Miracle-dz/UniFAR-FTUs huggingface dataset:
DAIRRy-BLUP: A High-Performance Computing Approach to Genomic Prediction

In genomic prediction, common analysis methods rely on a linear mixed-model framework to estimate SNP marker effects and breeding values of animals or plants. Ridge regression–best linear unbiased prediction (RR-BLUP) is based on the assumptions that SNP marker effects are normally distributed, are uncorrelated, and have equal variances. We propose DAIRRy-BLUP, a parallel, Distributed-memory RR-BLUP implementation, based on single-trait observations (y), that uses the Average Information algorithm for restricted maximum-likelihood estimation of the variance components. The goal of DAIRRy-BLUP is to enable the analysis of large-scale data sets to provide more accurate estimates of marker effects and breeding values. A distributed-memory framework is required since the dimensionality of the problem, determined by the number of SNP markers, can become too large to be analyzed by a single computing node. Initial results show that DAIRRy-BLUP enables the analysis of very large-scale data sets (up to 1,000,000 individuals and 360,000 SNPs) and indicate that increasing the number of phenotypic and genotypic records has a more significant effect on the prediction accuracy than increasing the density of SNP arrays.
The International Trade Network: weighted network analysis and modelling

Tools of the theory of critical phenomena, namely the scaling analysis and universality, are argued to be applicable to large complex web-like network structures. Using a detailed analysis of the real data of the International Trade Network we argue that the scaled link weight distribution has an approximate log-normal distribution which remains robust over a period of 53 years. Another universal feature is observed in the power-law growth of the trade strength with gross domestic product, the exponent being similar for all countries. Using the ‘rich-club’ coefficient measure of the weighted networks it has been shown that the size of the rich-club controlling half of the world’s trade is actually shrinking. While the gravity law is known to describe well the social interactions in the static networks of population migration, international trade, etc, here for the first time we studied a non-conservative dynamical model based on the gravity law which excellently reproduced many empirical features of the ITN.
Analysis of thresholds for braided block codes in BEC

Low-density parity-check (LDPC) codes, invented by Gallager [2], who described and analyzed a block variant of the codes, arouse great interest of researchers. These codes are widely used in practice since they can be decoded by using relatively simple iterative decoding algorithms. Several modifications of these codes are known, in particular, generalized LDPC codes [3]. In contrast to Gallager’s LDPC codes, using single parity-check codes as component codes, the generalized LDPC codes use as component codes arbitrary block codes. The convolutional version of Gallager’s codes, called convolutional LDPC codes, was described in [4]. These codes have better decoding reliability performance then the related LDPC block codes. Particularly, if the density of the parity-check matrices of convolutional LDPC codes increases, then their threshold (see below) tends to the Shannon limit [5], [6]. Braided block codes [1] and braided convolutional codes [7] can be considered as special constructions of generalized LDPC convolutional codes.
Jacobs Journal of Radiation Oncology Radiotherapy and Rosai-Dorfman Disease

Rosai–Dorfman disease (RDD) also known as histiocytosis with lymphadenopathy is uncommon, often self-limiting benign, not– Langerhans-cell histiocytic proliferative disorder. It usually affects young adults and children, with no predilection for sex. More than 80% of patients present with painless cervical lymphadenopathy, with or without fever. Other presentation sites include upper aero-digestive tract, orbits, and the paranasal sinuses. Extra nodal involvement can occur from 20% to more than 40% of cases, and common sites of involvement include the skin, upper airway, soft tissue, bones kidney, lower respiratory tract, liver, orbit and central nervous system.
MemGuard: A low cost and energy efficient design to support and enhance memory system reliability

Memory system reliability is increasingly a concern as memory cell density and capacity continue to grow. The conventional approach is to use redundant memory bits for error detection and correction, with significant storage, cost and power overheads. In this paper, we propose a novel, system-level scheme called MemGuard for memory error detection. With OS-based checkpointing, it is also able to recover program execution from memory errors. The memory error detection of MemGuard is motivated by memory integrity verification using log hashes. It is much stronger than SECDED in error detection, incurs negligible hardware cost and energy overhead and no storage overhead, and is compatible with various memory organizations. It may play the role of ECC memory in consumer-level computers and mobile devices, without the shortcomings of ECC memory. In server computers, it may complement SECDED ECC or Chipkill Correct by providing even stronger error detection. We have comprehensively investigated and evaluated the feasibility and reliability of MemGuard. We show that using an incremental multiset hash function and a non-cryptographic hash function, the performance and energy overheads of Mem-Guard are negligible. We use the mathematical deduction and synthetic simulation to prove that MemGuard is robust and reliable.
XMM-Newton Detection of the Supernova Remnant G337.2+0.1

