Miracle-dz/UniFAR-FTUs huggingface dataset:
iGraph in action: performance analysis of disk-based graph indexing techniques

Graphs provide a powerful way to model complex structures such as chemical compounds, proteins, images, and program dependence. The previous practice for experiments in graph indexing techniques is that the author of a newly proposed technique does not implement existing indexes on his own code base, but instead uses the original authors' binary executables and reports only the wall clock time. However, we observed that this practice may result in several problems [6]. In order to address these problems, we have implemented all representative graph indexing techniques on a common framework called iGraph [6]. In this demonstration we showcase iGraph and its visual tools using several real datasets and their workloads. For selected queries of the workloads, we show several unique features including visual performance analysis.
Risk Perceptions in a Resource Community and Communication Implications: Emotion, Stigma, and Identity

Communication targeting resource communities, sites of potentially damaging industries such as forestry, mining, and logging, requires an understanding of risk perceptions among residents living within these communities. Among concerns facing these communities is social stigmatization, an actual or feared negative psychological experience associated with living in a community with an undesirable industry. This study of a coal‐mining resource community was conducted with the purpose of exploring a range of perceptions associated with ongoing exposure to a resource industry, including the experience of social stigma. This study used focus group interviews with stakeholders to highlight the personal voices of the resource community experience. A model of stakeholders’ perceptions of industry risks and benefits is introduced, and important distinctions between hypothetical risk perceptions and perceptions of resource community stakeholders are explored. Implications for communicating with resource communities are also discussed.
Algorithms for Learning Good Step Sizes

Many common algorithms in machine learning, from logistic regression to neural networks and beyond, rely on hyperparameters to function well. In gradient descent, too large a step size can cause the iteration to blow up and not terminate; too small a step size and the iteration doesn’t converge fast enough. Tuning these parameters can be very difficult: the manual for the popular linear and integer programming solver CPLEX has a 200page parameter manual that covers 135 parameters, and advises simply that “you may need to experiment with them” [1]. Existing methods for parameter tuning include just hand-tuning, a brute-force or random search, and grid search on the full set of training data, none of which are especially satisfying. For example, [2] gives a comparison between random and grid search on various problems, concluding that random search is better in many cases. [3] and [4] go further by applying a gradient-descent-like algorithm to the hyperparameters themselves. There is even work on determining whether it is even important to optimize hyperparameters [5]. However, all of these articles focus on hyperparameter optimization by repeatedly training on the full training set with different hyperparameters, and seeing which is best. If the training set is large or the model is complex, this may be highly impractical. According to the theoretical framework proposed by Prof. Rishi Gupta and Prof. Tim Roughgarden [1], we can learn these hyper parameters by using grid search on a significantly smaller subset of the full training set. We examine specifically the case of tuning the step size ρ used in gradient descent. More formally, let D be an hidden1 probability distribution over a set of functions that can be optimized by gradient descent2. For a function f in the support of D, let Cost(f ; ρ, ν) be the number of steps it takes gradient descent to converge such that the gradient ∇f(ρ) has norm less than ν. We would like an algorithm that learns the hyperparameter ρ that minimizes the expected cost C(ρ) ≡ Ef∼D[Cost(f ; ρ, ν)]. Intuitively, D defines a “family” of related optimization problems, and we would
Congenital anomalies and rhabdoid tumor associated with 22q11 germline deletion and somatic inactivation of the SMARCB1 tumor suppressor

