the scheduler itself schedules applications correctly according to the scheduling parameters and the chosen scheduling policy. A faulty scheduler can affect all applications in a negative way. Hence, being able to guarantee that the scheduler is correct is of great importance. Therefore, in this paper, we study how properties of hierarchical scheduling can be verified. We model a hierarchically scheduled system using task automata, and we conduct verification with model checking using the Times tool. Further, we generate C-code from the model and we execute the hierarchical scheduler in the Vx Works kernel. The CPU and memory overhead of the modelled scheduler is compared against an equivalent manually coded two-level hierarchical scheduler. We show that the worst-case memory consumption is similar and that there is a considerable difference in CPU overhead.
Simple robot suggests physical interlimb communication is essential for quadruped walking

Quadrupeds have versatile gait patterns, depending on the locomotion speed, environmental conditions and animal species. These locomotor patterns are generated via the coordination between limbs and are partly controlled by an intraspinal neural network called the central pattern generator (CPG). Although this forms the basis for current control paradigms of interlimb coordination, the mechanism responsible for interlimb coordination remains elusive. By using a minimalistic approach, we have developed a simple-structured quadruped robot, with the help of which we propose an unconventional CPG model that consists of four decoupled oscillators with only local force feedback in each leg. Our robot exhibits good adaptability to changes in weight distribution and walking speed simply by responding to local feedback, and it can mimic the walking patterns of actual quadrupeds. Our proposed CPG-based control method suggests that physical interaction between legs during movements is essential for interlimb coordination in quadruped walking.
Performance on Adaptive Path Selection Scheme for Cooperative Communication Networks

In future communications, cooperative communication with relay networks will be the one of the most effective scheme to enlarge coverage area and to boost data rate. In the recent research results, the path selection, power allocation and relay protocols on relay networks are the most important factors to improve the system performance. However, the channel quality of direct transmission path and the relay path will be the influential effect on the performance of relay networks. Therefore, in this paper, we proposed an adaptive path selection (APS) scheme to effectively select the optimal path for cooperative communications.
Glycated Collagen Induces α11 Integrin Expression Through TGF‐β2 and Smad3

The adhesion of cardiac fibroblasts to the glycated collagen interstitium in diabetics is associated with de novo expression of the α11 integrin, myofibroblast formation and cardiac fibrosis. We examined how methylglyoxal‐glycated collagen regulates α11 integrin expression. In cardiac fibroblasts plated on glycated collagen but not glycated fibronectin, there was markedly increased α11 integrin and α‐smooth muscle actin expression. Compared with native collagen, binding of purified α11β1 integrin to glycated collagen was reduced by >fourfold, which was consistent with reduced fibroblast attachment to glycated collagen. Glycated collagen strongly enhanced the expression of TGF‐β2 but not TGF‐β1 or TGF‐β3. The increased expression of TGF‐β2 was inhibited by triple helical collagen peptides that mimic the α11β1 integrin binding site on type I collagen. In cardiac fibroblasts transfected with α11 integrin luciferase promoter constructs, glycated collagen activated the α11 integrin promoter. Analysis of α11 integrin promoter truncation mutants showed a novel Smad2/3 binding site located between −809 and −1300 nt that was required for promoter activation. We conclude that glycated collagen in the cardiac interstitium triggers an autocrine TGF‐β2 signaling pathway that stimulates α11 integrin expression through Smad2/3 binding elements in the α11 integrin promoter, which is important for myofibroblast formation and fibrosis. J. Cell. Physiol. 230: 327–336, 2015. © 2014 Wiley Periodicals, Inc.
The HATP hierarchical planner: Formalisation and an initial study of its usability and practicality