We report the first XMM-Newton detection of the SNR candidate G337.2+0.1 (=AX J1635.9-4719). The object shows centrally filled and diffuse X-ray emission. The emission peaks in the hard 3.0-10.0 keV band. A spatially resolved spectral study confirms that the column density of the central part of the SNR is about NH ~ 5.9(±1.5) × 1022 cm-2 and its X-ray spectrum is well represented by a single power law with a photon index Γ = 0.96 ± 0.56. The nondetection of line emission in the central spectrum is consistent with synchrotron radiation from a population of relativistic electrons. Detailed spectral analysis indicates that the outer region is highly absorbed and quite softer than the inner region, with NH ~ 16.2(±5.2) × 1022 cm-2 and kT = 4.4(±2.8) keV. Such characteristics are already observed in other X-ray plerions. On the basis of the morphological and spectral X-ray information, we confirm the SNR nature of G337.2+0.1 and suggest that the central region of the source is a pulsar wind nebula, originated by an energetic although yet undetected pulsar, that is currently losing energy at a rate of ~1036 ergs s-1.
Low-ω3 Fatty Acid and Soy Protein Attenuate Alcohol-Induced Fatty Liver and Injury by Regulating the Opposing Lipid Oxidation and Lipogenic Signaling Pathways

Chronic ethanol-induced downregulation of peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC1α) and upregulation of peroxisome proliferator-activated receptor gamma coactivator 1-beta (PGC1β) affect hepatic lipid oxidation and lipogenesis, respectively, leading to fatty liver injury. Low-ω3 fatty acid (Low-ω3FA) that primarily regulates PGC1α and soy protein (SP) that seems to have its major regulatory effect on PGC1β were evaluated for their protective effects against ethanol-induced hepatosteatosis in rats fed with Lieber-deCarli control or ethanol liquid diets with high or low ω3FA fish oil and soy protein. Low-ω3FA and SP opposed the actions of chronic ethanol by reducing serum and liver lipids with concomitant decreased fatty liver. They also prevented the downregulation of hepatic Sirtuin 1 (SIRT1) and PGC1α and their target fatty acid oxidation pathway genes and attenuated the upregulation of hepatic PGC1β and sterol regulatory element-binding protein 1c (SREBP1c) and their target lipogenic pathway genes via the phosphorylation of 5′ adenosine monophosphate-activated protein kinase (AMPK). Thus, these two novel modulators attenuate ethanol-induced hepatosteatosis and consequent liver injury potentially by regulating the two opposing lipid oxidation and lipogenic pathways.
A Volumetric Approach to Predictive Rendering of Fabrics

Efficient physically accurate modeling and rendering of woven cloth at a yarn level is an inherently complicated task due to the underlying geometrical and optical complexity. In this paper, a novel and general approach to physically accurate cloth rendering is presented. By using a statistical volumetric model approximating the distribution of yarn fibers, a prohibitively costly explicit geometrical representation is avoided. As a result, accurate rendering of even large pieces of fabrics containing orders of magnitudes more fibers becomes practical without sacrifying much generality compared to fiber‐based techniques. By employing the concept of local visibility and introducing the effective fiber density, limitations of existing volumetric approaches regarding self‐shadowing and fiber density estimation are greatly reduced.
Autonomic responses to cold face stimulation in sickle cell disease: a time-varying model analysis

Sickle cell disease (SCD) is characterized by sudden onset of painful vaso‐occlusive crises (VOC), which occur on top of the underlying chronic blood disorder. The mechanisms that trigger VOC remain elusive, but recent work suggests that autonomic dysfunction may be an important predisposing factor. Heart‐rate variability has been employed in previous studies, but the derived indices have provided only limited univariate information about autonomic cardiovascular control in SCD. To circumvent this limitation, a time‐varying modeling approach was applied to investigate the functional mechanisms relating blood pressure (BP) and respiration to heart rate and peripheral vascular resistance in healthy controls, untreated SCD subjects and SCD subjects undergoing chronic transfusion therapy. Measurements of respiration, heart rate, continuous noninvasive BP and peripheral vascular resistance were made before, during and after the application of cold face stimulation (CFS), which perturbs both the parasympathetic and sympathetic nervous systems. Cardiac baroreflex sensitivity estimated from the model was found to be impaired in nontransfused SCD subjects, but partially restored in SCD subjects undergoing transfusion therapy. Respiratory‐cardiac coupling gain was decreased in SCD and remained unchanged by chronic transfusion. These results are consistent with autonomic dysfunction in the form of impaired parasympathetic control and sympathetic overactivity. As well, CFS led to a significant reduction in vascular resistance baroreflex sensitivity in the nontransfused SCD subjects but not in the other groups. This blunting of the baroreflex control of peripheral vascular resistance during elevated sympathetic drive could be a potential factor contributing to the triggering of VOC in SCD.
Extraction and Compilation of Events and Sub-events from Twitter

