Miracle-dz/UniFAR-FTUs huggingface dataset:
Somatic Mutation Allelic Ratio Test Using ddPCR (SMART-ddPCR): An Accurate Method for Assessment of Preferential Allelic Imbalance in Tumor DNA

The extent to which heritable genetic variants can affect tumor development has yet to be fully elucidated. Tumor selection of single nucleotide polymorphism (SNP) risk alleles, a phenomenon called preferential allelic imbalance (PAI), has been demonstrated in some cancer types. We developed a novel application of digital PCR termed Somatic Mutation Allelic Ratio Test using Droplet Digital PCR (SMART-ddPCR) for accurate assessment of tumor PAI, and have applied this method to test the hypothesis that heritable SNPs associated with childhood acute lymphoblastic leukemia (ALL) may demonstrate tumor PAI. These SNPs are located at CDKN2A (rs3731217) and IKZF1 (rs4132601), genes frequently lost in ALL, and at CEBPE (rs2239633), ARID5B (rs7089424), PIP4K2A (rs10764338), and GATA3 (rs3824662), genes located on chromosomes gained in high-hyperdiploid ALL. We established thresholds of AI using constitutional DNA from SNP heterozygotes, and subsequently measured allelic copy number in tumor DNA from 19–142 heterozygote samples per SNP locus. We did not find significant tumor PAI at these loci, though CDKN2A and IKZF1 SNPs showed a trend towards preferential selection of the risk allele (p = 0.17 and p = 0.23, respectively). Using a genomic copy number control ddPCR assay, we investigated somatic copy number alterations (SCNA) underlying AI at CDKN2A and IKZF1, revealing a complex range of alterations including homozygous and hemizygous deletions and copy-neutral loss of heterozygosity, with varying degrees of clonality. Copy number estimates from ddPCR showed high agreement with those from multiplex ligation-dependent probe amplification (MLPA) assays. We demonstrate that SMART-ddPCR is a highly accurate method for investigation of tumor PAI and for assessment of the somatic alterations underlying AI. Furthermore, analysis of publicly available data from The Cancer Genome Atlas identified 16 recurrent SCNA loci that contain heritable cancer risk SNPs associated with a matching tumor type, and which represent candidate PAI regions warranting further investigation.
Narcissistic Rage and the Murder of Allison Baden-Clay

The trial and the appeals in relation to the killing of Allison Baden-Clay in Queensland in 2012 focused attention upon the role of relevance of motive and thereby intention in what was ultimately found to be the murderous conduct of her husband Gerard Baden-Clay. There are strong grounds for concluding that he had narcissistic personality disorder, a consequence of which can be particular susceptibility to narcissistic injury and thereafter narcissistic rage if the person perceives themselves threatened by attack to their reputation and integrity. This article reviews the extensive clinical literature on narcissism, insofar as it has potential relevance to the commission of crimes of violence and argues that identifying Baden-Clay as having the disorder provides a useful psychological insight into his conduct.
Effects of Gamma Irradiation on Bacterial Microflora Associated with Human Amniotic Membrane

Human amniotic membrane is considered a promising allograft material for the treatment of ocular surface reconstruction, burns, and other skin defects. In order to avoid the transmission of any diseases, grafts should be perfectly sterile. Twenty-five amniotic sacs were collected to determine the microbiological quality of human amniotic membrane, to analyze the radiation sensitivity pattern of the microorganism, and to detect the radiation decimal reduction dose (D10) values. All the samples were found to be contaminated, and the bioburden was ranged from 3.4 × 102 to 1.2 × 105 cfu/g. Initially, a total fifty bacterial isolates were characterized according to their cultural, morphological, and biochemical characteristics and then tested for the radiation sensitivity in an incremental series of radiation doses from 1 to 10 KGy. The results depict gradual decline in bioburden with incline of radiation doses. Staphylococcus spp. were the most frequently isolated bacterial contaminant in tissue samples (44%). The D10 values of the bacterial isolates were ranged from 0.6 to 1.27 KGy. Streptococcus spp. were found to be the highest radioresistant strain with the radiation sterilization dose (RSD) of 11.4 KGy for a bioburden level of 1000. To compare the differences, D10 values were also calculated by graphical evaluations of the data with two of the representative isolates of each bacterial species which showed no significant variations. Findings of this study indicate that lower radiation dose is quite satisfactory for the sterilization of amniotic membrane grafts. Therefore, these findings would be helpful to predict the efficacy of radiation doses for the processing of amniotic membrane for various purposes.
Topology-preserving perceptual segmentation using the Combinatorial Pyramid