HTN planners have generally relied on specialised languages for domain and problem representations. To facilitate adoption by other communities such as robotics, however, and integration with real world applications written in standard programming languages, we need HTN planners that are based on more familiar concepts from structured programming, and that come ready with features supporting integration. In this paper, we demonstrate how the HATP (Hierarchical Agent-based Task Planner) HTN planner offers such “syntactic sugar” and some of these features. Moreover, since it has a conceptually distinct syntax compared to traditional HTN planners, we also develop a formalism to unambiguously capture HATP's syntax and an important subset of its semantics, which we then use to compare against the formalism of a well understood family of HTN planners and to show that the former is sound. Finally, we demonstrate that despite quite possibly using “heavier” data structures to naturally capture HATP's syntax/semantics, and thereby facilitate extensions to HATP and integration with other applications, the implementation still performs acceptably.
Inverse Arithmetic Operators for Fuzzy Intervals

Fuzzy arithmetic is a powerful tool in many engineering problems such as decision making, control theory, fuzzy systems and approximate reasoning. However, it is well known that the practical use of standard fuzzy arithmetic operators gives results more imprecise than necessary or in some cases, even incorrect. This problem is due to the overestimation effect induced by computing fuzzy arithmetic operations. In this paper a modified implementation for fuzzy unimodal interval arithemtics is defined where new subtraction and division operators are proposed. These new operators are exactly the inverse of the addition and multiplication operators. The effectiveness of the proposed methodology is illustrated by simulation examples.
The in vivo role of stem cell factor (c‐kit ligand) on mastocytosis and host protective immunity to the intestinal nematode Trichinella spiralis in mice

The role of stem cell factor (SCF) in the generation of intestinal mast cell hyperplasia and host protective immunity following helminth infection was investigated using the Trichinella spiralis/mouse model. In vivo administration of a monoclonal antibody specific for the receptor for SCF (c‐kit) was found to completely prevent the generation of intestinal mastocytosis normally observed following T. spiralis infection. This was reflected by markedly reduced intestinal mast cell protease (IMCP) levels in both tissue and serum. Moreover, animals treated with anti‐c‐kit antibody failed to show any evidence of worm expulsion from the gut. The data demonstrate for the first time, a critical role for the SCF in the generation of mucosal mastocytosis and host protective immunity following an intestinal helminth infection.
Daily Rhythms in Olfactory Discrimination Depend on Clock Genes but Not the Suprachiasmatic Nucleus

The suprachiasmatic nucleus (SCN) regulates a wide range of daily behaviors and has been described as the master circadian pacemaker. The role of daily rhythmicity in other tissues, however, is unknown. We hypothesized that circadian changes in olfactory discrimination depend on a genetic circadian oscillator outside the SCN. We developed an automated assay to monitor olfactory discrimination in individual mice throughout the day. We found olfactory sensitivity increased approximately 6-fold from a minimum during the day to a peak in the early night. This circadian rhythm was maintained in SCN-lesioned mice and mice deficient for the Npas2 gene but was lost in mice lacking Bmal1 or both Per1 and Per2 genes. We conclude that daily rhythms in olfactory sensitivity depend on the expression of canonical clock genes. Olfaction is, thus, the first circadian behavior that is not based on locomotor activity and does not require the SCN.
Characterization of PBSX, a defective prophage of Bacillus subtilis

PBSX, a defective Bacillus subtilis prophage, maps to the metA-metC region of the chromosome. DNA (33 kilobases) from this region of the chromosome was cloned and analyzed by insertional mutagenesis with the integrating plasmid pWD3. This plasmid had a promoterless alpha-amylase gene (amyL) that provided information on the direction and level of transcription at the site of integration. Transcription under the control of the PBSX repressor proceeded in the direction metA to metC over a distance of at least 18 kilobases. Electrophoretic analysis of proteins produced by different integrant strains upon PBSX induction and by fragments subcloned in Escherichia coli allowed the identification of early and late regions of the prophage. A set of contiguous fragments directing mutagenic integration suggested that the minimum size of an operon that encodes phage structural proteins is 19 kilobases. The adaptation of PBSX transcriptional and replicational functions to a chromosomally based, thermoinducible expression system is discussed.
Exploiting Heterogeneous Treebanks for Parsing

