Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of target genes of cediranib in alveolar soft part sarcoma using a gene microarray

The aim of the present study was to identify the target genes of cediranib and the associated signaling pathways in alveolar soft part sarcoma (ASPS). A microarray dataset (GSE32569) was obtained from the Gene Expression Omnibus database. The R software package was used for data normalization and screening of differentially expressed genes (DEGs). The Database for Annotation, Visualization and Integrated Discovery was used to perform Gene Ontology analysis. Gene Set Enrichment Analysis was performed to obtain the up- and downregulated pathways in ASPS. The Distant Regulatory Elements of co-regulated genes database was used to identify the transcription factors (TFs) that were enriched in the signaling pathways. A protein-protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins database and was visualized using Cytoscape software. A total of 71 DEGs, including 59 upregulated genes and 12 downregulated genes, were identified. Gene sets associated with ASPS were enriched primarily in four signaling pathways: The phenylalanine metabolism pathway, the mitogen-activated protein kinase (MAPK) signaling pathway, the taste transduction pathway and the intestinal immune network for the production of immunoglobulin A. Furthermore, 107 TFs were identified to be enriched in the MAPK signaling pathway. Certain genes, including those coding for Fms-like tyrosine kinase 1, kinase insert domain receptor, E-selectin and platelet-derived growth factor receptor D, that were associated with other genes in the PPI network, were identified. The present study identified certain potential target genes and the associated signaling pathways of cediranib action in ASPS, which may be helpful in understanding the efficacy of cediranib and the development of new targets for cediranib.
Myocardial metabolism of fatty acids.

The myocardium is able to utilize both carbohydrates and noncarbohydrates for the performance of its work (1). Extraction of an individual substrate is usually determined by its arterial level. Thus, after a carbohydrate meal the heart derives much of its energy from the metabolism of carbohydrates; however, in the fasting state myocardial energy production is dependent upon noncarbohydrates, primarily fatty acids (1). Recent studies (2, 3) have shown that the principal lipid fraction of plasma concerned with the transport and metabolism of fatty acids is the plasma nonesterified or free fatty acid (FFA) fraction. Previous studies have already demonstrated that the heart uses a considerable amount of FFA (3). The present study was undertaken to determine further the role of fatty acids in myo-cardial metabolism. Most of the methods used in this investigation have been described in detail in previous studies from this laboratory. Coronary sinus blood was obtained from a catheter placed in the coronary sinus, and blood samples from metabolic studies were simultaneously obtained from arterial and coronary sinus blood (1). The coronary blood flow was determined with the nitrous oxide desaturation method (4). Blood glucose was determined by the method of Hagedorn and Jensen (5) using Somogyi's method to prepare the blood filtrate (6).
The effect of Er,Cr:YSGG laser and air abrasion on shear bond strength of a fissure sealant to enamel.

PURPOSE The authors conducted an in vitro study to evaluate the shear bond strength of a fissure sealant to enamel pretreated with erbium,chromium:yttrium, scandium,gallium,garnet (Er,Cr:YSGG) laser or air abrasion followed by acid etching. METHODS The authors sectioned extracted sound premolars mesiodistally and used the buccal and lingual surfaces for experimental analysis. They divided specimens randomly into three groups of 15 each according to the enamel surface pretreatment methods: group A, 37 percent phosphoric acid; group B, air abrasion followed by acid etching with 37 percent phosphoric acid; group C, irradiation with Er,Cr:YSGG laser followed by acid etching with 37 percent phosphoric acid. After applying a bonding system, the authors bonded cylinders of sealant to the enamel surfaces by using transparent gelatin tubes (0.7 millimeter in diameter and 1 mm in height) and then polymerized them. They stored all specimens in distilled water at 37 degrees C for 24 hours. They tested shear bond strength by using a universal testing machine with a crosshead speed of 0.5 mm per second. The authors analyzed the data by means of one-way analysis of variance and Tukey-Kramer post hoc tests (alpha = .05). RESULTS The bond strength of group B specimens was statistically higher than those of group A and group C specimens (P < .05). The authors found no statistically significant differences in shear bond strength between surfaces treated with Er,Cr:YSGG laser and those treated with acid etching alone (P > .05). CONCLUSION Pretreatment of enamel surfaces with air abrasion increased the bond strength of fissure sealant, but pretreatment with Er,Cr:YSGG laser did not increase the effectiveness of conventional acid etching of enamel in sealant bonds.
Sensitive Screening Tests for Suspected Class A Carbapenemase Production in Species of Enterobacteriaceae