Scene understanding and other high-level visual tasks usually rely on segmenting the captured images for dealing with a more efficient mid-level representation. Although this segmentation stage will consider topological constraints for the set of obtained regions (e.g., their internal connectivity), it is typical that the importance of preserving the topological relationships among regions will be not taken into account. Contrary to other similar approaches, this paper presents a bottom-up approach for perceptual segmentation of natural images which preserves the topology of the image. The segmentation algorithm consists of two consecutive stages: firstly, the input image is partitioned into a set of blobs of uniform colour (pre-segmentation stage) and then, using a more complex distance which integrates edge and region descriptors, these blobs are hierarchically merged (perceptual grouping). Both stages are addressed using the Combinatorial Pyramid, a hierarchical structure which can correctly encode relationships among image regions at upper levels. The performance of the proposed approach has been initially evaluated with respect to groundtruth segmentation data using the Berkeley Segmentation Dataset and Benchmark. Although additional descriptors must be added to deal with small regions and textured surfaces, experimental results reveal that the proposed perceptual grouping provides satisfactory scores. Keyworks topology-preserving image segmentation, perceptual grouping, irregular pyramids, combinatorial pyramids.
Study on the Key Techniques of Emergency Logistics System Based on GIS

This paper illustrates applications of GIS in the phases of Preparation and Response, proposes methods to design the emergency logistics GIS system and discusses the main problems during system design and the key technologies to solve these problems - the techniques of correlating space data with attribute data as well as the MapX technique based on module, so as to provide new ways for further systematic realization.
Adaptive working window for impulse noise reduction

We propose an effective method to choose an adaptive working window for impulse noise reduction. Every pixel has the pixel-correlation between itself and its neighbor pixels in an image. Based on the pixel-correlation, we define a formula to gather the statistics for impulse noise intensity estimation. Because the image corrupted by impulse noise would degrade the pixel-correlation, a simple rule is introduced for different median-based filters which are developed with adaptive working window to reduce impulse noise. The reported multi-state median (MSM) filter and switching median (SM) filter are simulated with the simple rule. The experimental results show that our method would improve the reliability of MSM filter and SM filter for impulse noise reduction.
The eye of the beholder: designing the OWL

Preliminary requirements and possible technological solutions for the next generation of ground-based optical telescopes were laid down at ESO in 1998. Since then, a phase A study has been commissioned, the objective of which is to produce a conceptual design compatible, to the maximum possible extent, with proven technology, and establish realistic plans for detailed design, site selection, construction and operation for a 100-m class optical, diffraction-limited telescope. There was no doubt about how daunting such a challenge would be, but, somewhat surprisingly, it turns out to be firmly confined to adaptive optics concepts and technologies. The telescope itself appears to be feasible within the allocated budget and without reliance on exotic assumptions. Fabrication of key subsystems is fully within the reach of a properly engineered, industrialized process. A consolidated baseline is taking shape, and alternative system and subsystem solutions are being explored, strengthening the confidence that requirements could be met. Extensive development of wavefront measurement techniques enlarges the palette of solutions available for active wavefront control of a segmented, active telescope. At system level, ESO is developing enabling experiments to validate multi-conjugate adaptive optics (MAD for Multi-conjugate Adaptive optics Demonstrator) and telescope wavefront control (APE, for Active Phasing Experiment).
Reducing the Calibration Effort for Probabilistic Indoor Location Estimation

