Miracle-dz/UniFAR-FTUs huggingface dataset:
Outlier Detection with One-Class Classifiers from ML and KDD

The problem of outlier detection is well studied in the fields of Machine Learning (ML) and Knowledge Discovery in Databases (KDD). Both fields have their own methods and evaluation procedures. In ML, Support Vector Machines and Parzen Windows are well-known methods that can be used for outlier detection. In KDD, the heuristic local-density estimation methods LOF and LOCI are generally considered to be superior outlier-detection methods. Hitherto, the performances of these ML and KDD methods have not been compared. This paper formalizes LOF and LOCI in the ML framework of one-class classification and performs a comparative evaluation of the ML and KDD outlier-detection methods on real-world datasets. Experimental results show that LOF and SVDD are the two best-performing methods. It is concluded that both fields offer outlier-detection methods that are competitive in performance and that bridging the gap between both fields may facilitate the development of outlier-detection methods.
Insights into lava fountain eruptions at Mt. Etna by improved source location of the volcanic tremor

We analysed volcanic tremor recorded during ten lava fountain eruptions at Mount Etna volcano over the second half of 2011. The seis- mic signal, recorded by a network of 19 broadband stations, was corrected for site effects. The site amplification factors obtained for all the seismic stations were calculated using 18 regional earthquakes. To quantitatively estimate the goodness of the site correction, the vol- canic tremor source locations obtained by using site corrections were compared with those performed without such corrections. The seismic signal was filtered in two different frequency bands before applying correction: (i) the band 1-2 Hz, which contains most of the tremor energy, and (ii) the band 5-10 Hz, in which, likely due to scattering phenomena, the assumption of isotropic radiation behind the volcanic tremor source location method is valid. The results revealed that the seismic signal correction for site effects improved the tremor location results. Such improved tremor locations, together with volcanological and geodetic data, allowed us to identify two dis- tinct periods characterised by different tremor locations during lava fountains (July - August 20 and August 20 - November 15). Such differences were probably due to magma recharge phenomena, taking place during the former period.
Modeling Extractive Sentence Intersection via Subtree Entailment

Sentence intersection captures the semantic overlap of two texts, generalizing over paradigms such as textual entailment and semantic text similarity. Despite its modeling power, it has received little attention because it is difficult for non-experts to annotate. We analyze 200 pairs of similar sentences and identify several underlying properties of sentence intersection. We leverage these insights to design an algorithm that decomposes the sentence intersection task into several simpler annotation tasks, facilitating the construction of a high quality dataset via crowdsourcing. We implement this approach and provide an annotated dataset of 1,764 sentence intersections.
Gene Expression Profiling of B Cell Chronic Lymphocytic Leukemia Reveals a Homogeneous Phenotype Related to Memory B Cells

B cell–derived chronic lymphocytic leukemia (B-CLL) represents a common malignancy whose cell derivation and pathogenesis are unknown. Recent studies have shown that >50% of CLLs display hypermutated immunoglobulin variable region (IgV) sequences and a more favorable prognosis, suggesting that they may represent a distinct subset of CLLs which have transited through germinal centers (GCs), the physiologic site of IgV hypermutation. To further investigate the phenotype of CLLs, their cellular derivation and their relationship to normal B cells, we have analyzed their gene expression profiles using oligonucleotide-based DNA chip microarrays representative of ∼12,000 genes. The results show that CLLs display a common and characteristic gene expression profile that is largely independent of their IgV genotype. Nevertheless, a restricted number of genes (<30) have been identified whose differential expression can distinguish IgV mutated versus unmutated cases and identify them in independent panels of cases. Comparison of CLL profiles with those of purified normal B cell subpopulations indicates that the common CLL profile is more related to memory B cells than to those derived from naive B cells, CD5+ B cells, and GC centroblasts and centrocytes. Finally, this analysis has identified a subset of genes specifically expressed by CLL cells of potential pathogenetic and clinical relevance.
Hierarchical Deployment Optimization for Wireless Sensor Networks