The most common microdeletion in humans involves the 22q11 region. Congenital anomalies associated with 22q11 loss include cardiac and facial defects. Less frequent is the co‐presentation of malignant rhabdoid tumors that are highly aggressive childhood malignancies typically found in renal or extra‐renal soft tissues and central nervous system. A newborn patient presented with multiple congenital anomalies consistent with 22q11 deletion syndrome including cleft lip and palate, ear tags and ventricular septal defects co‐presenting with an axillary rhabdoid tumor. Comparative genomic hybridization revealed a 2.8 Mb germline deletion in the 22q11.2 region containing genes required for normal fetal development and the SMARCB1 tumor suppressor gene. Analysis of tumor DNA revealed a somatic deletion of exon 7 in the second allele of SMARCB1. Expression of SMARCB1 was absent, while tumor markers including MYC, GFAP, and CLAUDIN‐6 were upregulated. The presence of tandem oriented BCRL modules located within interspersed low copy repeat elements throughout the 22q11 distal region may predispose this area for microdeletions through nonalleleic homologous recombination. © 2011 Wiley‐Liss, Inc.
Lessons from a domain-based reengineering effort

The author presents the lessons and insights learned from a domain-centered reengineering effort. Using a method developed in a previous work, he sets about trying to understand and convert a complete legacy system from COBOL to an executable domain model. His work suggests that a domain-based approach is very promising but a number of issues need to be better understood. Among these are questions about domain completeness, scoping, interleaving and evolution; concept matching at the granularity of both the program architecture and details of the source code; thoroughness and representation of the legacy program coverage, as well as the problems inherent to the transition of a multi-program system. He discusses these issues in details using examples. Implications on future work in the area are suggested.
An Efficient Approximation of Betweenness Centrality for Uncertain Graphs

Betweenness centrality measures the centrality of nodes and edges in a graph based on the concept of shortest paths. However, such a definition is unsuitable for uncertain graphs due to the uncertainty of links. In the possible-world semantics, the Monte Carlo method is proposed to estimate the betweenness centrality of uncertain graphs. However, this method is computationally intensive. To address this challenging issue, in this paper, we propose the concept of possible shortest paths and develop a metric to approximate the betweenness centrality for uncertain graphs. We demonstrate that the new metric of betweenness centrality generalizes the deterministic one. Unfortunately, it is NP-hard to enumerate all possible shortest paths between two nodes exhaustively. To tackle this difficulty, we design a heuristic algorithm to explore the majority of possible shortest paths efficiently. Our method avoids the sampling process in the Monte Carlo method, and thus significantly improves the computational efficiency. We conduct extensive experiments to evaluate the effectiveness and efficiency of our method. The experimental results show that our approach can approximate the centrality of uncertain graphs accurately with high efficiency. Finally, we apply our method to the Internet network to evaluate the importance of autonomous systems.
Phylogenetic Analysis of Enteroaggregative Escherichia coli (EAEC) Isolates from Japan Reveals Emergence of CTX-M-14-Producing EAEC O25:H4 Clones Related to Sequence Type 131

ABSTRACT Enteroaggregative Escherichia coli (EAEC) causes acute or persistent diarrhea. The aggR gene is widely used as a marker for typical EAEC. The heterogeneity of EAEC is well known; however, there are few reports on the phylogenetic relationships of EAEC. Recently, CTX-M extended-spectrum β-lactamase (ESBL)-producing EAEC strains have been reported worldwide. To characterize EAEC strains in Japan, we investigated the population structure of EAEC. A total of 167 aggR-positive strains isolated from stool specimens from diarrheal patients in Kagoshima (139 strains) and Osaka (28 strains), Japan, between 1992 and 2010 were examined for the prevalence of EAEC virulence markers, the bla CTX-M gene, and the capacity to form biofilms. Multilocus sequence typing was also conducted. EAEC strains were widely distributed across four major E. coli phylogroups. Strains of O111:H21/clonal group 40 (CG40) (30 strains), O126:H27/CG200 (13 strains), and O86a:H27/CG3570 (11 strains) in phylogroup B1 are the historical EAEC clones in Japan, and they exhibited strong biofilm formation. Twenty-nine strains of EAEC O25:H4/CG131 were identified in phylogroup B2, 79% of which produced CTX-M-14. This clone has emerged since 2003. The clone harbored plasmid-encoded EAEC virulence genes but not chromosomal virulence genes and had lower biofilm-forming capacity than historical EAEC strains. This clone most likely emerged from a pandemic uropathogenic O25:H4/sequence type 131 clone by acquiring an EAEC virulence plasmid from canonical EAEC. Surveillance of the horizontal transfer of both virulence and ESBL genes among E. coli strains is important for preventing a worldwide increase in antimicrobial drug resistance.
Sex impact on the quality of fatty liver and its genetic determinism in mule ducks.