WLAN location estimation based on 802.11 signal strength is becoming increasingly prevalent in today's pervasive computing applications. Among the well-established location determination approaches, probabilistic techniques show good performance and, thus, become increasingly popular. For these techniques to achieve a high level of accuracy, however, a large number of training samples are usually required for calibration, which incurs a great amount of offline manual effort. In this paper, we aim to solve the problem by reducing both the sampling time and the number of locations sampled in constructing a radio map. We propose a novel learning algorithm that builds location-estimation systems based on a small fraction of the calibration data that traditional techniques require and a collection of user traces that can be cheaply obtained. When the number of sampled locations is reduced, an interpolation method is developed to effectively patch a radio map. Extensive experiments show that our proposed methods are effective in reducing the calibration effort. In particular, unlabeled user traces can be used to compensate for the effects of reducing the calibration effort and can even improve the system performance. Consequently, manual effort can be reduced substantially while a high level of accuracy is still achieved
SMOOTHNESS OF CARRYING SIMPLICES FOR THREE-DIMENSIONAL COMPETITIVE SYSTEMS : A COUNTEREXAMPLE

For a dissipative totally competitive system of ODEs ẋ = xf (x), ∂f /∂x < 0, i, j = 1, 2, 3, on the nonnegative octant K in R for which 0 is a repeller, M. W. Hirsch proved the existence of an invariant unordered Lipschitz surface (the carrying simplex) attracting all points in K \{0}. We give an example (of a Lotka–Volterra type) showing that the carrying simplex need not be of class C. AMS (MOS) subject classification: Primary 34C30.
Crystal structure of a human CD3-ε/δ dimer in complex with a UCHT1 single-chain antibody fragment

The alpha/beta T cell receptor complex transmits signals from MHC/peptide antigens through a set of constitutively associated signaling molecules, including CD3-epsilon/gamma and CD3-epsilon/delta. We report the crystal structure at 1.9-A resolution of a complex between a human CD3-epsilon/delta ectodomain heterodimer and a single-chain fragment of the UCHT1 antibody. CD3-epsilon/delta and CD3-epsilon/gamma share a conserved interface between the Ig-fold ectodomains, with parallel packing of the two G strands. CD3-delta has a more electronegative surface and a more compact Ig fold than CD3-gamma; thus, the two CD3 heterodimers have distinctly different molecular surfaces. The UCHT1 antibody binds near an acidic region of CD3-epsilon opposite the dimer interface, occluding this region from direct interaction with the TCR. This immunodominant epitope may be a uniquely accessible surface in the TCR/CD3 complex, because there is overlap between the binding site of the UCHT1 and OKT3 antibodies. Determination of the CD3-epsilon/delta structure completes the set of TCR/CD3 globular ectodomains and contributes information about exposed CD3 surfaces.
Iris Biometric Security Challenges and Possible Solutions

1053-5888/15©2015IEEE B iometrics were originally developed for identification, such as for criminal investigations. More recently, biometrics have been also utilized for authentication. Most biometric authentication systems today match a user’s biometric reading against a stored reference template generated during enrollment. If the reading and the template are sufficiently close, the authentication is considered successful and the user is authorized to access protected resources. This binary matching approach has major inherent vulnerabilities. An alternative approach to biometric authentication proposes to use fuzzy extractors (also known as biometric cryptosystems), which derive cryptographic keys from noisy sources, such as biometrics. In theory, this approach is much more robust and can enable cryptographic authorization. Unfortunately, for many biometrics that provide high-quality identification, fuzzy extractors provide no security guarantees. Digital Object Identifier 10.1109/MSP.2015. 2439717
The effect of E-service category on consumers' perceived risk

Whether consumers' risk perception differs or not when purchasing different services online? 115 participants were investigated to discover the differences in the lab experiment, and the results indicated that: a) Consumers perceived higher risk in buying professional services than mass services, interactive services, and supporting services online, while the differences among the latter three services were not significant, b) The constructs of risk perception in different E-services differ: consumers perceived performance risk when purchasing mass services; financial risk and psychological risk were perceived in interactive services; when buying the supportive services, financial risk was perceived; financial risk, social risk and psychological risk were perceived in buying professional services online.
Constrained closed loop inverse kinematics