Sensor nodes deployment is very crucial for wireless sensor networks (WSNs). Current methods are apt to enlarge the coverage by achieving a nearly even deployment with similar density in the whole network. However, in some specific applications, the even distribution may not satisfy the sensing requirements. This paper proposes a virtual force directed coevolutionary particle swarm optimization (VFCPSO) algorithm, which uses a combined objective function to achieve the tradeoff of coverage and energy consumption. By considering deployment as an optimization problem, VFCPSO is more reliable and flexible for WSNs, since it can satisfy the combined requirements instead of only enlarging coverage. For investigating the performance of different paradigms, centralized VFCPSO is extended to distributed VFCPSO, heterogeneous hierarchical VFCPSO and homogeneous hierarchical VFCPSO (Homo-H-VFCPSO), and the solution of preferential deployment in interested region is also analyzed. Simulation results show that the Homo-H-VFCPSO has the best performance, i.e., it is more efficient than other three VFCPSO algorithms and the VF-style algorithms in terms of computation time, coverage and efficient moving energy consumption. It is obvious that the Homo-H-VFCPSO has good global searching ability and scalability, and it can rapidly and effectively achieve the sensor nodes deployment in WSNs.
Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures

We show how a basic pairwise alignment procedure can be improved to more accurately align conserved structural regions, by using variable, position-dependent gap penalties that depend on secondary structure and by taking the consensus of a number of suboptimal alignments. These improvements, which are novel for structural alignment, are direct analogs of what is possible with normal sequences alignment. They are feasible for us since our basic structural alignment procedure, unlike others, is so similar to normal sequence alignment. We further present preliminary results that show how our procedure can be generalized to produce a multiple alignment of a family of structures. Our approach is based on finding a "median" structure from doing all possible pairwise alignments and then aligning everything to it.
Helminth Fauna in Captive European Gray Wolves (Canis lupus lupus) in Germany

Captive as well as free-ranging wolves, which are currently recolonizing Germany, may harbor a variety of gastrointestinal parasites. This study investigated endoparasites in captive European gray wolves (Canis lupus lupus) using coproscopical methods. Fecal samples were collected monthly between October 2012 and November 2013 from 18 wolf enclosures in 14 German zoological gardens, representing 72 individual wolves. In total, 1,041 fecal samples including 26 bulk samples were analyzed by the sedimentation and flotation method. The most frequently detected egg morphotypes included five nematodes [Ancylostomatidae (Ancylostoma or Uncinaria spp.), Toxocara canis, Toxascaris leonina, Trichuris vulpis, and Capillaria/Eucoleus spp. ], one cestode (Taeniidae) and one trematode (Alaria alata). 44.76% of all samples were positive for at least one of these egg morphotypes. Overall, Ancylostomatidae showed the highest frequency (30.84% of all samples), followed by Capillaria/Eucoleus spp. (19.88%), Toxocara canis (5.19%), taeniids (3.75%), Trichuris vulpis and Alaria alata (3.65% each), and Toxascaris leonina (1.25%). As fecal samples were collected from the environment and could not be assigned to individual wolves, sample results were combined per zoo and month. General linear mixed models were employed to analyze the effect of season and management factors on the occurrence of Ancylostomatidae, Capillaria/Eucoleus spp. , Toxocara canis and taeniids. No statistically significant effect of season was found, whereas anthelmintic treatment negatively affected Ancylostomatidae egg excretion. Detected parasites and their prevalences are comparable to previous studies on wolf parasitism conducted elsewhere in Europe. As many of the most prevalent helminths are of zoonotic importance, routine anthelmintic treatment of captive wolves should be recommended.
Energy efficiency of joint base station and relay sleeping in heterogeneous networks

Energy efficiency (EE) is an important criterion in devising emerging mobile networks. One of the techniques that has been proposed to reduce energy consumption of base stations (BSs) in cellular networks is BS sleep mode. In this work, the effect of sleep mode on throughput, coverage and EE of relay assisted heterogeneous cellular networks is analysed. A cooperative relay-BS sleep mode-based algorithm for heterogeneous networks is proposed and its performance analytically evaluated. It is shown that the proposed algorithm has a considerably higher EE compared with a homogeneous network without sleep mode or a heterogeneous network with relay-only sleep mode.
Hearing Voices and Listening to What They Say: The Importance of Voice Content in Understanding and Working With Distressing Voices