Twitter has emerged as a great source to provide insights about upcoming planned and unplanned events of social, economic and political relevance. Big events are publicized and known in advance, but smaller, unplanned sub-events around them are not always advertised. These unplanned events may have a large localized impact. If known in advance, knowledge about events like threats, protests, demonstrations etc. or even about large flash mobs can be utilized by planners and event managers. Given the large volumes of tweets floating around at any given time, identifying relevant sub-events is a non-trivial task. In this paper, we explore machine learning techniques to identify, extract and build a map of small sub-events around a big, popular event. We use CRFs to extract event components from tweets. Events are resolved for uniqueness and compiled into a complete calendar. The model is evaluated on tweets around Olympic Games. The framework is generic enough to be adapted to other domains.
Metric Operator in Pseudo-Hermitian Quantum Mechanics and the Imaginary Cubic Potential

We present a systematic perturbative construction of the most general metric operator (and positive-definite inner product) for quasi-Hermitian Hamiltonians of the standard form, H = 1 2 p 2 + v(x), in one dimension. We show that this problem is equivalent to solving an infinite system of iteratively decoupled hyperbolic partial differential equations in (1 + 1)-dimensions. For the case that v(x} is purely imaginary, the latter have the form of a nonhomogeneous wave equation which admits an exact solution. We apply our general method to obtain the most general metric operator for the imaginary cubic potential, v(x) = i∈x 3 . This reveals an infinite class of previously unknown CPT- as well as non-CPT-inner products. We compute the physical observables of the corresponding unitary quantum system and determine the underlying classical system. Our results for the imaginary cubic potential show that, unlike the quantum system, the corresponding classical system is not sensitive to the choice of the metric operator. As another application of our method we give a complete characterization of the pseudo-Hermitian canonical quantization of a free particle moving in R that is consistent with the usual choice for the quantum Hamiltonian. Finally, we discuss subtleties involved with higher dimensions and systems having a fixed length scale.
WB4SP: A tool to build the word base for specific programs

Software becomes increasingly complex with its continuous maintenance activities. Given a system under maintenance, developers used to employing code search techniques to locate the code of their interests. However, they may have difficulties in understanding the source code elements and the relationship among them in the searching results. If there is a word base for a specific system, the developers can refer it to help locate and recover the source code elements and their relationships, which can improve the maintenance efficiency. In this paper, we present a tool, WB4SP(Word Base for Specific Programs), which focuses on building the word base for a specific system. WB4SP can retrieve the words, recover the relationship between them, and display the evolution of these words during the software evolution.
Cognitive maps assess news viewer ethical sensitivity

~Et h i c a l sensitivity is investigated in an illustrative analysis of two female television nezos viewers. Transcripts of structured, in-depth interviews were analyzed according to four critical content dimensions of ethical sensitivity reflecting interviewees' mentions of story characteristics, ethical issues, consequences, and stakeholders. Cognitive maps illustrate the reasoning processes ofthe two viewers, one with relatively high and the other with relatively low ethical sensitivity. This study provides a detailed description of a new application of a research procedure, and gives detailed examples of how subdimensions of ethical sensitivity interact and relate to a person's reasoning processes. The study is a pilot demonstration of a promising methodology and a precursor to more investigations on more viewers, more types of content, and more media.
Adolescents' perceptions of national identification and socialization: A grounded analysis

This paper examines the perceived influence of parents and family and the construction of national and religious identification amongst adolescents theoretically sampled from along the border between the Irish Republic and the Northern Ireland. Two hundred and sixty-one young people wrote essays on the meaning of their national identity and the influence of parents, families and the border on national and religious identities. Lengthy and detailed responses were subjected to a grounded analysis. Results revealed the complexity of young people's identification processes and their opinions and experiences of religious and national socialization. The majority of respondents attached a great deal of significance to their national identity. Identity was represented across a range of meanings including sport, government policy, culture, folklore and characteristics thought typical of a given nationality. Diversity was valued though national and religious categories were defined exclusively. Parents and family were viewed as important sources of socialization and the intergenerational transmission of identity was viewed as natural and inevitable. There was a widespread belief that national and religious identity overlapped and though many asserted that religion could promote tolerance and inclusion there was an implicit acceptance that it could also fuel intergroup hostilities.
Bureaucratic Morality in the United Kingdom

A model of bureaucratic morality is developed in which a hierarchy of four levels of expectation is associated with a hierarchy of control systems. The four levels of expectation are: bureaucratic discipline (time-keeping, following instructions, etc.); bureaucratic trust (probity, rectitude, care for the public purse); bureaucratic fairness (impartiality, doing right); and bureaucratic professional honour (loyalty, commitment). The four systems of control are: supervision within the bureaucracy; monitoring by other bureaucracies; check by extra-bureaucratic mechan isms ; and élite socialization. Recent cases and current anxieties in the United Kingdom are described under each head.
Identification of the anticancer effects of a novel proteasome inhibitor, ixazomib, on colorectal cancer using a combined method of microarray and bioinformatics analysis