ABSTRACT The detection of class A serine-carbapenemases among species of Enterobacteriaceae remains a challenging issue. Methods of identification for routine use in clinical microbiology laboratories have not been standardized to date. We developed a novel screening methodology suitable for countries with high basal levels of carbapenem resistance due to non-carbapenemase-mediated mechanisms and standardized several simple confirmatory methods that allow the recognition of bacteria producing class A carbapenemases, including KPC, Sme, IMI, NMC-A, and GES, by using boronic acid (BA) derivatives. A total of 28 genetically unrelated Enterobacteriaceae strains producing several class A carbapenemases were tested. Thirty-eight genetically unrelated negative controls were included. The isolates were tested against imipenem (IPM), meropenem (MEM), and ertapenem (ETP) by MIC and disk diffusion assays in order to select appropriate tools to screen for suspected carbapenemase production. It was possible to differentiate class A carbapenemase-producing bacteria from non-carbapenemase-producing bacteria by using solely the routine IPM susceptibility tests. The modified Hodge test was evaluated and found to be highly sensitive, although false-positive results were documented. Novel BA-based methods (a double-disk synergy test and combined-disk and MIC tests) using IPM, MEM, and ETP, in combination with 3-aminophenylboronic acid as an inhibitor, were designed as confirmatory tools. On the basis of the performance of these methods, a sensitive flow chart for suspicion and confirmation of class A carbapenemase production in species of Enterobacteriaceae was designed. By using this methodology, isolates producing KPC, GES, Sme, IMI, and NMC-A carbapenemases were successfully distinguished from those producing other classes of β-lactamases (extended-spectrum β-lactamases, AmpCs, and metallo-β-lactamases, etc). These methods will rapidly provide useful information needed for targeting antimicrobial therapy and appropriate infection control.
A K-band compact fully integrated transformer power amplifier in 0.18-μm CMOS

A K-band, 24 GHz, fully integrated transformer power amplifier (PA) is designed and fabricated in the standard 0.18-μm deep N-well (DNW) CMOS technology. This power amplifier is a 2-stage design using cascode RF NMOS configuration. The on-chip transformers are adopted for the power combining and impedance transformation for the matching network with a small size. The measurement results of this PA are linear gain of 15 dB, OP1dB of 18 dBm and PSAT of 23.5 dBm with power added efficiency (PAE) of 12%. Due to the small size of transformer, the size of the chip is only 0.86 × 0.56 mm2. To the author's knowledge, this PA not only demonstrates the highest output power among the CMOS PA in a 0.18-μm CMOS process, but also achieves the highest ratio of output power to chip size among the all reported K-band CMOS PAs.
Heart Rate Variability: New Perspectives on Physiological Mechanisms, Assessment of Self-regulatory Capacity, and Health risk

