Miracle-dz/UniFAR-FTUs huggingface dataset:
Composite likelihood method for inferring local pedigrees

Pedigrees contain information about the genealogical relationships among individuals and are of fundamental importance in many areas of genetic studies. However, pedigrees are often unknown and must be inferred from genetic data. Despite the importance of pedigree inference, existing methods are limited to inferring only close relationships or analyzing a small number of individuals or loci. We present a simulated annealing method for estimating pedigrees in large samples of otherwise seemingly unrelated individuals using genome-wide SNP data. The method supports complex pedigree structures such as polygamous families, multi-generational families, and pedigrees in which many of the member individuals are missing. Computational speed is greatly enhanced by the use of a composite likelihood function which approximates the full likelihood. We validate our method on simulated data and show that it can infer distant relatives more accurately than existing methods. Furthermore, we illustrate the utility of the method on a sample of Greenlandic Inuit. Author Summary Pedigrees contain information about the genealogical relationships among individuals. This information can be used in many areas of genetic studies such as disease association studies, conservation efforts, and learning about the demographic history and social structure of a population. Despite their importance, pedigrees are often unknown and must be estimated from genetic information. However, pedigree inference remains a difficult problem due to the high cost of likelihood computation and the enormous number of possible pedigrees we must consider. These difficulties limit existing methods in their ability to infer pedigrees when the sample size or the number of markers is large, or when the sample contains only distant relatives. In this report, we present a method that circumvents these computational barriers in order to infer pedigrees of complex structure for a large number of individuals. From our simulation studies, we found that our method can infer distant relatives much more accurately than existing methods. Our ability to infer pedigrees with a greater accuracy opens up possibilities for developing or improving pedigree-based methods in many areas research such as linkage analysis, demographic inference, association studies, and conservation.
Encyclopedia of Soviet life

A by-product of the amazing changes now taking place within the Soviet Union is a change in rhetoric no less than reality. Under Gorbachev, the Russian language has been changing parallel with novoe politichaskoe myshenie - new political thinking - with the effect that such new expressions as have flooded the Russian language clash with the less yielding realities of Soviet economy and society. The purpose of this volume is to clarify this dynamic in Soviet life, in which stagnation and decay confront hopes and expectations for liberalization. Zemtsov argues that the Soviet political language is self-contradictory, fractured into polarities of good and evil and thus depriving the Russian language of its basic subtlety, coherence, and inner logic. This work brings to life the Orwellian world of double-speak in a post-totalitarian environment. The Soviet language has two basic components: fictions which Communist ideology proclaims as reality, and realities that are portrayed in the guise of fictions. In this sense, Zemtsov undertakes to do for the Soviet language what the great H. L. Mencken achieved for the American language -show the reality of Soviet life by making plain the fictive qualities of Soviet ideology. This is a basic library reference work, a volume of indispensable utility for political scientists, area experts, and policy analysts. It offers a taxonomy enriched by a deep, personal knowledge of the Russian language by its author. Encyclopedia of Soviet Life is at one and the same time a basic primer of Soviet contemporary politics, a deep portrait of the psychology of totalitarian manipulation, and a sensitive appreciation of the nobler aspirations of the Russian people that is part and parcel of their great language.
Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes

One of the greatest challenges that modern molecular biology is facing is the understanding of the complex mechanisms regulating gene expression. A fundamental step in this process requires the characterization of regulatory motifs playing key roles in the regulation of gene expression at transcriptional and post-transcriptional levels. In particular, transcription is modulated by the interaction of transcription factors with their corresponding binding sites. Weeder Web is a web interface to Weeder, an algorithm for the automatic discovery of conserved motifs in a set of related regulatory DNA sequences. The motifs found are in turn likely to be instances of binding sites for some transcription factor. Other than providing access to the program, the interface has been designed so to make usage of the program itself as simple as possible, and to require very little prior knowledge about the length and the conservation of the motifs to be found. In fact, the interface automatically starts different runs of the program, each one with different parameters, and provides the user with an overall summary of the results as well as some 'advice' on which motifs look more interesting according to their statistical significance and some simple considerations. The web interface is available at the address www.pesolelab. it by following the 'Tools' link.
PSO based path planner of an autonomous mobile robot