The content of auditory hallucinations is sometimes dismissed as having little diagnostic/therapeutic importance. There is growing evidence that voice content may be crucial to understanding and working therapeutically with this experience. The aim of the present study is to explore, in a general population sample, the content and impact of voice-hearers' auditory hallucinations. A self-selected sample of 154 participants completed questionnaires about voice-hearing. A subsample of 50 participants completed semi-structured interviews. Participants experienced a range of voice content of high personal relevance, with most experiencing both positive and negative content. Voice content was the only significant predictor of emotional distress and the strongest predictor of contact with mental health services. These findings suggest that content is an important characteristic of auditory hallucinations and should be explored with voice-hearers who find themselves in clinical settings.
The Returns to U.S. Congressional Seats in the Mid-19th Century 1

In many political economy models, endogenous \rents" from o±ce can cause large distortions in policy and even reduce economic growth. However, there is little systematic evidence about the actual magnitude of such rents. We have collected data on wealth for a large sample of individuals who served in the U.S. House of Representatives during the period 1845-1875, using the censuses of 1850, 1860 and 1870. We use this data to estimate the monetary returns to holding o±ce. We nd no evidence of large returns for the 1850's or late 1860's. We do nd evidence of signi cant returns for the early 1860's. This pattern suggests that although the returns to a seat in the House were low during \normal" times, they increased during the Civil War years { perhaps not coincidentally, a period of dramatically higher federal spending.
Stabilized Sparse Scaling Algorithms for Entropy Regularized Transport Problems

Scaling algorithms for entropic transport-type problems have become a very popular numerical method, encompassing Wasserstein barycenters, multi-marginal problems, gradient flows and unbalanced transport. However, a standard implementation of the scaling algorithm has several numerical limitations: the scaling factors diverge and convergence becomes impractically slow as the entropy regularization approaches zero. Moreover, handling the dense kernel matrix becomes unfeasible for large problems. To address this, we combine several modifications: A log-domain stabilized formulation, the well-known epsilon-scaling heuristic, an adaptive truncation of the kernel and a coarse-to-fine scheme. This permits the solution of larger problems with smaller regularization and negligible truncation error. A new convergence analysis of the Sinkhorn algorithm is developed, working towards a better understanding of epsilon-scaling. Numerical examples illustrate efficiency and versatility of the modified algorithm.
Prevalence of depression and anxiety disorders in HIV-positive outpatients in rural Tanzania

Abstract HIV/AIDS is associated with significant mental health morbidity in high-income countries, and depression associated with HIV/AIDS has been linked with faster disease progression and reduced drug adherence. However, research on mental health is scarce in sub-Saharan Africa where infection levels are highest. This cross-sectional study of 220 HIV-positive outpatients at a dedicated Tanzanian HIV/AIDS care centre assessed sociodemographics, clinical variables and prevalence of ICD-10 common mental health diagnoses via a standardised psychiatric questionnaire (the Clinical Interview Schedule – Revised). Depression or mixed anxiety and depression was identified in 15.5% of subjects, with 4.5% suffering from other anxiety disorders. This suggests routine HIV care in sub-Saharan Africa should include assessment and treatment of mental health issues.
Redundant and unique roles of retinol dehydrogenases in the mouse retina