Heart rate variability, the change in the time intervals between adjacent heartbeats, is an emergent property of interdependent regulatory systems that operates on different time scales to adapt to environmental and psychological challenges. This article briefly reviews neural regulation of the heart and offers some new perspectives on mechanisms underlying the very low frequency rhythm of heart rate variability. Interpretation of heart rate variability rhythms in the context of health risk and physiological and psychological self-regulatory capacity assessment is discussed. The cardiovascular regulatory centers in the spinal cord and medulla integrate inputs from higher brain centers with afferent cardiovascular system inputs to adjust heart rate and blood pressure via sympathetic and parasympathetic efferent pathways. We also discuss the intrinsic cardiac nervous system and the heart-brain connection pathways, through which afferent information can influence activity in the subcortical, frontocortical, and motor cortex areas. In addition, the use of realtime HRV feedback to increase self-regulatory capacity is reviewed. We conclude that the heart's rhythms are characterized by both complexity and stability over longer time scales that reflect both physiological and psychological functional status of these internal self-regulatory systems.
Visual analytics tools for analysis of movement data

With widespread availability of low cost GPS devices, it is becoming possible to record data about the movement of people and objects at a large scale. While these data hide important knowledge for the optimization of location and mobility oriented infrastructures and services, by themselves they lack the necessary semantic embedding which would make fully automatic algorithmic analysis possible. At the same time, making the semantic link is easy for humans who however cannot deal well with massive amounts of data. In this paper, we argue that by using the right visual analytics tools for the analysis of massive collections of movement data, it is possible to effectively support human analysts in understanding movement behaviors and mobility patterns. We suggest a framework for analysis combining interactive visual displays, which are essential for supporting human perception, cognition, and reasoning, with database operations and computational methods, which are necessary for handling large amounts of data. We demonstrate the synergistic use of these techniques in case studies of two real datasets.
MULTIPRED: a computational system for prediction of promiscuous HLA binding peptides

MULTIPRED is a web-based computational system for the prediction of peptide binding to multiple molecules (proteins) belonging to human leukocyte antigens (HLA) class I A2, A3 and class II DR supertypes. It uses hidden Markov models and artificial neural network methods as predictive engines. A novel data representation method enables MULTIPRED to predict peptides that promiscuously bind multiple HLA alleles within one HLA supertype. Extensive testing was performed for validation of the prediction models. Testing results show that MULTIPRED is both sensitive and specific and it has good predictive ability (area under the receiver operating characteristic curve AROC > 0.80). MULTIPRED can be used for the mapping of promiscuous T-cell epitopes as well as the regions of high concentration of these targets—termed T-cell epitope hotspots. MULTIPRED is available at .
On the origins of Bisimulation, Coinduction, and Fixed Points

The origins of bisimulation and bisimilarity are examined, in the three fields where they have been independently discovered: Computer Science, Philosophical Logic (precisely, Modal Logic), Set Theory. Bisimulation and bisimilarity are coinductive notions, and as such are intimately related to fixed points, in particular greatest fixed points. Therefore also the appearance of coinduction and fixed points are discussed, though in this case only within Computer Science. The paper ends with some historical remarks on the main fixed-point theorems (such as Knaster-Tarski) that underpin the fixed-point theory presented.
Improving power efficiency of D-NUCA caches

D-NUCA caches are cache memories that, thanks to banked organization, broadcast search and promotion/demotion mechanism, are able to tolerate the increasing wire delay effects introduced by technology scaling. As a consequence, they will outperform conventional caches (UCA, Uniform Cache Architectures) in future generation cores. Due to the promotion/demotion mechanism, we have found that, in a D-NUCA cache, the distribution of hits on the ways varies across applications as well as across different execution phases within a single application. In this paper, we show how such a behavior can be utilized to improve D-NUCA power efficiency as well as to decrease its access latencies. In particular, we propose a new D-NUCA structure, called Way Adaptable D-NUCA cache, in which the number of active (i.e. powered-on) ways is dynamically adapted to the need of the running application. Our initial evaluation shows that a consistent reduction of both the average number of active ways (42% in average) and the number of bank access requests (29% in average) is achieved, without significantly affecting the IPC.
Accurate Estimation of Posture and Velocity with Application to Coordinated Motion Control of Twin Hoisting-Girder Transporters