Purpose The study aimed to explore the anticancer effects of a novel proteasome inhibitor, ixazomib, on colorectal cancer (CRC) using a combined method of microarray and bioinformatics analysis. Materials and methods Cell proliferation was tested by Cell Counting Kit-8 (CCK-8) assay for SW620 cells treated with different concentrations of ixazomib and different treatment times. The microarray analysis was conducted for six samples, including three samples of SW620 cells untreated with ixazomib and three samples of SW620 cells treated with ixazomib. The differentially expressed genes (DEGs) between untreated and treated samples were identified by the Linear Models for Microarray data (LIMMA) package in R language. The Gene Ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed for the DEGs using the Database for Annotation, Visualization and Integrated Discovery (DAVID) and KEGG Orthology-Based Annotation System (KOBAS) online tool. The protein–protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, and module analysis was performed for the PPI network. Results Ixazomib could inhibit the proliferation of SW620 cells in a dose-dependent and time-dependent manner. A total of 743 DEGs, including 203 upregulated DEGs such as HSPA6 and 540 downregulated DEGs such as APCDD1, were identified. Eighty-three GO terms were enriched for DEGs, which were mainly related to protein folding, apoptotic process, transcription factor activity, and proteasome. Thirty-seven KEGG pathways were perturbed, including pathway of apoptosis and cell cycle. Forty-six hub genes, such as TP53, JUN, and ITGA2, were screened out, and three modules with important functions were mined from the PPI network. Conclusion The novel proteasome inhibitor ixazomib significantly inhibited the proliferation of human CRC SW620 cells. It exerted anticancer effects through targeting the expression of DEGs, such as HSPA6, APCDD1, TP53, and JUN, and affecting the signaling pathways including apoptosis and cell cycle pathway, which demonstrated the promising potential of ixazomib for CRC therapy.
Towards a vehicular cloud - using parked vehicles as a temporary network and storage infrastructure

We investigate the potentials of a vehicular cloud based on parked vehicles as a spatio-temporal network and storage infrastructure. Vehicular networking solutions have been investigated for more than a decade but recent standardization efforts just enable a broad use of this technology to build large scale Intelligent Transportation Systems (ITS). One of the key questions is whether some pre-deployed infrastructure is needed to enable and to boost vehicular networks. We see many benefits in such infrastructure to store information and to provide connectivity among the vehicles. Yet, instead of using Roadside Units (RSUs), we envision to rely on parked vehicles to provide such vehicular cloud services. In this paper, we demonstrate the feasibility of this idea using the Virtual Cord Protocol (VCP) protocol to enable dynamic cloud services. Our simulation results indicate that this concept is sound and scales even with a highly dynamic number of parkers on the streets.
A capacitive-coupling technique with phase noise and phase error reduction for multi-phase clock generation

This paper presents a capacitive-coupling technique for multi-phase oscillators. The proposed capacitive coupling techniques can improve the phase noise performance while maintain good phase accuracy over wide frequency range for multi-phase oscillators. A prototype two-phase VCO is analyzed using injection-locking theory and implemented to demonstrate the effectiveness of the capacitive-coupling technique for low-power and low-noise multiple phase clock generation. The 4.3-5.3 GHz two-phase VCO prototype was implemented in a 130 nm CMOS technology and achieved a measured phase noise of -120 to -124.04 dBc /Hz @ 1 MHz offset and a measured phase error of 0.23-0.91° across the 1 GHz tuning range.
Reduction of the Hodgkin-Huxley Equations to a Single-Variable Threshold Model

It is generally believed that a neuron is a threshold element that fires when some variable u reaches a threshold. Here we pursue the question of whether this picture can be justified and study the four-dimensional neuron model of Hodgkin and Huxley as a concrete example. The model is approximated by a response kernel expansion in terms of a single variable, the membrane voltage. The first-order term is linear in the input and its kernel has the typical form of an elementary postsynaptic potential. Higher-order kernels take care of nonlinear interactions between input spikes. In contrast to the standard Volterra expansion, the kernels depend on the firing time of the most recent output spike. In particular, a zero-order kernel that describes the shape of the spike and the typical after-potential is included. Our model neuron fires if the membrane voltage, given by the truncated response kernel expansion, crosses a threshold. The threshold model is tested on a spike train generated by the Hodgkin-Huxley model with a stochastic input current. We find that the threshold model predicts 90 percent of the spikes correctly. Our results show that, to good approximation, the description of a neuron as a threshold element can indeed be justified.