Miracle-dz/UniFAR-FTUs huggingface dataset:
Align human interactome with phenome to identify causative genes and networks underlying disease families

MOTIVATION Understanding the complexity in gene-phenotype relationship is vital for revealing the genetic basis of common diseases. Recent studies on the basis of human interactome and phenome not only uncovers prevalent phenotypic overlap and genetic overlap between diseases, but also reveals a modular organization of the genetic landscape of human diseases, providing new opportunities to reduce the complexity in dissecting the gene-phenotype association. RESULTS We provide systematic and quantitative evidence that phenotypic overlap implies genetic overlap. With these results, we perform the first heterogeneous alignment of human interactome and phenome via a network alignment technique and identify 39 disease families with corresponding causative gene networks. Finally, we propose AlignPI, an alignment-based framework to predict disease genes, and identify plausible candidates for 70 diseases. Our method scales well to the whole genome, as demonstrated by prioritizing 6154 genes across 37 chromosome regions for Crohn's disease (CD). Results are consistent with a recent meta-analysis of genome-wide association studies for CD. AVAILABILITY Bi-modules and disease gene predictions are freely available at the URL http://bioinfo.au. tsinghua.edu. cn/alignpi/
FEASIBILITY AND FUNCTIONALITY OF AUTONOMOUS OBJECTS IN THE HLA

The generality, autonomy, and mobility of autonomous objects open up new possibilities for supporting a broad range of requirements of federates and federations under the High Level Architecture (HLA). Their generality allows them to execute arbitrarily complex behaviors in heterogeneous environments without modification while their autonomy and mobility allow them to arrive at solutions collectively in a distributed environment without the bottlenecks of static, stationary s stems. The feasibility of integrating autonomous objects systems into federates and federations is examined. Integration solutions considered include using the HLA and its Run-Time Infrastructure (RTI) as currently specified, extending the HLA to specifically support autonomous objects systems, and allowing autonomous objects to perform management functions outside the HLA. The range of functionality that autonomous objects can provide via the identified integration strategies is extrapolated. This functionality may include extension of global functionality or infrastructure, extension of a federate’s model, and federation management or oversight.
Non-invasive tumor localization by 3D registration of range sensor and computer tomography images.

This paper describes a patient positioning method that allows a non-invasive localization of tumors in the field of conformal radiotherapy for the treatment of cancers located in the head. The proposed methodology uses computer tomography and range sensor images of the patient's head; on the one hand tomography data has information of tumor localization related to the patient's head and on the other hand range sensor images has information of patient's face localization into the treatment's room. A 3D multimodality registration of computer tomography and range sensor images and the calibration of range sensor at radiotherapy treatment room avoid the use of stereotactic frame for patient's positioning. Tests performed with human data proved that the registration algorithm is accurate (0.1 mm mean distance between homologous points) and robust even for facial expression changes.
Concentration-Dependent Chemical Expansion in Lithium-Ion Battery Cathode Particles

In this work, the effect of the concentration-dependent chemical-expansion coefficient, b, on the chemo-elastic field in lithium-ion cathode particles is examined. To accomplish this, an isotropic linear-elastic model is developed for a single idealistic particle subjected to potentiostatic-discharge and charge conditions. It is shown that b can be a key parameter in demarcating the chemo-stress–strain state of the cathode material undergoing nonlinear volumetric strains. As an example, such strains develop in the hexagonal-to-monoclinic-phase region of LixCoO2 (0.37 x 0.55) and, subsequently, the corresponding b is a linear function of concentration. Previous studies have assumed a constant value for b. Findings suggest that the composition-generated chemo-elastic field that is based on a linear-b dramatically affects both the interdiffusion and the mechanical behavior of the LixCoO2 cathode particle. Because the chemo-elastic phenomena emanate in a reciprocal fashion, the resulting linear b-based hydrostatic-stress gradients significantly aid the diffusion of lithium. Thus, diffusion is accelerated in either electrochemical process that the cathode material undergoes. [DOI: 10.1115/1.4027833]
A Secure Middleware Architecture for Web Services

Current web service platforms (WSPs) often perform all web servicesrelated processing, including security-sensitive information handling, in the same protection domain. Consequently, the entire WSP may have access to securitysensitive information such as credit card numbers, forcing us to trust a large and complex piece of software. To address this problem, we propose ISO-WSP, a new middleware architecture that decomposes current WSPs into two parts executing in separate protection domains: (1) a small trusted T-WSP to handle security-sensitive data, and (2) a large, legacy untrusted U-WSP that provides the normal WSP functionality, but uses the T-WSP for security-sensitive data handling. By restricting security-sensitive data access to T-WSP, ISO-WSP reduces the software complexity of trusted code, thereby improving the testability of ISO-WSP. To achieve end-to-end security, the application code is also decomposed into two parts, isolating a small trusted part from the remaining untrusted code. The trusted part encapsulates all accesses to security-sensitive data through a Secure Functional Interface (SFI). To ease the migration of legacy applications to ISO-WSP, we developed tools to translate direct manipulations of security-sensitive data by the untrusted part into SFI invocations. Using a prototype implementation based on the Apache Axis2 WSP, we show that ISO-WSP reduces software complexity of trusted components by a factor of five, while incurring a modest performance overhead of few milliseconds per request. We also show that existing applications can be migrated to run on ISO-WSP with minimal effort: a few tens of lines of new and modified code.
Efficient variational inference for the dynamic harmonic model