We address the issue of using heterogeneous treebanks for parsing by breaking it down into two sub-problems, converting grammar formalisms of the treebanks to the same one, and parsing on these homogeneous treebanks. First we propose to employ an iteratively trained target grammar parser to perform grammar formalism conversion, eliminating predefined heuristic rules as required in previous methods. Then we provide two strategies to refine conversion results, and adopt a corpus weighting technique for parsing on homogeneous treebanks. Results on the Penn Treebank show that our conversion method achieves 42% error reduction over the previous best result. Evaluation on the Penn Chinese Treebank indicates that a converted dependency treebank helps constituency parsing and the use of unlabeled data by self-training further increases parsing f-score to 85.2%, resulting in 6% error reduction over the previous best result.
Neutrophils Infiltrate Resistance-Sized Vessels of Subcutaneous Fat in Women With Preeclampsia

We examined if there is systemic vascular inflammation and neutrophil infiltration in women with preeclampsia. Resistance-sized vessels (10 to 200 μm) of subcutaneous fat were evaluated from normal nonpregnant women, normal pregnant women, and preeclamptic women. Immunohistochemical staining was performed for: (1) interleukin-8 (IL-8), a potent neutrophil chemokine; (2) intercellular adhesion molecule-1 (ICAM-1; CD54), an endothelial cell adhesion molecule; and (3) CD66b, a neutrophil antigen. Vessels of preeclamptic patients had intense IL-8 staining in the endothelium and vascular smooth muscle, as compared with little or no staining for normal pregnant and normal nonpregnant patients. ICAM-1 was expressed on the endothelium of all patient groups. In preeclamptic patients, ICAM-1 was also expressed on vascular smooth muscle. Vessels of preeclamptic patients had significantly more CD66b staining of neutrophils than did normal pregnant or normal nonpregnant patients. There were significantly more vessels stained, more vessels with neutrophils flattened and adhered to endothelium, more vessels with neutrophils infiltrated into the intima, and more neutrophils per vessel. In conclusion, in women with preeclampsia, there was significant infiltration of neutrophils into maternal systemic vasculature associated with inflammation of the vascular smooth muscle indicated by increased expression of IL-8 and ICAM-1. Neutrophil infiltration provides a reasonable explanation for endothelial and vascular smooth muscle dysfunction in preeclampsia because neutrophils produce toxic substances, which may explain clinical symptoms.
Evaluation methods for Web application clustering

Clustering of the entities composing a Web application (static and dynamic pages) can be used to support program understanding, However, several alternative options are available when a clustering technique is designed for Web applications. The entities to be clustered can be described in different ways (e.g., by their structure, by their connectivity, or by their content), different similarity measures are possible, and alternative procedures can be used to form the clusters. The problem is how to evaluate the competing clustering techniques in order to select the best for program understanding purposes. In this paper, two methods for clustering evaluation are considered, the gold standard and the task oriented approach. The advantages and disadvantages of both of them are analyzed in detail. Definition of a gold standard (reference clustering) is difficult and prone to subjectivity. On the other side, an evaluation based on the level of support given to task execution is expensive and requires careful experimental design. Guidelines and examples are provided for the implementation of both methods.
Climate change, cash transfers and health

Abstract The forecast consequences of climate change on human health are profound, especially in low- and middle-income countries and among the most disadvantaged populations. Innovative policy tools are needed to address the adverse health effects of climate change. Cash transfers are established policy tools for protecting population health before, during and after climate-related disasters. For example, the Ethiopian Productive Safety Net Programme provides cash transfers to reduce food insecurity resulting from droughts. We propose extending cash transfer interventions to more proactive measures to improve health in the context of climate change. We identify promising cash transfer schemes that could be used to prevent the adverse health consequences of climatic hazards. Cash transfers for using emission-free, active modes of transport – e.g. cash for cycling to work – could prevent future adverse health consequences by contributing to climate change mitigation and, at the same time, improving current population health. Another example is cash transfers provided to communities that decide to move to areas in which their lives and health are not threatened by climatic disasters. More research on such interventions is needed to ensure that they are effective, ethical, equitable and cost–effective.
Cardiac output estimation with a new Doppler device after off-pump coronary artery bypass surgery.