Recent changes to French regulations now allow farmers to produce "foie gras" from both male and female mule ducks. The aim of this study was to assess the quality of female fatty liver and to compare, from a phenotypic and genetic point of view, liver quality in males and females. A total of 914 mule ducks (591 males and 323 females), hatched in a single pedigree batch, were reared until 86 d of age and then force-fed for 12 d, before being slaughtered. Carcasses and livers were weighed and liver quality was assessed by grading the extent of liver veining and measuring the liver melting rate, either after sterilization of 60 g of liver or pasteurization of 180 g of liver. Sexual dimorphism was observed in favor of males, with a difference of approximately 10% in carcass and liver weights and up to 54% for the liver melting rate. Moreover, one-third of female livers showed moderate to high veining, whereas this was not the case for male livers. The fatty livers of female mule ducks are, therefore, of poorer quality and could not be transformed into a product with the appellation "100% fatty liver. " According to sex and parental line, heritability values ranged from 0.12 ± 0.05 to 0.18 ± 0.07 for fatty liver weight and from 0.09 ± 0.05 to 0.18 ± 0.05 for the 2 melting rate traits. The genetic correlations between the fatty liver weight and both melting rates were high (greater than +0.80) in the Muscovy population, whereas in the Pekin population, the liver weight and melting rates were less strongly correlated (estimates ranging from +0.36 ± 0.30 to +0.45 ± 0.28). Selection for lower liver melting rates without reducing the liver weight would, therefore, be easier to achieve in the Pekin population. Finally, as the 2 melting rate measurements are highly correlated (0.91 and over 0.95 for phenotypic and genetic correlations, respectively), we suggest using the easiest method, that is, sterilization of 60 g of liver.
A bi-annual forecasting model of currency crises

ABSTRACT This study proposes a novel approach that combines random forests and discrete wavelet transform (DWT) to construct a bi-annual forecasting model of currency crises. The proposed model can achieve a reasonably high level of accuracy in predicting crises and demonstrates that the DWT of monthly real exchange rates and foreign reserves can serve as reliable predictors. The predicted probability of crises in individual countries is visualized through a map, which indicates that the risk of crises has increased substantially across regions in the second half of 2018.
Resource Allocation for Millimeter Wave Self-Backhaul Network Using Markov Approximation

Millimeter wave (mmW) self-backhaul has been regarded as a high-capacity and low-cost solution to deploy dense small cell networks but its performance depends on a resource allocation strategy, which can effectively reduce interference (including co-tier interference, cross-tier interference, and self-interference). Taking the use of beamforming and the advantage of mmW short-range communication into account, this paper formulates a resource allocation problem in which sub-channels can be shared among low-interference links while orthogonal sub-channels can be used at the links that suffer high-level interference among them. The objective is to maximize the sum data rates of all users while ensuring the data rate of backhaul link at each small cell base station is greater than or equal to the sum data rates of all its served users in the access links. Besides, the data rate of each user should achieve its minimum traffic demand. The optimization problem is a combinatorial integer programming problem with a series of inequality constraints, which is difficult to solve. By introducing penalty function and penalty factors into it, the problem is transferred to an equivalent problem without any inequality, and then it can be addressed by the Markov approximation method. First, by leveraging the log-sum-exp method to approximate the equivalent problem, we deduce the near optimal solution. However, it is difficult to calculate the deduced solution since that it needs all possible solution information, and thus a Markov chain is then utilized to converge to the near optimal solution. The numerical results are shown to verify the performance of the proposed algorithm.
Unique active site promotes error-free replication opposite an 8-oxo-guanine lesion by human DNA polymerase iota