This paper proposed a novel method providing high-update rate vehicle posture and velocity estimation using real-time kinematics global position system (RTK-GPS) and simple in-vehicle speed sensors. The RTK-GPS noise processing techniques are used to discard the noises that do not satisfy the Kalman filter model. Combining the RTK-GPS and speed sensors using extended Kalman filter (EKF) provided a high-update rate estimation that can satisfy the need of the coordinated control of the vehicles fleet. The experimental and practical application results illustrate that the ability of the method meet the accuracy and robustness requirements of the control system.
Efficient connectivity preserving clustering protocol for mobile sensor network

Ensuring connectivity among mobile nodes is significantly important to the success of many critical applications, like military, where the loss of connectivity can lead to the failure of the mission and also proved to be challenging in particular when mobiles nodes have heterogeneous mobility pattern i.e., they are moving in several directions at different speeds. In this paper, we propose a new Heterogonous Mobility Pattern Clustering (HMPC) algorithm in which spatial and temporal densities are used. In our approach, we implement Density Based Spatial Clustering Application Noise (DBSCAN) in which the temporal aspect of a Minimum Period of Connectivity (MPC) is taken into consideration. Border nodes are used to reestablish connectivity among disconnected sub-clusters by increasing the communication range of the best suitable border nodes. Using three different mobility scenarios, simulation results show that the proposed HMPC outperforms two other typical clustering algorithms LEACH and HEED in term of connectivity as it provides better packets delivery ratio and smaller packets loss ratio.
Validation of the Friedewald Equation for Evaluation of Plasma LDL-Cholesterol

In most clinical laboratories, low density lipoprotein (LDL) cholesterol is usually estimated indirectly with the Friedewald equation or directly with the N-geneous assay. We assessed LDL-cholesterol values obtained by both methods to find an appropriate fasting period and to assess the influence of the energy content of the last meal. Blood samples were taken from 28 healthy volunteers who had consumed a standard meal (107 g of carbohydrate, 658 kcal) followed by a fasting period of 12 and 18 h, or a high-energy meal (190 g of carbohydrate, 1011 kcal) with a fasting period of 12 h. Prolongation of the fasting period from 12 h to 18 h decreased glucose level, but did not decrease triacylglycerol, total cholesterol, or high density lipoprotein (HDL) cholesterol. LDL-cholesterol levels measured with the N-geneous assay did not change (94.0 ± 21.5 to 96.3 ± 19.1 mg/dl). LDL-cholesterol levels calculated with the Friedewald equation were also similar after fasting periods of 12 h (98.5 ± 21.4 mg/dl) and 18 h (99.7 ± 20.2 mg/dl). The high-energy meal did not change the level of LDL-cholesterol measured with the N-geneous assay (96.1 ± 21.2 mg/dl), or the glucose, triacylglycerol, total cholesterol, or HDL-cholesterol level, but LDL-cholesterol levels evaluated from the Friedewald equation (92.6 ± 20.3 mg/dl) became significantly lower. A fasting time longer than 12 h is not necessary to obtain reasonable blood lipid levels. The Friedewald equation gave higher LDL-cholesterol levels than N-geneous assay in young Japanese females who had eaten a low-energy meal, and lower values when they had eaten a high-energy meal. Thus, it may be necessary to pay attention to energy of nigh meal prior to blood withdrawal.
Growth of nano-wrinkles on photoresist-derived carbon microelectrode array