In this paper, we develop a class of probability models that are potentially useful for various music applications such as polyphonic transcription, source separation, restoration or denoising. This class unifies and extends several models such as sinusoidal and harmonic models, additive synthesis model, Gabor regression and probabilistic phase vocoder. We overcome computational intractability issues by introducing structured variational (mean-field) approximations that lead to efficient local message passing algorithms
Classical conditioning for preserving the effects of short melatonin treatment in children with delayed sleep: a pilot study

Melatonin treatment is effective in treating sleep onset problems in children with delayed melatonin onset, but effects usually disappear when treatment is discontinued. In this pilot study, we investigated whether classical conditioning might help in preserving treatment effects of melatonin in children with sleep onset problems, with and without comorbid attention deficit hyperactivity disorder (ADHD) or autism. After a baseline week, 16 children (mean age: 9.92 years, 31% ADHD/autism) received melatonin treatment for 3 weeks and then gradually discontinued the treatment. Classical conditioning was applied by having children drink organic lemonade while taking melatonin and by using a dim red light lamp that was turned on when children went to bed. Results were compared with a group of 41 children (mean age: 9.43 years, 34% ADHD/autism) who received melatonin without classical conditioning. Melatonin treatment was effective in advancing dim light melatonin onset and reducing sleep onset problems, and positive effects were found on health and behavior problems. After stopping melatonin, sleep returned to baseline levels. We found that for children without comorbidity in the experimental group, sleep latency and sleep start delayed less in the stop week, which suggests an effect of classical conditioning. However, classical conditioning seems counterproductive in children with ADHD or autism. Further research is needed to establish these results and to examine other ways to preserve melatonin treatment effects, for example, by applying morning light.
The project fragmentation problem in personal information management

The project fragmentation problem in personal information management occurs when someone who is working on a single project stores and retrieves information items relating to that project from separate format-related collections (documents, emails and favorite Web sites). This study was aimed to test empirically users' working habits in order to shed light on the project fragmentation problem. Twenty personal computer users participated in the study. Data collection tools included an interview, screen captures and a questionnaire. Results indicate that users tend to store and retrieve project-related information items based on different formats in one project folder when the interface design encourages it. However, they store and retrieve project- related information items in different folders (documents, emails and favorite Web sites) when the design encourages such fragmentation. Two types of attempts to solve the project fragmentation problem are reviewed and a new possible solution is suggested.
Let’s Not “Taint” Stigma Research With Legitimacy, Please

We propose that stigma and legitimacy are distinct constructs. Drawing from extant research, empirical observations, and the theoretical assumptions of both constructs we assert that, in spite of increasing efforts to equate stigma as illegitimacy, the opposite of legitimacy, that it is not. Specifically, we argue that organizations and their actors can be both stigmatized and legitimate at the same time. With this recognized, we propose a stigma-focused research agenda, separate from - and untainted by - legitimacy. Further, we propose an agenda that broadens conceptualizations of audiences and their dynamics, addresses how normal “deviants” take action in the face of stigma, and reconceptualises how audiences and the stigmatized interact.
The classification of doubly periodic minimal tori with parallel ends

Let K be the space of properly embedded minimal tori in quotients of R 3 by two independent translations, with any fixed (even) number of parallel ends. After an appropriate normalization, we prove that K is a 3-dimensional real analytic manifold that reduces to the finite coverings of the examples defined by Karcher, Meeks and Rosenberg in (9, 10, 15). The degenerate limits of surfaces in K are the catenoid, the helicoid and three 1-parameter families of surfaces: the simply and doubly periodic Scherk minimal surfaces and the Riemann minimal examples.
Multi-Antenna Diversity — A New Transmit Diversity Scheme for Wireless Communications

In this paper, we propose multi-antenna diversity (MAD), a new transmit diversity scheme for wireless communications. Specifically, MAD selects the optimal transmit antenna with the best channel quality to send data. Due to its greatly simplified architecture, MAD guarantees the simple decoding without imposing any constraints on the issues such as code delay, code rate, antenna number, and modulation method, etc. We also develop the analytical framework to evaluate the performance of MAD from different perspectives. We show that MAD performs better than space-time block codes (STBC), while the processing complexity is lower than STBC. The superiority of MAD over STBC increases significantly as the number of transmit antennas gets larger.
Minimizing discovery time in bluetooth networks using localization techniques

