Miracle-dz/UniFAR-FTUs huggingface dataset:
Learning Oncogenic Pathways from Binary Genomic Instability Data

Summary Genomic instability, the propensity of aberrations in chromosomes, plays a critical role in the development of many diseases. High throughput genotyping experiments have been performed to study genomic instability in diseases. The output of such experiments can be summarized as high‐dimensional binary vectors, where each binary variable records aberration status at one marker locus. It is of keen interest to understand how aberrations may interact with each other, as it provides insight into the process of the disease development. In this article, we propose a novel method, LogitNet, to infer such interactions among these aberration events. The method is based on penalized logistic regression with an extension to account for spatial correlation in the genomic instability data. We conduct extensive simulation studies and show that the proposed method performs well in the situations considered. Finally, we illustrate the method using genomic instability data from breast cancer samples.
The relationship between visceral ischemia, proinflammatory cytokines, and organ injury in patients undergoing thoracoabdominal aortic aneurysm repair

ObjectivesPlasma proinflammatory, anti-inflammatory cytokine, and soluble tumor necrosis factor (TNF) receptor concentrations were examined in hospitalized patients after abdominal and thoracoabdominal aortic aneurysm (TAAA) repair, with and without left atrial femoral bypass. Changes in plasma cytokine concentrations were related to the duration of visceral ischemia and the frequency rate of postoperative, single, or multiple system organ dysfunction (MSOD). DesignProspective, observational study. SettingTwo academic referral centers in the United States and The Netherlands. PatientsWe included 16 patients undergoing TAAA repair without left atrial femoral bypass, 12 patients undergoing TAAA repair with left atrial femoral bypass, and nine patients undergoing infrarenal aortic aneurysm repair. Measurements and Main ResultsTimed, arterial blood sampling for proinflammatory and anti-inflammatory cytokine and soluble TNF receptor concentrations (p55 and p75), and prospective assessment of postoperative single and MSOD. Plasma appearance of TNF-&agr;, interleukin (IL)-6, IL-8, and IL-10 peaked 1 to 4 hrs after TAAA repair, and concentrations were significantly elevated compared with infrarenal abdominal aortic aneurysm repair (p < .05). Left atrial femoral bypass significantly reduced the duration of visceral ischemia (p < .05) and the systemic TNF-&agr;, p75, and IL-10 responses (p < .05). Plasma TNF-&agr; concentrations >150 pg/mL were more common in patients with extended visceral ischemia times (>40 mins). Additionally, patients with early peak TNF-&agr; concentrations >150 pg/mL and IL-6 levels >1,000 pg/mL developed MSOD more frequently than patients without these elevated plasma cytokine levels (both p < .05). ConclusionsThoracoabdominal aortic aneurysm repair results in the increased plasma appearance of TNF-&agr;, IL-6, IL-8, IL-10, and shed TNF receptors. The frequency and magnitude of postoperative organ dysfunction after TAAA repair is associated with an increased concentration of the cytokines, TNF-&agr;, and IL-6 and the increased plasma levels of these cytokines appear to require extended visceral ischemia times.
Overview of future directions in high energy-density and high-field science using ultra-intense lasers

The increasing proliferation of 100TW class ultrashort pulse lasers and the near completion of a number of petawatt class lasers world wide is opening many frontiers in laser science. Some of the most exciting frontiers rest in high energydensity science and high field physics. A multi-TW laser can create heated matter with pressure in excess of a Gbar and can create electric fields of ten to one hundred atomic units. In this paper some of the recent advances in high energy density science and high field physics made using high intensity short pulse lasers will be reviewed with illustrative examples from work performed at the University of Texas and Lawrence Livermore National Laboratory. r 2004 Elsevier Ltd. All rights reserved.
A distance protection based on the estimation of system model parameters

Most of the distance relays base their operation on the measured apparent fault impedance. These relays are bound to have an error inflicted by the unknown remote end parameters and fault resistance. This paper presents a method, which diminishes such errors using optimization techniques. The proposed method executes a system model unknown parameter estimation by adjusting model output to measurements from the same substation with the Monte Carlo method in sequence to pre-fault and fault regimes. This allows the elimination of uncertainty, caused by incomplete scope of information, available to classic relays. The proposed method was tested on a three machine system with a fault in one of parallel lines bounded by a mutual inductance and was proved to obtain fault parameters with an acceptable tolerance. The proposed method can be applied in a standalone application or it can provide reliable fault parameter data and improve the distance protection sensitivity.
Sizing up the heart: development redux in disease.