A novel fabrication method for integrating nano-wrinkles to carbon microelectromechanical systems (C-MEMS) posts on a silicon substrate is proposed in this paper. In the fabrication of carbon microelectrode array, SU-8, a negative photoresist is patterned by photolithography and subsequently pyrolysed at high temperatures in an oxygen-free environment. In this process, the SU-8 posts are slowly converted to the desired carbon posts with properties resembling those of glassy carbon, and the carbon posts have shrinkage in both vertical and radial directions. As we deposit a thin layer (nanoscale order) of carbon before pyrolysis, nano-wrinkle patterns can be generated with the shrinking of the photoresist due to a large difference in the elastic moduli as well as high compressive stress. The nano-wrinkles generated in carbon films can greatly enlarge specific surface area, which significantly enhances the electrochemical performance compared to the blank posts. Since the carbon nano-wrinkles have the same nature as the carbon posts, the stability and biological compatibility of nano-wrinkles integrated microelectrodes are greatly enhanced.
Grid based PHD filtering by Fast Fourier Transform

We propose an approach to calculate the Probability Hypothesis Density function on a numerical grid by using a method based on the convolution theorem and Fast Fourier transform. This approach provides a representation of the PHD over a discretized domain and, unlike other techniques, does not require Gaussian assumptions on the target and observation model. By using the Fast Fourier Transform it results reasonably competitive in comparison to existing implementations, especially in low dimensional state spaces.
Entrepreneurial Scripts and the New Transaction Commitment Mindset: Extending the Expert Information Processing Theory Approach to Entrepreneurial Cognition Research

In this study, we extend the expert information processing theory approach to entrepreneurial cognition research through an empirical exploration of the new transaction commitment mindset among business people in Canada, Mexico, and the United States. Using analysis of covariance, multivariate analysis of variance, and hierarchical regression analysis of data from a cross–sectional sample of 417 respondents, our results provide a foundation for additional cross–level theory development, with related implications for increasing the practicality of expert information processing theory–based entrepreneurial cognition research. Specifically, this paper: (1) clarifies the nature of the relationship between entrepreneurial expert scripts and constructs that might represent an entrepreneurial mindset at the individual level of analysis; (2) identifies analogous relationships at the economy level of analysis, where the structure found at the individual level informs an economy–level problem; (3) presents a North American Free Trade Agreement–based illustration analysis to demonstrate the extent to which cognitive findings at the individual level can be used to explain economy–level phenomena; and (4) extrapolates from our analysis some of the ways in which script–based comparisons across country or culture can inform the more general task of making information processing–based comparisons among entrepreneurs across other contexts.
In situ observation of kink-band formation in a unidirectional carbon fiber reinforced plastic by X-ray computed tomography imaging

A compression test of a unidirectional carbon fiber reinforced plastic (CFRP) rectangular coupon was performed in an X-ray computed tomography (CT) system. Internal compressive failure of the CFRP was observed under loading. Two-dimensional fiber microbuckling developed non-uniformly in the specimen, and enlarged locally at one side. Fiber failure then initiated at the side edge and propagated through the whole cross section. A two-dimensional kink-band developed as a result of two-dimensional fiber microbuckling. The out-of-plane and in-plane band widths and band angles were almost the same. The coupon specimen twisted slightly owing to the two-dimensional kink-band, which resulted, macroscopically, in a transverse and through-thickness shear failure mode. The scenario of kink-band failure in a unidirectional CFRP coupon was revealed by X-ray CT imaging.
Challenges faced by mental health peer support workers: peer support from the peer supporter's point of view.

OBJECTIVE This study aimed to identify the various challenges encountered by peer support workers in Western Australia in the course of their work and to identify possible solutions to those challenges. METHOD We used the nominal group technique to collect and analyze the data. RESULTS The main challenge encountered by participants was a lack of understanding of the peer support worker role which caused them to experience a sense of exclusion. The main solution focused on strategies to educate consumers, managers, and health professionals about the peer support worker role. CONCLUSION AND IMPLICATIONS FOR PRACTICE Managers have a responsibility to be informed about the peer support worker role and communicate role related information to other team members to ensure that peer support workers are included as part of the health team. Implications for practice therefore center on training for managers and inclusion of the peer support worker role in orientation programs. Further, if these steps are not undertaken, a valuable resource could be lost to a health service to the detriment of persons with a mental illness.