OBJECTIVE To compare cardiac output (CO), stroke volume (SV), and cardiac index (CI) as estimated with a new, noninvasive Doppler device (Ultrasonic Cardiac Output Monitor [USCOM]; USCOM Ltd, Sydney, Australia) with those measured with the bolus thermodilution (TD) technique. DESIGN Prospective nonrandomized study. SETTING Postcardiac surgery recovery unit of a tertiary cardiac center. PARTICIPANTS Fifty patients after off-pump coronary artery bypass (OPCAB) surgery. MEASUREMENT AND MAIN RESULTS Both right-sided and left-sided CO were estimated with a USCOM continuous-wave (CW) Doppler device, and CO was determined with the bolus TD technique performed in triplicate. On comparing the right-sided CO, SV, and CI with those of TD, the mean bias was 0.03 L/min, 1.6 mL, and 0.02 L/min/m(2), respectively. The comparison of left-sided CO, SV, and CI with those of TD revealed a means bias of 0.14 L/min, 1.0 mL, and 0.08 L/min/m(2), respectively. CONCLUSION This study showed excellent agreement between the values for CO, SV, and CI as determined with USCOM and TD. Since there was only 1 time period for CO estimation in each patient with both methods, the stability of this correlation needs to be further investigated over time.
Time-frequency analysis for power transformer fault detection using vibration method

The vibration methods are widely employed in the machinery condition monitoring and the time-frequency analysis has been applied in many fault detection applications. In this paper, the study of the vibrations using Wigner-Ville distribution is presented to assess the power transformer condition. First, the distribution contour plots of power transformer vibrations under different conditions are compared. Then, the pattern recognition based on the energy distribution similarity is presented. Finally, a health metric is proposed to represent the transformer health state. The results from more than 10 transformers are compared, and the preliminary study shows that the proposed method is effective to assess the power transformer condition.
MADNESS: A Multiresolution, Adaptive Numerical Environment for Scientific Simulation

MADNESS (multiresolution adaptive numerical environment for scientific simulation) is a high-level software environment for solving integral and differential equations in many dimensions that uses adaptive and fast harmonic analysis methods with guaranteed precision that are based on multiresolution analysis and separated representations. Underpinning the numerical capabilities is a powerful petascale parallel programming environment that aims to increase both programmer productivity and code scalability. This paper describes the features and capabilities of MADNESS and briefly discusses some current applications in chemistry and several areas of physics.
Filtering microblogging messages for social tv

Social TV was named one of the ten most important emerging technologies in 2010 by the MIT Technology Review. Manufacturers of set-top boxes and televisions have recently started to integrate access to social networks into their products. Some of these systems allow users to read microblogging messages related to the TV program they are currently watching. However, such systems suffer from low precision and recall when they use the title of the show as keywords when retrieving messages, without any additional filtering. We propose a bootstrapping approach to collecting microblogging messages related to a given TV program. We start with a small set of annotated data, in which, for a given show and a candidate message, we annotate the pair to be relevant or irrelevant. From this annotated data set, we train an initial classifier. The features are designed to capture the association between the TV program and the message. Using our initial classifier and a large dataset of unlabeled messages we derive broader features for a second classifier to further improve precision.
Complexity and performance analysis of spectrum sensing techniques for Cognitive Radios

Spectrum sensing is a vital part of Cognitive Radios (CRs). Success of CRs for opportunistic spectrum access depends upon the underlying spectrum sensing technique. Prior to choosing a particular technique among others, one of the biggest challenges faced is the hardware requirements of these techniques as they govern the cost of CR. This paper presents the complexity and performance analysis of filter bank spectrum estimation techniques while taking classical spectral estimation techniques as reference. This analysis can be very useful for radio designers as the obtained results can be used to optimize their designs.