A novel approach based on particle swarm optimization has been presented in this paper for solving mobile robot navigation task. The proposed technique tries to optimize the path generated by an intelligent mobile robot from its source position to destination position in its work space. For solving this problem, a new fitness function has been modelled, which satisfies the obstacle avoidance and optimal path traversal conditions. From the obtained fitness values of each particle in the swarm, the robot moves towards the particle which is having optimal fitness value. Simulation results are provided to validate the feasibility of the developed methodology in various unknown environments.
Person Identification Using Eye Movements and Post Saccadic Oscillations

A novel person identification approach using eye movements is presented and evaluated. The method incorporates both physical and behavioral characteristics of the human eye and is specifically based on eye movements and post saccadic oscillations. In an experiment with 12 participants the method achieved an identification accuracy of 86.4 % using random forest classification.
Biological agents as weapons 1: smallpox and botulism

1. Early recognition by clinicians of illnesses suggesting a biological attack is integral to the public health response. 2. The four biological agents of most concern are smallpox virus, botulinum toxin, and anthrax and plague bacteria. 3. Smallpox is distinguishable from chickenpox by the prominent prodromal period and lesions that develop at the same pace and, on any part of the body, appear identical to each other, evolve slowly and are peripherally distributed. 4. The degree of protection conferred by smallpox vaccination given 20 or more years ago is unknown. 5. Foodborne and inhalational botulism could result from deliberate release of toxin. 6. Botulism presents with cranial nerve palsies and descending paralysis in a patient with normal conscious state and no fever.
Experiences with using iBeacons for Indoor Positioning

iBeacon is a protocol standardized by Apple based on Bluetooth Low Energy which allows broadcasting devices (e.g. beacons) to emit signals and a compatible receiver (e.g. smartphone) to capture and interpret the same. iBeacon seems useful in indoor positioning and proximity based solutions. This paper talks about our experiences with iBeacon and establishing its effectiveness in indoor positioning. We placed multiple beacons in a room and recorded received signal strength (RSSI) at designated points (fingerprinting) to create a RSSI fingerprint database. This was used to establish location of a user in real time based on the measured RSSI in the user's mobile device. We found beacon signal strength is inconsistent and is dependent on height, position, direction of device and obstacles. RSSI fingerprinting is time consuming and must be redone if beacons are moved or if room is rearranged. Our conclusion was that iBeacon was more suitable for applications around proximity rather than positioning.
The major form of hepatitis C virus alternate reading frame protein is suppressed by core protein expression

Hepatitis C virus (HCV) is a human RNA virus encoding 10 proteins in a single open reading frame. In the +1 frame, an ‘alternate reading frame’ (ARF) overlaps with the core protein-encoding sequence and encodes the ARF protein (ARFP). Here, we investigated the molecular regulatory mechanisms of ARFP expression in HCV target cells. Chimeric HCV-luciferase reporter constructs derived from the infectious HCV prototype isolate H77 were transfected into hepatocyte-derived cell lines. Translation initiation was most efficient at the internal AUG codon at position 86/88, resulting in the synthesis of a truncated ARFP named 86/88ARFP. Interestingly, 86/88ARFP synthesis was markedly enhanced in constructs containing an inactivated core protein reading frame. This enhancement was reversed by co-expression of core protein in trans, demonstrating suppression of ARFP synthesis by HCV core protein. In conclusion, our results indicate that translation of ARFP occurs mainly by alternative internal initiation at position 86/88 and is regulated by HCV core protein expression. The suppression of ARFP translation by HCV core protein suggests that ARFP expression is inversely linked to the level of viral replication. These findings define key mechanisms regulating ARFP expression and set the stage for further studies addressing the function of ARFP within the viral life cycle.
Role of Perfusion CT in Glioma Grading and Comparison with Conventional MR Imaging Features