￻￻ Following gastrulation and establishment of the three embryonic germ layers, the first definitive organ to form in the embryo is the heart, whose morphogenesis, growth, and integrated function are essential to embryonic survival, even by midgestation. Abnormalities in heart development result in congenital heart disease, the most frequent form of birth defects in humans. At the opposite end of the temporal spectrum, adult cardiac disease is the most common cause of death in the industrialized world, with congestive heart failure and inadequate pump function the end result of diverse disorders intrinsic to cardiac muscle cells, cardiac valves, systemic blood pressure, and the coronary blood supply. Despite recent therapeutic advances and mechanical devices to sustain cardiac function, only a minority of heart failure patients lives longer than 5yr. Death from heart disease therefore comprises an epidemic more prevalent than all cancers combined (Ries et al. 2003). Recent studies have begun to reveal the cellular circuitry that controls cardiac growth during development and disease. Intriguingly, many of the molecules and mechanisms that regulate growth of the embryonic heart are redeployed in the adult heart in response to stress signals that provoke cardiac enlargement and heart failure. Thus, understanding the mechanisms involved in heart development promises to provide insights into the molecular basis for pathogenesis of the adult heart, as well as to reveal novel therapeutic targets. In this review, we consider three aspects of cardiac development with significant implications for adult heart disease: (1) normal growth during organogenesis, (2) a “fetal” cardiac gene program reactivated in hypertrophy, and (3) restorative growth by undifferentiated progenitor cells that have cardiogenic potential. Each of these aspects of cardiac growth could be, itself, the subject of an in-depth review. Our goal, however, is not to comprehensively review these areas, but to identify common themes in developmental biology that are reiterated in settings of abnormal growth and dysfunction of the adult heart. Although we focus on development and disease of the myocardium, many of the same principles of allometric growth and homeostasis apply to other organs whose structure and function are influenced by physiological and pathological signaling.
Retinol activates tyrosine hydroxylase acutely by increasing the phosphorylation of serine40 and then serine31 in bovine adrenal chromaffin cells

Tyrosine hydroxylase is the rate‐limiting enzyme in the biosynthesis of the catecholamines. It has been reported that retinol (vitamin A) modulates tyrosine hydroxylase activity by increasing its expression through the activation of the nuclear retinoid receptors. In this study, we observed that retinol also leads to an acute activation of tyrosine hydroxylase in bovine adrenal chromaffin cells and this was shown to occur via two distinct non‐genomic mechanisms. In the first mechanism, retinol induced an influx in extracellular calcium, activation of protein kinase C and serine40 phosphorylation, leading to tyrosine hydroxylase activation within 15 min. This effect then declined over time. The retinol‐induced rise in intracellular calcium then led to a second slower mechanism; this involved an increase in reactive oxygen species, activation of extracellular signal‐regulated kinase 1/2 and serine31 phosphorylation and the maintenance of tyrosine hydroxylase activation for up to 2 h. No effects were observed with retinoic acid. These results show that retinol activates tyrosine hydroxylase via two sequential non‐genomic mechanisms, which have not previously been characterized. These mechanisms are likely to operate in vivo to facilitate the stress response, especially when vitamin supplements are taken or when retinol is used as a therapeutic agent.
Advanced Algorithms in Medical Computer Graphics

Advanced algorithms and efficient visualization techniques are of major importance in intra-operative imaging and image-guided surgery. The surgical environment is characterized by a high information flow and fast decisions, requiring efficient and intuitive presentation of complex medical data and precision in the visualization results. Regions or organs that are classified as risk structures are in this context of particular interest. This paper summarizes advanced algorithms for medical visualization with special focus on risk structures such as tumors, vascular systems and white matter fiber tracts. algorithms and techniques employed in intra-operative situations or virtual and mixed reality simulations are discussed. Finally, the prototyping and software development process of medical visualization algorithms is addressed.
Direct animation interfaces: an interaction approach to computer animation

Creativity tools for digital media have been largely democratised, offering a range from beginner to expert tools. Yet computer animation, the art of instilling life into believable characters and fantastic worlds, is still a highly sophisticated process restricted to the spheres of expert users. This is largely due to the methods employed: in keyframe animation dynamics are indirectly specified over abstract descriptions, while performance animation suffers from inflexibility due to a high technological overhead. The reverse trend in human-computer interaction to make interfaces more direct, intuitive, and natural to use has so far hardly touched the animation world: decades of interaction research have scarcely been linked to research and development of animation techniques. The hypothesis of this work is that an interaction approach to computer animation can inform the design and development of novel animation techniques. Three goals are formulated to illustrate the validity of this thesis. Computer animation methods and interfaces must be embedded in an interaction context. The insights this brings for designing next generation animation tools must be examined and formalised. The practical consequences for the development of motion creation and editing tools must be demonstrated with prototypes that are more direct, efficient, easy-to-learn, and flexible to use. The foundation of the procedure is a conceptual framework in the form of a comprehensive discussion of the state of the art, a design space of interfaces for time-based visual media, and a taxonomy for mappings between user and medium space-time. Based on this, an interaction-centred analysis of computer animation culminates in the concept of direct animation interfaces and guidelines for their design. These guidelines are tested in two point designs for direct input devices. The design, implementation and test of a surface-based performance animation tool takes a system approach, addressing interaction design issues as well as challenges in extending current software architectures to support novel forms of animation control. The second, a performance timing technique, shows how concepts from video browsing can be applied to motion editing for more direct and efficient animation timing.
CATEGORY RECOGNITION ON RGB-D DATA