This paper introduces a kinematically constrained closed loop inverse kinematics algorithm for motion control of robots or other articulated rigid body systems. The proposed strategy utilizes gradients of collision and joint limit potential functions to arrive at an appropriate weighting matrix to penalize and dampen motion approaching constraint surfaces. The method is particularly suitable for self collision avoidance of highly articulated systems which may have multiple collision points among several segment pairs. In that respect, the proposed method has a distinct advantage over existing gradient projection based methods which rely on numerically unstable null-space projections when there are multiple intermittent constraints. We also show how this approach can be augmented with a previously reported method based on redirection of constraints along virtual surface manifolds. The hybrid strategy is effective, robust, and does not require parameter tuning. The efficacy of the proposed algorithm is demonstrated for a self collision avoidance problem where the reference motion is obtained from human observations. We show simulation and experimental results on the humanoid robot ASIMO.
An approach to diagnostic radiology dosimetry

In 2003 at the World Congress at Medical Physics in Sydney I heard a talk by František Pernička, late of the International Atomic Energy Agency (IAEA), speaking on an international code of practice for diagnostic radiology (now known as TRS457 [1]). At the time it appeared to me that there was little new or special. Now, over 10 years later, I find I need to review this assumption. From my perspective much has changed in the last decade. The perception of the importance of diagnostic radiology dosimetry has broadened. Its application now crosses speciality boundaries where technology is posing increasing dosimetric challenges with the needs for standardisation and direction ever present. Perhaps a good place to start is with the basis of the dosimetry. Unlike dosimetry in radiation therapy which, according to the cover of TRS398 [2], is based on absorbed dose in water, diagnostic radiology dosimetry is based on air kerma [1, 3]. We should accept this basis, as indeed the National Council of Radiation Protection and measurement (NCRP) has in a recent standard on interventional procedures [4] where the units used in that document follow the ICRU report No 74 [3]. Indeed the use of the letter K replacing the letter D is being seen more commonly, for example, kerma area product (KAP) is beginning to replace the former dose area product (DAP) as seen in the new edition of the UK text from Martin and Sutton [5]. The ICRU nomenclature is indeed a little challenging, with the air kerma-area product notated as PK,A, similarly air kerma-length product notated as PK,L, however this does reinforce an interesting dosimetric principle that is probably not commonly found in radiotherapy. While radiotherapy dosimetry has a number of parameters designed to monitor dose distributions, a primary dosimetric objective is to determine point doses, which can be related to a severity of radiation damage from a tissue reaction effect. There is often little need for an integral dose metric which could be related to a probability of cancer induction. Typically the reverse is true in diagnostic radiology dosimetry, and hence the usefulness of PK,A generally in diagnostic radiology and PK,L which describes the measurement of a pencil ionisation chamber, as used typically in dental or CT dosimetry. The initial ICRU nomenclature for CT dosimetry [3], was the use of the CK family to replace the IEC [6] defined CTDI terminology, however the recent ICRU publication on CT dosimetry [7] sees the return of CTDI usage. At the end of chapter 3 in TRS457 there is found a small equation (3.21) that has had profound effect on my view of D. McLean (&) Canberra Hospital, Canberra 2605, Australia e-mail: donald.mclean@act.gov. au
$L^{2}$-spectral gaps, weak-reversible and very weak-reversible Markov chains