Bluetooth is a short range wireless communication protocol. However, the discovery process to establish connection in Bluetooth network is very time consuming process. This paper presents localization techniques for Bluetooth networks. There is an increasing interest in location identification, and communication with other Bluetooth devices within a local area network. The idea behind localization techniques is to address position estimation in Bluetooth networks in order to reduce the time taken for device discovery to establish connection process. In this paper Received Signal Strength Indicator (RSSI) is obtained using Inverse square law. The Received Power (Prx) is obtained indirectly by converting RSSI values to Prx using Friis equation. Positioning is based on Prx and converted to estimate the distance using simple radio propagation model based on Friis equation. The advantage of positioning is to know the object actual position with respect to the distance from the transmitter. The relationship obtained from positioning using Prx will be used to minimize the discovery time in connection establishment process in Bluetooth networks. This work is part of the design process of roaming protocol for Bluetooth networks.
CHANDRA OBSERVATIONS OF NUCLEAR X-RAY EMISSION FROM LOW SURFACE BRIGHTNESS GALAXIES

We present Chandra detections of X-ray emission from the active galactic nuclei (AGN) in two giant low surface brightness (LSB) galaxies, UGC 2936 and UGC 1455. Their X-ray luminosities are 1.8 × 1042 ergs s−1 and 1.1 × 1040 ergs s−1 respectively. Of the two galaxies, UGC 2936 is radio loud. Together with another LSB galaxy UGC 6614 (XMM-Newton archival data) both appear to lie above the X-ray–radio fundamental plane, and their AGN have black hole masses that are low compared to similar galaxies lying on the correlation. However, the bulges in these galaxies are well developed, and we detect diffuse X-ray emission from four of the eight galaxies in our sample. Our results suggest that the bulges of giant LSB galaxies evolve independently of their halo-dominated disks which are low in star formation and disk dynamics. The centers follow an evolutionary path similar to that of bulge-dominated normal galaxies on the Hubble sequence, but the LSB disks remain unevolved. Thus, the bulge and disk evolution are decoupled and so whatever star formation processes produced the bulges did not affect the disks.
Transformation of a Modern Newsroom Workforce

Digital transformation continues to impact the news industry and news organizations are adapting accordingly through shifts in required skills and prescribed job positions of journalists. In order to examine the changing nature of the modern journalist, a case study was conducted examining the employment histories of New York City journalists (n = 3587). Social network analysis was used to better understand the career trajectories of journalists within the dataset, with a specific focus on understanding the development of new jobs for journalists in data, analytic, social, and mobile-oriented job positions. Findings demonstrate important differences between traditional employment patterns and those of employees in jobs requiring new skills and knowledge of new technology.
Handover Mechanisms for Planned Cell Outage in Twin State Green Wireless Networks

This paper investigates possible handover mechanisms for a twin state network aimed at energy saving. We propose the twin state network as a viable 'Green' option and illustrate the possible energy savings. The challenge of conducting multiple handovers within the transit times of the twin state network, while maintaining the service quality is discussed. The possible handover solutions through multi-carrier operation, FFR and incremental coverage extension are presented in the context of LTE standards.
The Champagne Wine Industry : An Economic Dynamic Model of Production and Consumption

This paper reports on the development of an economic system dynamics (SD) model designed to simulate both the short term and the long term production dynamics of the Champagne wine industry. The model captures the main structural details of the Champagne business activity. The goal of the SD model is to study the nonlinear and dynamic behavior observed in the Champagne wine industry, and the long feedback delays involved in fixed asset investments supporting the production of grapes and wine. All industry operators have to face production, price and stock risks. Because it takes about three years to sell Champagne wine after the vintage of grapes, industry operators have to cope with the uncertainty associated to long time delays in the formation of price expectations, in the adjustment of supply, seasonal production and demand. Thus, the model integrates structural elements of price expectations, short term and long term supply responses, demand substitution and inventory fluctuation. Perspectives are open to link the model to forecast profitability and financial leverage.
REVIEW-ARTIFICIAL INTELLIGENCE BASED MODELLING OF HYDROLOGICAL PROCESSES

Hydrological processes such as runoff and contaminant transport are usually affected by various complex interrelated variables. Moreover, uncertainties in variables estimate are the common stamp of these processes. Due to this complex nature, Physical modeling of any hydrological system requires availability of large, accurate and detailed data related to all influencing variables, which are not always available due to financial and technical constraints. This may lead to deficiencies in model’s performance which in turn, negatively affect hydrological planning and policy drawing. To address these shortcomings, artificial intelligence (AI) based techniques have been recently used as alternative tools to traditional physical hydrological models. These techniques have been proved to be successful and effective in tackling wide spectrum of challenging hydrological processes. This article is intended to serve as an introductory review of application of two AI techniques namely, artificial neural networks (ANNs) and support vector machine (SVM) in various hydrological applications. In this article, ANNs and SVM theoretical background coupled with their strength points that make them suitable for hydrological modeling were briefly described. Moreover, various examples of successful applications of ANNs and SVM for modeling different hydrological processes were also provided.
Performance of Fortran Coarrays on the Cray XE 6