Sensors for RGB-D data have gained high popularity in the computer vision community. We present an efficient ensemble classifier that combines visual and depth data and achieves higher recognition rates than the individual classifiers or a classifier exploiting visual and depth data at the same time. The presented approach was evaluated in practice on a mobile robot during the RoCKIn robotics challenge in 2014.
Effect of heat treatment on the change in color and dimensional stability of acacia hybrid wood

Acacia hybrid (Acacia mangium x auriculiformis), a wood species of low dimensional stability which is used almost exclusively for pulp, paper, or as firewood, was heat treated in nitrogen at 210-230 ºC for 2 to 6 hours. The changes in color and anti-swelling efficiency (ASE) of wood after heat treatment were determined for the different heat treatment conditions. The results show that heat treatment mainly resulted in the darkening of wood tissues, and heat-treated wood had better dimensional stability than those of the control samples. Chemical modifications of wood components were determined by FT-IR analysis. Spectra indicated that the hydroxyl group content was reduced by increased treatment intensity. This result coincides with the increase in dimensional stability of heat-treated wood. Heat treatment of acacia hybrid wood shows an interesting potential to improve the quality and value for solid wood products from plantation-grown wood species.
Adaptive Arrays and Diversity Antenna Configurations for Handheld Wireless Communication Terminals

This dissertation reports results of an investigation into the performance of adaptive beamforming and diversity combining using antenna arrays that can be mounted on handheld radios. Handheld arrays show great promise for improving the coverage, capacity, and power efficiency of wireless communication systems. Diversity experiments using a handheld antenna array testbed (HAAT) are reported here. These experiments indicate that signals received by the antennas in two-element handheld antenna arrays with spacing of 0.15 wavelength or greater can be combined to provide 7-9 dB diversity gain against fading at the 99% reliability level in non line-of-sight multipath channels. Thus, peer-to-peer systems of handheld transceivers that use antenna arrays can achieve reliability comparable to systems of single-antenna handheld units, with only one-fifth the transmitter power, resulting in lower overall power consumption and increased battery life. Similar gains were observed for spatial, polarization, and pattern diversity. Adaptive beamforming with single- and multi-polarized four-element arrays of closely spaced elements was investigated by experiment using the HAAT, and by computer simulation using a polarization-sensitive vector multipath propagation simulator developed for this purpose. Small and handheld adaptive arrays were shown to provide 25 to 40 dB or more of interference rejection in the presence of a single interferer in rural, suburban, and urban channels including line-of-sight and non line-of-sight cases. In multipath channels, these performance levels were achieved even when there was no separation between the transmitters in azimuth angle as seen from the receiver, and no difference in the orientations of the two transmitting antennas. This interference rejection capability potentially allows two separate spatial channels to coexist in the same time/frequency channel, doubling system capacity.
Nucleotide sequence of the Escherichia coli regulatory gene mprA and construction and characterization of mprA-deficient mutants

In high copy number, the Escherichia coli mprA gene reduces the synthesis of peptide microcins B17 and C7 (MccB17 and MccC7) and blocks the osmoinduction of the proU operon at the transcriptional level. mprA has been sequenced and shown to encode a polypeptide of 176 amino acids (Mr, 20,563). Insertion and deletion mutant mprA alleles were constructed and then transferred to the chromosome by allelic replacement. In these mutants, expression of two mcb-lacZ fusions was fivefold derepressed, indicating a negative regulatory role of mprA on the mcb operon (MccB17). In contrast, no effect of the MprA- mutations on the expression of mcc operon (MccC7) or on the osmoinduction of proU operon was observed.
A Design and Evaluation of a Secure Neighborhood Awareness Framework for Vehicular Ad-Hoc Networks