The theory of $L^2$-spectral gaps for reversible Markov chains has been studied by many authors. In this paper we consider positive recurrent general state space Markov chains with stationary transition probabilities. Replacing the assumption of reversibility by a less strong one, we still obtain a simple necessary and sufficient condition for the spectral gap property of the associated Markov operator in terms of isoperimetric constant. Moreover, we define a new sequence of isoperimetric constants which provides a necessary and sufficient condition for the existence of a spectral gap in a very general setting. Finally, these results are used to obtain simple sufficient conditions for the existence of a spectral gap in terms of the first and second order transition probabilities.
A Novel Virus Detected in Papillomas and Carcinomas of the Endangered Western Barred Bandicoot (Perameles bougainville) Exhibits Genomic Features of both the Papillomaviridae and Polyomaviridae

ABSTRACT Conservation efforts to prevent the extinction of the endangered western barred bandicoot (Perameles bougainville) are currently hindered by a progressively debilitating cutaneous and mucocutaneous papillomatosis and carcinomatosis syndrome observed in captive and wild populations. In this study, we detected a novel virus, designated the bandicoot papillomatosis carcinomatosis virus type 1 (BPCV1), in lesional tissue from affected western barred bandicoots using multiply primed rolling-circle amplification and PCR with the cutaneotropic papillomavirus primer pairs FAP59/FAP64 and AR-L1F8/AR-L1R9. Sequencing of the BPCV1 genome revealed a novel prototype virus exhibiting genomic properties of both the Papillomaviridae and the Polyomaviridae. Papillomaviral properties included a large genome size (∼7.3 kb) and the presence of open reading frames (ORFs) encoding canonical L1 and L2 structural proteins. The genomic organization in which structural and nonstructural proteins were encoded on different strands of the double-stranded genome and the presence of ORFs encoding the nonstructural proteins large T and small t antigens were, on the other hand, typical polyomaviral features. BPCV1 may represent the first member of a novel virus family, descended from a common ancestor of the papillomaviruses and polyomaviruses recognized today. Alternatively, it may represent the product of ancient recombination between members of these two virus families. The discovery of this virus could have implications for the current taxonomic classification of Papillomaviridae and Polyomaviridae and can provide further insight into the evolution of these ancient virus families.
Defining Risk Drinking

Many efforts to prevent alcohol-related harm are aimed at reducing risk drinking. This article outlines the many conceptual and methodological challenges to defining risk drinking. It summarizes recent evidence regarding associations of various aspects of alcohol consumption with chronic and acute alcohol-related harms, including mortality, morbidity, injury, and alcohol use disorders, and summarizes the study designs most appropriate to defining risk thresholds for these types of harm. In addition, it presents an international overview of low-risk drinking guidelines from more than 20 countries, illustrating the wide range of interpretations of the scientific evidence related to risk drinking. This article also explores the impact of drink size on defining risk drinking and describes variation in what is considered to be a standard drink across populations. Actual and standard drink sizes differ in the United States, and this discrepancy affects definitions of risk drinking and prevention efforts.
Optimal Double Via Insertion With On-Track Preference

As on-track double vias take less routing resources and have better electrical characteristics, we study in this paper the problem of double via insertion with a preference for on-track double vias (DVI/ON) in a postrouting stage. The primary goal is to insert as many double vias as possible, and maximizing the number of on-track double vias is a secondary objective. We present a zero-one integer linear program-based approach to optimally solve the DVI/ON problem. Moreover, we also discuss a special case of the DVI/ON problem and present a maximum-weighted bipartite matching-based optimal approach. Experimental results indicate that our approaches outperform existing algorithms in terms of solution quality.
Factors Affecting the Effective Implementation ofE-learning in Educational Institutions

E-learning is an essential trend in education for the 21st century. In fact, students need the ability to use knowledge to communicate, collaborate, analyze, create, innovate, and solve problems in order to be successful in a global economy. The implementation of electronic learning (e-learning) systems impact on the educational environments and offer learners great flexibility, encourage risk taking, help students to be active learners and enhance their higher order thinking. This paper reviews the literature as it pertains to factors affecting effective implementation of e-learning for instructors andstudents in educational institutions. It is concluded that e-learning practice needs a good ICT infrastructure and active and collaborative involvement of a number of other people. Access to the technologies and pedagogical issues and institutional support services are important in the successful e-learning practice.