The 8-oxo-guanine (8-oxo-G) lesion is the most abundant and mutagenic oxidative DNA damage existing in the genome. Due to its dual coding nature, 8-oxo-G causes most DNA polymerases to misincorporate adenine. Human Y-family DNA polymerase iota (polι) preferentially incorporates the correct cytosine nucleotide opposite 8-oxo-G. This unique specificity may contribute to polι’s biological role in cellular protection against oxidative stress. However, the structural basis of this preferential cytosine incorporation is currently unknown. Here we present four crystal structures of polι in complex with DNA containing an 8-oxo-G lesion, paired with correct dCTP or incorrect dATP, dGTP, and dTTP nucleotides. An exceptionally narrow polι active site restricts the purine bases in a syn conformation, which prevents the dual coding properties of 8-oxo-G by inhibiting syn/anti conformational equilibrium. More importantly, the 8-oxo-G base in a syn conformation is not mutagenic in polι because its Hoogsteen edge does not form a stable base pair with dATP in the narrow active site. Instead, the syn 8-oxo-G template base forms the most stable replicating base pair with correct dCTP due to its small pyrimidine base size and enhanced hydrogen bonding with the Hoogsteen edge of 8-oxo-G. In combination with site directed mutagenesis, we show that Gln59 in the finger domain specifically interacts with the additional O8 atom of the lesion base, which influences nucleotide selection, enzymatic efficiency, and replication stalling at the lesion site. Our work provides the structural mechanism of high-fidelity 8-oxo-G replication by a human DNA polymerase.
Focusing Bistatic SAR Data in Airborne/Stationary Configuration

This paper presents a frequency-domain-based focusing algorithm for the bistatic synthetic aperture radar (BiSAR) data in airborne/stationary configuration. In this bistatic configuration, only the moving platform contributes to the azimuth modulation, whereas the stationary platform introduces a range offset (RO) to the range migration trajectories of targets at the same range. The offset is determined by the azimuth position of different targets with respect to the stationary platform. Since the RO is position dependent, monostatic SAR imaging algorithms are not able to focus the bistatic data collected in this configuration. In this paper, an analytical bistatic point-target reference spectrum is derived, and then, a frequency-domain-based algorithm is developed to focus the bistatic data. It uses an interpolation-free wavenumber-domain algorithm as a basis and performs a range-variant interpolation to correct the position-dependent RO in the image domain after coarse focusing. The proposed algorithm is validated by the simulated data and the real BiSAR data acquired by the Forschungsgesellschaft fu¿r Angewandte Naturwissenschaften's airborne SAR system, PAMIR, in December 2007. In this BiSAR experiment, an X-band transmitter was stationary operated on a hill with PAMIR as the receiver mounted on a Transall C-160.
Weakly Supervised Dual Learning for Facial Action Unit Recognition

Current research on facial action unit (AU) recognition typically requires fully AU-annotated facial images. Compared to facial expression labeling, AU annotation is a time-consuming, expensive, and error-prone process. Inspired by dual learning, we propose a novel weakly supervised dual learning mechanism to train facial action unit classifiers from expression-annotated images. Specifically, we consider AU recognition from facial images as the main task, and face synthesis given AUs as the auxiliary task. For AU recognition, we force the recognized AUs to satisfy the expression-dependent and expression-independent AU dependencies, i.e., the domain knowledge about expressions and AUs. For face synthesis given AUs, we minimize the difference between the synthetic face and the ground truth face, which has identical recognized and given AUs. By optimizing the dual tasks simultaneously, we successfully leverage their intrinsic connections as well as domain knowledge about expressions and AUs to facilitate the learning of AU classifiers from expression-annotated image. Furthermore, we extend the proposed weakly supervised dual learning mechanism to semi-supervised dual learning scenarios with partially AU-annotated images. Experimental results on three benchmark databases demonstrate the effectiveness of the proposed approach for both tasks.
The Pathophysiology, Diagnosis and Therapy of the Transurethral Resection of the Prostate Syndrome