Vehicular ad-hoc networks (VANETs) are envisioned to provide many road and safety applications that will improve drivers’ awareness and enhance the driving experience. Many of proposed applications are location-based that depend on sharing the location information of vehicles and events among neighboring nodes. The location-based applications should provide vehicle operators with knowledge of the current surrounding conditions to help them make appropriate traveling decisions, such as avoiding traffic congestion. Drivers expect to receive accurate and reliable information from other vehicles. Therefore, securing localization service integrity is important to support a VANET’s overall system reliability. In this thesis, we study the exchanged location information in VANETs and designed a framework to prevent potential security threats that will violate users’ privacy and overcome limitations that can impact the exchanged data integrity and reliability. The solution developed a secure neighborhood awareness service and shared localization information management protocol in a VANET. The proposed framework is constructed through several components: (i) a location verification protocol that will secure location information by providing a non-line-of-sight (NLOS) verification protocol to overcome moving obstacle effects; (ii) privacy-preserving location information management to detect data inconsistency and provide a recovery process while preventing attackers from tracking individual vehicles; (iii) a trust model evaluation mechanism based on neighborhood awareness; (iv) an adaptive beacon protocol that will reduce the number of messages and provide quality of service(QoS) control for network managers and authorities. We also propose a security evaluation model that quantifies the security attributes for the localization service in a VANET. The model will help evaluate an integrated security measures that are provided by different components of the network services.
On the Design of Multi-Dimensional Irregular Repeat-Accumulate Lattice Codes

Most multi-dimensional (more than two dimensions) lattice partitions only form additive quotient groups and lack multiplication operations. This prevents us from constructing lattice codes based on multi-dimensional lattice partitions directly from non-binary linear codes over finite fields. In this paper, we design lattice codes from Construction A lattices where the underlying linear codes are non-binary irregular repeat-accumulate (IRA) codes. Most importantly, our codes are based on multi-dimensional lattice partitions with finite constellations. We propose a novel encoding structure that adds randomly generated lattice sequences to the encoder’s messages, instead of multiplying lattice sequences to the encoder’s messages. We prove that our approach can ensure that the decoder’s messages exhibit permutation-invariance and symmetry properties. With these two properties, the densities of the messages in the iterative decoder can be modeled by Gaussian distributions described by a single parameter. With Gaussian approximation, extrinsic information transfer charts for our multi-dimensional IRA lattice codes are developed and used for analyzing the convergence behavior and optimizing the decoding thresholds. Simulation results show that our codes can approach the unrestricted Shannon limit within 0.46 dB and outperform the previously designed lattice codes with 2-D lattice partitions and existing lattice coding schemes for large codeword length.
Service system and cognitive outcomes for young children with autism spectrum disorders in a rural area of Taiwan

Chiayi is a rural county located in southwestern Taiwan, and the effectiveness of its early intervention service system for autism spectrum disorders was studied in detail. A total of 71 children with autism spectrum disorders (n = 35) and developmental delay (n = 36) aged 2.5 years were referred from the only Early Intervention Reporting and Referral Center in Chiayi and followed up at 4 years. Results showed relatively low and varied services of early intervention for both groups during two time-point periods and a relative lack of specific early intervention programs for children with autism spectrum disorders. It was found, however, that cognitive abilities were increased for autism spectrum disorders and developmental delay groups. Additionally, the Early Learning Score at the initial evaluation could contribute to the high learner autism spectrum disorders subgroup. Parental socio-economic level was also determined to benefit the high learner developmental delay subgroup.
Self‐organization of rat cardiac cells into contractile 3‐D cardiac tissue

The mammalian heart is not known to regenerate following injury. Therefore, there is great interest in developing viable tissue‐based models for cardiac assist. Recent years have brought numerous advances in the development of scaffold‐based models of cardiac tissue, but a self‐organizing model has yet to be described. Here, we report the development of an in vitro cardiac tissue without scaffolding materials in the contractile region. Using an optimal concentration of the adhesion molecule laminin, a confluent layer of neonatal rat cardiomyogenic cells can be induced to self‐organize into a cylindrical construct, resembling a papillary muscle, which we have termed a cardioid. Like endogenous heart tissue, cardioids contract spontaneously and can be electrically paced between 1 and 5 Hz indefinitely without fatigue. These engineered cardiac tissues also show an increased rate of spontaneous contraction (chronotropy), increased rate of relaxation (lusitropy), and increased force production (inotropy) in response to epinephrine. Cardioids have a developmental protein phenotype that expresses both α‐ and β‐tropomyosin, very low levels of SERCA2a, and very little of the mature isoform of cardiac troponin T.
Neural Machine Translation with Source Dependency Representation

Source dependency information has been successfully introduced into statistical machine translation. However, there are only a few preliminary attempts for Neural Machine Translation (NMT), such as concatenating representations of source word and its dependency label together. In this paper, we propose a novel NMT with source dependency representation to improve translation performance of NMT, especially long sentences. Empirical results on NIST Chinese-to-English translation task show that our method achieves 1.6 BLEU improvements on average over a strong NMT system.