Highly abundant short-chain alcohol dehydrogenases (RDHs) in the retina were assumed to be involved in the recycling of 11-cis-retinal chromophore in the visual cycle. Mutations in human RDH genes are associated with Fundus albipunctatus, a mild form of night blindness (RDH5) and an autosomal recessive, childhood-onset severe retinal dystrophy (RDH12). Rdh12 knockout mice were found to be susceptible to light-induced photoreceptor apoptosis, whereas Rdh5 and Rdh8 knockout mice displayed only delayed dark adaptation. However, each knockout mouse eventually regenerated normal levels of visual pigments, suggesting that RDHs compensate for each other in the visual cycle. Here, we established RDH double knockout (Rdh8−/−Rdh12−/−) and triple knockout (Rdh5−/−Rdh8−/−Rdh12−/−) mice generated on various genetic backgrounds including a rod α-transducin knockout to test cone function. RDH activity was severely reduced in Rdh8−/−Rdh12−/− retina extracts, whereas Rdh8−/− RDH activity was intermediate and Rdh12−/− RDH activity was reduced only slightly. Surprisingly, all multiple knockout mice produced sufficient amounts of the chromophore to regenerate rhodopsin and cone pigments in vivo. Three-month-old Rdh8−/−Rdh12−/− mice characteristically displayed a slowly progressing rod–cone dystrophy accompanied by accumulation of N-retinylidene-N-retinylethanolamine (A2E), a toxic substance known to contribute to retinal degeneration. A2E accumulation and retinal degeneration were prevented by application of retinylamine, a potent retinoid cycle inhibitor. The results suggest that RDH8 and RDH12 are dispensable in support of the visual cycle but appear to be key components in clearance of free all-trans-retinal, thereby preventing A2E accumulation and photoreceptor cell death.
Regulation of Pituitary MT1 Melatonin Receptor Expression by Gonadotrophin-Releasing Hormone (GnRH) and Early Growth Response Factor-1 (Egr-1): In Vivo and In Vitro Studies

Melatonin receptor expression exhibits profound developmental changes through poorly understood mechanisms. In mammals, a current model suggests that pubertal reactivation of gonadotrophin-releasing hormone (GnRH) secretion down-regulates MT1 melatonin receptors in pituitary gonadotroph cells, via the induction of early growth response factor-1 (EGR-1). Here we have examined this model by testing the hypotheses that inhibition of Mt1 expression by GnRH occurs directly in gonadotroph cells, can be reversed in adulthood by blockade of GnRH receptors, and requires EGR-1. We first confirmed the endogenous expression of Mt1 mRNA in the αT3-1 gonadotroph cell line. Stimulation of these cells with a GnRH agonist resulted in a rapid increase of Egr-1 mRNA expression, which peaked after 30–60 minutes, and a more prolonged elevation of nuclear EGR-1 immunoreactivity. Moreover, the GnRH agonist significantly decreased Mt1 mRNA. We then treated adult male rats with the GnRH antagonist cetrorelix or saline. After 4 weeks of daily injections, cetrorelix significantly reduced serum LH concentration and testis weight, with histological analysis confirming absence of spermatogenesis. Despite the successful inhibition of GnRH signalling, pituitary Mt1 expression was unchanged. Next we studied the proximal region of the rat Mt1 promoter. Consistent with previous work, over-expression of the transcription factor PITX-1 increased Mt1-luciferase reporter activity; this effect was dependent on the presence of consensus PITX-1 promoter binding regions. Over-expression of EGR-1 inhibited PITX-1-stimulated activity, even following mutation of the consensus EGR-1 binding site. Finally, we studied Egr1 −/− mice and observed no difference in pituitary Mt1 expression between Egr1 −/− and wild-type litter mates. This work demonstrates that GnRH receptor activation directly down-regulates Mt1 expression in gonadotroph cells. However, pituitary Mt1 expression in adults is unaltered by blockade of GnRH signalling or absence of EGR-1. Our data therefore suggest that melatonin receptor regulation by GnRH is not reversible in adulthood and doesn't require EGR-1.
TATR: target-aimed triangular routing algorithm for mobile ad hoc networks