BACKGROUND AND PURPOSE: Perfusion imaging using CT can provide additional information about tumor vascularity and angiogenesis for characterizing gliomas. The purpose of our study was to demonstrate the usefulness of various perfusion CT (PCT) parameters in assessing the grade of treatment-naïve gliomas and also to compare it with conventional MR imaging features. MATERIALS AND METHODS: PCT was performed in 19 patients with glioma (14 high-grade gliomas and 5 low-grade gliomas). Normalized ratios of the PCT parameters (normalized cerebral blood volume [nCBV], normalized cerebral blood flow [nCBF], normalized mean transit time [nMTT]) were used for final analysis. Conventional MR imaging features of these tumors were assessed separately and compared with PCT parameters. Low- and high-grade gliomas were compared by using the nonparametric Wilcoxon 2-sample tests. RESULTS: Mean nCBV in the high- and low-grade gliomas was 3.06 ± 1.35 and 1.44 ± 0.42, respectively, with a statistically significant difference between the 2 groups (P = .005). Mean nCBF for the high- and low-grade gliomas was 3.03 ± 2.16 and 1.16 ± 0.36, respectively, with a statistically significant difference between the 2 groups (P = .045). Cut points of >1.92 for nCBV (85.7% sensitivity and 100% specificity), >1.48 for nCBF (71.4% sensitivity and 100% specificity), and <1.94 for nMTT (92.9% sensitivity and 40% specificity) were found to identify the high-grade gliomas. nCBV was the single best parameter; however, using either nCBV of >1.92 or nCBF of >1.48 improved the sensitivity and specificity to 92.9% and 100%, respectively. The sensitivity and specificity for diagnosing a high-grade glioma with conventional MR imaging were 85.7% and 60%, respectively. CONCLUSIONS: PCT can be used for preoperative grading of gliomas and can provide valuable complementary information about tumor hemodynamics, not available with conventional imaging techniques. nCBV was the single best parameter correlating with glioma grades, though using nCBF when nCBV was <1.92 improved the sensitivity. An nCBV threshold of >1.92 was found to identify the high-grade gliomas.
Two integral membrane proteins located in the cis-middle and trans-part of the Golgi system acquire sialylated N-linked carbohydrates and display different turnovers and sensitivity to cAMP-dependent phosphorylation

The localization and chemical characteristics of two Golgi integral membrane proteins (GIMPs) have been studied using monoclonal antibodies. The two proteins are segregated in different parts of the Golgi system and whereas GIMPc(130 kD) is located in the cis and medial cisternae, GIMPt (100 kD) is confined in the trans-most cisterna and trans-tubular network. Both GIMPs are glycoproteins that contain N- and O-linked carbohydrates. The N-linked carbohydrates were exclusively of the complex type. Although excluded from the trans-side of the Golgi system, where sialylation is believed to occur, GIMPc acquires sialic acid in both its N- and O-linked carbohydrates. Sialic acid was also detected in the N-linked carbohydrates of GIMPt. GIMPc is apparently phosphorylated in the luminal domain in vivo. Phosphorylation occurred exclusively on serine and was stimulated by dibutyryl cyclic AMP. GIMPc and GIMPt displayed half-lives of 20 and 9 h, respectively.
DRDO – IISc Programme on Advanced Research in Mathematical Engineering Exponential Diversity Achieving Spatio-Temporal Power Allocation Scheme for Fading Channels

In this paper, we analyze optimum (in space and time) adaptive power transmission policies for fading channels when the channel state information (CSI) at the transmitter (CSIT) and receiver (CSIR) is available. The transmitter has a long-term (time) average power constraint. There can be multiple antennas at the transmitter and receiver. The channel experiences Rayleigh fading. We consider beamforming and space-time coded systems with perfect/imperfect CSIT and CSIR. We also consider an inner convolutional code (with beamforming or an outer space-time code). The performance measure is the bit error rate (BER). We show that in both coded and uncoded systems, our power allocation policy provides exponential diversity gain if perfect CSIT is available. We also show that, if the quality of CSIT degrades then the exponential diversity is retained only in the low SNR region but we get only polynomial diversity in the high SNR region.
The Relationship between Phytoplankton Distribution and Water Column Characteristics in North West European Shelf Sea Waters