Coarrays are a feature of the Fortran 2008 standard that enable parallelism using a small number of additional language elements. The execution model is that of a Partitioned Global Address Space (PGAS) language. The Cray XE architecture is particularly interesting for studying PGAS languages: it scales to very large numbers of processors; the underlying GEMINI interconnect is ideally suited to the PGAS model of direct remote memory access; the Cray compilers support PGAS natively. In this paper we present a detailed analysis of the performance of key coarray operations on XE systems including the UK national supercomputer HECToR, a 90,000-core Cray XE6 operated by EPCC at the University of Edinburgh. The results include a wide range of communications patterns and synchronisation methods relevant to real applications. Where appropriate, these are compared to the equivalent operation implemented using MPI. Keywords-Fortran; parallel programming; benchmark.
Quantifying the influence of surface water–groundwater interaction on nutrient flux in a lowland karst catchment

Abstract. Nutrient contamination of surface waters and groundwaters is an issue of growing importance as the risks associated with agricultural run-off escalate due to increasing demands on global food production. In this study, the influence of surface water–groundwater interaction on the nutrient flux in a lowland karst catchment was investigated with the aid of alkalinity sampling and a hydrological model. The objective of the study was to determine the impact of ephemeral karst lakes (turloughs) on the surface water–groundwater nutrient flux, and whether these lakes act as sources or sinks of nutrients within the groundwater flow system. Water samples were tested from a variety of rivers, turloughs, boreholes and springs at monthly intervals over 3 years. Alkalinity sampling was used to elucidate the contrasting hydrological functioning between different turloughs. Such disparate hydrological functioning was further investigated with the aid of a hydrological model which allowed for an estimate of allogenically and autogenically derived nutrient loading into the karst system. The model also allowed for an investigation of mixing within the turloughs, comparing observed behaviours with the hypothetical conservative behaviour allowed for by the model. Within the turloughs, recorded nutrient concentrations were found to reduce over the flooded period, even though the turloughs hydrological functioning (and the hydrological model) suggested this would not occur under conservative conditions. As such, it was determined that nutrient loss processes were occurring within the system. Denitrification during stable flooded periods (typically 3–4 months per year) was deemed to be the main process reducing nitrogen concentrations within the turloughs, whereas phosphorus loss is thought to occur mostly via sedimentation and subsequent soil deposition. The results from this study suggest that, in stable conditions, ephemeral lakes can impart considerable nutrient losses on a karst groundwater system.
An investigation of quantization table modification on JPEG steganography

Imperceptibility and the embedding capacity are the two most important aspects to be concerned in any image based steganographic research studies. It is necessarily considered to maximize the amount of embedding capacity while preserving the security against detection by unauthorized people in any steganographic methods. Many research studies have exposed that the modified quantization tables significantly reduce the distortion in the quality of stego-images and increase the embedding capacity of stego-images in DCT based steganographic techniques. In this paper, we investigate the aforementioned requirements in JPEG based steganographic techniques with the existing quantization table modification techniques by evaluating the experimental results and derive modified quantization tables to compare the previous results of some existing quantization modification techniques. Our experimental results reveal that the modified tables can provide a significance improvement in information-hiding capacity and visual quality than the other methods tested.
Transposable Prophage Mu Is Organized as a Stable Chromosomal Domain of E. coli

The E. coli chromosome is compacted by segregation into 400–500 supercoiled domains by both active and passive mechanisms, for example, transcription and DNA-protein association. We find that prophage Mu is organized as a stable domain bounded by the proximal location of Mu termini L and R, which are 37 kbp apart on the Mu genome. Formation/maintenance of the Mu ‘domain’ configuration, reported by Cre-loxP recombination and 3C (chromosome conformation capture), is dependent on a strong gyrase site (SGS) at the center of Mu, the Mu L end and MuB protein, and the E. coli nucleoid proteins IHF, Fis and HU. The Mu domain was observed at two different chromosomal locations tested. By contrast, prophage λ does not form an independent domain. The establishment/maintenance of the Mu domain was promoted by low-level transcription from two phage promoters, one of which was domain dependent. We propose that the domain confers transposition readiness to Mu by fostering topological requirements of the reaction and the proximity of Mu ends. The potential benefits to the host cell from a subset of proteins expressed by the prophage may in turn help its long-term stability.