In this paper, we propose a Target-Aimed Triangular Routing (TATR) protocol that uses global positioning system (GPS). The TATR uses geographical position information to achieve the minimum number of intermediate nodes that form a routing path and to create a progressive routing path that always aims for the target (destination) node. In entire networks, the routing path which is constructed by minimum number of the intermediate nodes can reduce an electric power consumption of nodes that do not participate in routing path. And the routing path that always aims for the target node prevents unnecessary increase of intermediate nodes. In this scheme, we first decide a projection-line, which is the line between the sender node and the target node, and then three types of route request (RREQ) packets are exchanged by a sender node and its neighboring nodes. The neighboring node with the largest shadow-line value is chosen as the next sender node. The routing path that used a TATR scheme minimized the number of intermediate nodes. Finally, simulation results show that the proposed TATR scheme can reduce the number of intermediate nodes in the routing path below that of location-aided routing (LAR).
In Vitro and In Vivo Differentiation of Progenitor Stem Cells Obtained After Mechanical Digestion of Human Dental Pulp

Human population is facing a revolutionary change in the demographic structure with an increasing number of elderly people requiring an unmet need to ensure a smooth aging process and dental care is certainly an important aspect that has to be considered. To date, dentistry has been conservative and the need of transferring the scientific models of regenerative dentistry into clinical practice is becoming a necessity. The aim of this study was to characterize the differentiation commitment (in vitro) and the clinical grafting ability (in vivo) of a population of progenitor stem cells obtained after mechanical digestion of dental pulp with an innovative system recently developed. This approach was successfully used in previous studies to obtain a clinical‐grade ready to use dental pulp fragments that could be grafted in autologous tissues to obtain bone. We are thus showing that micro grafts resulting from mechanical digestion contain stem cells with a mesenchymal phenotype, able to differentiate toward different cell types and to generate new bone in patients. We are providing data for the establishment of standardized and routinely oral surgery approaches, having outlined the cellular properties of human stem cells obtained from the dental pulp. This method can represent a valid tool for both regenerative medicine and tissue engineering purposes not only applicable to the cranio‐maxillofacial region but, likely, to different bone pathologies for a fastening and healing recovering of patients. J. Cell. Physiol. 232: 548–555, 2017. © 2016 Wiley Periodicals, Inc.
Flexibility in Research Designs in Empirical Software Engineering

Problem outline: It is common to classify empirical research designs as either qualitative or quantitative. Typically, particular research methods (e.g., case studies, action research, experiments and surveys) are associated with one or the other of these types of design. Studies in empirical software engineering (ESE) are often exploratory and often involve software developers and development organizations. As a consequence, it may be difficult to plan all aspects of the studies, and to be successful, ESE studies must often be designed to handle possible changes during the conduct of the study. A problem with the above classification is that it does not cater for flexibility in design. Position: This paper suggests viewing research in ESE along the axis of flexible and fixed designs, which is both orthogonal to the axis of quantitative and qualitative designs, and independent of the particular research method. According to the traditional view of ESE, changes to the research design in the course of a study are typically regarded as threats to the validity of the results. However, viewing the study designs as flexible, practical challenges can provide useful information. The validity of the results of studies with flexible research designs can be established by applying techniques that are traditionally used for qualitative designs. This paper urges an increased recognition of flexible designs in ESE and discusses techniques for establishing the trustworthiness in flexible designs.
Transformed Low-Rank Model for Line Pattern Noise Removal

This paper addresses the problem of line pattern noise removal from a single image, such as rain streak, hyperspectral stripe and so on. Most of the previous methods model the line pattern noise in original image domain, which fail to explicitly exploit the directional characteristic, thus resulting in a redundant subspace with poor representation ability for those line pattern noise. To achieve a compact subspace for the line pattern structure, in this work, we incorporate a transformation into the image decomposition model so that maps the input image to a domain where the line pattern appearance has an extremely distinct low-rank structure, which naturally allows us to enforce a low-rank prior to extract the line pattern streak/stripe from the noisy image. Moreover, the random noise is usually mixed up with the line pattern noise, which makes the challenging problem much more difficult. While previous methods resort to the spectral or temporal correlation of the multi-images, we give a detailed analysis between the noisy and clean image in both local gradient and nonlocal domain, and propose a compositional directional total variational and low-rank prior for the image layer, thus to simultaneously accommodate both types of noise. The proposed method has been evaluated on two different tasks, including remote sensing image mixed random-stripe noise removal and rain streak removal, all of which obtain very impressive performances.