Phytoplankton underpin the marine food web in shelf seas, with some species having properties that are harmful to human health and coastal aquaculture. Pressures such as climate change and anthropogenic nutrient input are hypothesized to influence phytoplankton community composition and distribution. Yet the primary environmental drivers in shelf seas are poorly understood. To begin to address this in North Western European waters, the phytoplankton community composition was assessed in light of measured physical and chemical drivers during the “Ellett Line” cruise of autumn 2001 across the Scottish Continental shelf and into adjacent open Atlantic waters. Spatial variability existed in both phytoplankton and environmental conditions, with clear differences not only between on and off shelf stations but also between different on shelf locations. Temperature/salinity plots demonstrated different water masses existed in the region. In turn, principal component analysis (PCA), of the measured environmental conditions (temperature, salinity, water density and inorganic nutrient concentrations) clearly discriminated between shelf and oceanic stations on the basis of DIN∶DSi ratio that was correlated with both salinity and temperature. Discrimination between shelf stations was also related to this ratio, but also the concentration of DIN and DSi. The phytoplankton community was diatom dominated, with multidimensional scaling (MDS) demonstrating spatial variability in its composition. Redundancy analysis (RDA) was used to investigate the link between environment and the phytoplankton community. This demonstrated a significant relationship between community composition and water mass as indexed by salinity (whole community), and both salinity and DIN∶DSi (diatoms alone). Diatoms of the Pseudo-nitzschia seriata group occurred at densities potentially harmful to shellfish aquaculture, with the potential for toxicity being elevated by the likelihood of DSi limitation of growth at most stations and depths.
Single-trial EEG Discrimination between Five Hand Movement Imagery and Execution towards the control of a prosthetic / orthotic hand using a brain-computer interface

A brain computer interface (BCI) holds the potential to allow motor-impaired individuals to perform simple daily tasks by translating their neural intentions into movements of a robotic prosthetic/orthotic hand. These daily tasks can be facilitated through the performance of key kinematic hand movements; however, few BCI studies to date focus on functional kinematic unilateral hand movements. This paper presents the first attempt to discriminate the neural control signals for unilateral wrist extension and flexion, finger extension and flexion and the tripod pinch from single-trial electroencephalogram (EEG). High-resolution EEG was recorded from test subjects as they executed and imagined five essential hand movements using both hands. Independent component analysis (ICA) and time-frequency techniques were used to extract spectral features based on event-related (de)synchronisation (ERD/ERS). The Bhattacharyya distance (BD) was used for feature reduction, while Mahalanobis distance (MD) clustering and artificial neural networks (ANN) were used as classifiers. Average accuracies achieved ranged between 51 % and 63 %, however some subjects showed accuracies around 70 % for either real or imagined movements. This indicates the possibility of individual kinematic movement discrimination between this new combination of BCI hand movements. Keywords— Artificial neural networks (ANN), brain-computer interface (BCI), electroencephalogram (EEG), event-related (de)synchronisation (ERD/ERS), group classifier, independent component analysis (ICA), Mahalanobis distance (MD)
Position Paper: Measuring the Impact of Alphabet and Culture on Graphical Passwords

1. OUR POSITION Android’s graphical password scheme (sometimes referred to as the “password pattern”) is perhaps the most widely used and most studied graphical password system to date. With its launch, Android’s only authentication/unlock mechanism was the graphical password; however, other authentication systems are allowed today, such as PINs and text-based passwords. Despite the added authentication choices, the graphical password option remains a very popular choice among Android users [6, 7, 14].
On Secrecy Rate of the Generalized Artificial-Noise Assisted Secure Beamforming for Wiretap Channels