In this article, the authors analyze a syndrome first described by Creevy in the 1940s, which may occur during a transurethral resection of the prostate (TURP). The syndrome is characterized by cardiocirculatory and neurological problems due to rapid changes in intravascular volume and plasma solute concentrations caused by excess irrigating fluid absorption. This article reviews the available literature and reports on the experience of our clinic, a specialist department in the physiopathology, diagnosis, therapy and prevention of TURP syndrome.
Impedance matching considering cross coupling for wireless power transfer to multiple receivers

In this paper, a method of impedance matching for wireless power transfer (WPT) to multiple receivers is presented considering cross coupling effects between non-adjacent coils. For maximizing power transfer efficiency, design of a source coil and optimal load impedance are achieved based on circuit analysis and mutual inductance calculation. For verification, a WPT system of a transmitter and three receivers is fabricated. The fabricated WPT system can obtain reflection coefficient of under -11 dB for the maximum three receivers at once by using a circular single loop coil without capacitance compensation or additional impedance matching circuit. The simulated results show that the WPT system using the proposed method has more than 85% efficiency regardless of the number of receivers while efficiency for the conventional method is severely changed according to the number of the receivers. Measured results of the proposed method are consistent with calculation results.
Continuous monitoring of the sympatho-vagal balance through spectral analysis.

The activity of the autonomic nervous system is noninvasively studied by means of autoregressive (AR) frequency analysis of the heart-rate variability (HRV) signal. Some methods of noise rejection and robustness for AR recursive identification are presented that make on-line frequency analysis of the heart-rate variability signal more reliable. The performance of the algorithms is first tested through simulations, and then results obtained on real data during ischemic episodes are presented.
The Golden Hour: Improving the Stabilization of the Very Low Birth-Weight Infant

A term borrowed from emergency and cardiovascular medicine, the phrase “Golden Hour” refers to the first hour of an infant's life following delivery. The impact of implementation of a Golden Hour Protocol in a level III neonatal intensive care unit (NICU) for infants delivered at less than 28 weeks gestation was examined, with a focus on admission temperature, admission glucose, and time to the initiation of an intravenous glucose and amino acid administration. As part of a quality initiative project, data were collected before and after the implementation of the Golden Hour Protocol for infants born at less than 28 weeks gestational age from May 2008 through December 2011. Desired outcomes were admission axillary temperature within a range of 36.5°C to 37.4°C, admission glucose more than 50 mg/dL, and the initiation of a glucose and amino acid infusion within 1 hour of birth. Key components of the Golden Hour included the use of a protocolized script, which clearly defined the roles of the delivery room personnel, placing the infant in a polyethylene bag to prevent heat loss, the application of the isolette skin temperature probe within 10 minutes of age, and insertion of umbilical catheters before moving the infant from the resuscitation area to the NICU. Data were collected on 225 infants born less than 28 weeks gestation: 106 in the preprotocol group and 119 in the postprotocol group. Differences between the 2 groups were not statistically significant for birth weight and gestational age. There was a statistically significant difference in the number of infants with an admission temperature in-range (36.5°C–37.4°C) between the preprotocol and postprotocol infants (28.3% vs 49.6%; P = .002). There was a statistically significant difference in the incidence of admission glucose greater than 50 mg/dL between the pre- and postprotocol groups (55.7% vs 72%; P = .012). There was a highly statistically significant difference in the number of post–Golden Hour Protocol infants who received an intravenous administration of glucose and amino acids within 1 hour of life compared with the preprotocol group (61.3% vs 7%; P = 0.001). Our results suggest that the implementation of the Golden Hour Protocol can significantly improve the stabilization of infants delivered less than 28 weeks gestation.