In this paper we consider the secure transmission with multiple-input, single-output, single-antenna eavesdropper (MISOSE) in fast fading channels where the transmitter knows perfect legitimate channel state information but only the statistics of the eavesdropper's channel. For the MISOSE channels, the artificial noise assisted beamforming proposed by Goel and Negi is a promising technique, where the artificial noise is imposed on the null space of the legitimate channel to disrupt the eavesdropper's reception. Here we propose a generalized artificial noise scheme which allows the injection of the artificial noise to the legitimate channel. Although the generalized artificial noise may cause the leakage of artificial noise at the legitimate receiver, the secrecy rate can still be improved since the covariance matrix of it is more flexible than the heuristic one selected by Goel and Negi. To fully characterize the proposed scheme, we investigate the optimization of its secrecy rate. We first derive the conditions under which the beamformers of the message bearing signal and the generalized artificial noise being the same is optimal. Based on this choice, the complicated secrecy rate optimization problem over the covariance matrices of the message-bearing signal and the generalized artificial noise can be reduced to a much simpler power allocation problem. We also develop an efficient algorithm to solve this non-convex power allocation problem. Numerical results show that our generalized artificial noise scheme outperforms Goel and Negi's heuristic selection, especially in the near eavesdropper settings. In particular, with the aid of the proposed scheme, the regime with non-zero secrecy rate is enlarged, which can significantly improve the connectivity of the network.
IMPORTANCE OF MACRO‐ VERSUS MICROSTRUCTURE IN MODULATING LIGHT LEVELS INSIDE CORAL COLONIES 1

Adjusting the light exposure and capture of their symbiotic photosynthetic dinoflagellates (genus Symbiodinium Freud.) is central to the success of reef‐building corals (order Scleractinia) across high spatio‐temporal variation in the light environment of coral reefs. We tested the hypothesis that optical properties of tissues in some coral species can provide light management at the tissue scale comparable to light modulation by colony architecture in other species. We compared within‐tissue scalar irradiance in two coral species from the same light habitat but with contrasting colony growth forms: branching Stylophora pistillata and massive Lobophyllia corymbosa. Scalar irradiance at the level of the symbionts (2 mm into the coral tissues) were <10% of ambient irradiance and nearly identical for the two species, despite substantially different light environments at the tissue surface. In S. pistillata, light attenuation (90% relative to ambient) was observed predominantly at the colony level as a result of branch‐to‐branch self‐shading, while in L. corymbosa, near‐complete light attenuation (97% relative to ambient) was occurring due to tissue optical properties. The latter could be explained partly by differences in photosynthetic pigment content in the symbiont cells and pigmentation in the coral host tissue. Our results demonstrate that different strategies of light modulation at colony, polyp, and cellular levels by contrasting morphologies are equally effective in achieving favorable irradiances at the level of coral photosymbionts.
DWS-AQA: a cost effective approach for very large data warehouses

Data warehousing applications typically involve massive amounts of data that push database management technology to the limit. A scalable architecture is crucial, not only to handle very large amount of data but also to assure interactive response time to the users. Large data warehouses require a very expensive setup, typically based on high-end servers or high-performance clusters. In this paper we propose and evaluate a simple but very effective method to implement a data warehouse using the computers and workstations typically available in large organizations. The proposed approach is called data warehouse striping with approximate query answering (DWS-AQA). The goal is to use the processing and disk capacity normally available in large workstation networks to implement a data warehouse with a very reduced infrastructure cost. As the data warehouse shares computers that are also being used for other purposes, most of the times only a fraction of the computers will be able to execute the partial queries in time. However, as we show in the paper, the approximated answers estimated from partial results have a very small error for most of the plausible scenarios. Moreover, as the data warehouse facts are partitioned in a strict uniform way, it is possible to calculate tight confidence intervals for the approximated answers, providing the user with a measure of the accuracy of the query results. A set of experiments on the TPC-H benchmark database is presented to show the accuracy of DWS-AQA for a large number of scenarios.