Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of Non-HIV and HIV Risk Factors on Survival in HIV-Infected Patients on HAART: A Population-Based Nationwide Cohort Study

Background We determined the impact of three factors on mortality in HIV-infected patients who had been on highly active antiretroviral therapy (HAART) for at least one year: (1) insufficient response to (HAART) and presence of AIDS-defining diseases, (2) comorbidity, and (3) drug and alcohol abuse and compared the mortality to that of the general population. Methodology/Principal Findings In a Danish nationwide, population-based cohort study, we used population based registries to identify (1) all Danish HIV-infected patients who started HAART in the period 1 January 1998–1 July 2009, and (2) a comparison cohort of individuals matched on date of birth and gender (N = 2,267 and 9,068, respectively). Study inclusion began 1 year after start of HAART. Patients were categorised hierarchically in four groups according to the three risk factors, which were identified before study inclusion. The main outcome measure was probability of survival from age 25 to 65 years. The probability of survival from age 25 to age 65 was substantially lower in HIV patients [0.48 (95% confidence interval (CI) 0.42–0.55)] compared to the comparison cohort [0.88 (0.86 to 0.90)]. However, in HIV patients with no risk factors (N = 871) the probability of survival was equivalent to that of the general population [0.86 (95% CI 0.77–0.92)]. In contrast, the probability of survival was 0.58 in patients with HIV risk factors (N = 704), 0.30 in patients with comorbidities (N = 479), and 0.03 in patients with drug or alcohol abuse (N = 313). Conclusions The increased risk of death in HIV-infected individuals is mainly attributable to risk factors that can be identified prior to or in the initial period of antiretroviral treatment. Mortality in patients without risk factors on a successful HAART is almost identical to that of the non–HIV-infected population.
Using a J2EE cluster for parallel computation of join queries in distributed databases

In here we consider the problem of parallel execution of Join operation by a J2EE cluster. J2EE clusters are intended for coarse-grain distributed processing of multiple queries/business transactions over the Web. Thus, the possibility of using a J2EE cluster for fine-grain parallel computations (parallel Joins in our case) is intriguing and of practical interest. We have developed a new variant of the SFR algorithm for parallel computation of Cartesian Product in Join operations and proved its optimality in terms of communication/execution-time tradeoffs via a simple lower bound. Our experimental results show that despite the fact that J2EE is considered to be a platform that uses a complex interfaces and software entities, such as various types of Java beans, J2EE clusters can be efficiently used to execute Join operation in parallel.
Topographical organization of pathways from somatosensory cortex through the pontine nuclei to tactile regions of the rat cerebellar hemispheres

The granule cell layer of the cerebellar hemispheres contains a patchy and noncontinuous map of the body surface, consisting of a complex mosaic of multiple perioral tactile representations. Previous physiological studies have shown that cerebrocerebellar mossy fibre projections, conveyed through the pontine nuclei, are mapped in registration with peripheral tactile projections to the cerebellum. In contrast to the fractured cerebellar map, the primary somatosensory cortex (SI) is somatotopically organized. To understand better the map transformation occurring in cerebrocerebellar pathways, we injected axonal tracers in electrophysiologically defined locations in Sprague–Dawley rat folium crus IIa, and mapped the distribution of retrogradely labelled neurons within the pontine nuclei using three‐dimensional (3‐D) reconstructions. Tracer injections within the large central upper lip patch in crus IIa‐labelled neurons located centrally in the pontine nuclei, primarily contralateral to the injected side. Larger injections (covering multiple crus IIa perioral representations) resulted in labelling extending only slightly beyond this region, with a higher density and more ipsilaterally labelled neurons. Combined axonal tracer injections in upper lip representations in SI and crus IIa, revealed a close spatial correspondence between the cerebropontine terminal fields and the crus IIa projecting neurons. Finally, comparisons with previously published three‐dimensional distributions of pontine neurons labelled following tracer injections in face receiving regions in the paramedian lobule (downloaded from http://www.rbwb.org) revealed similar correspondence. The present data support the coherent topographical organization of cerebro‐ponto‐cerebellar networks previously suggested from physiological studies. We discuss the present findings in the context of transformations from cerebral somatotopic to cerebellar fractured tactile representations.
Type III Einstein-Yang-Mills solutions

We construct two distinct classes of exact type III solutions of the D = 4 Einstein-Yang-Mills system. The solutions are embeddings of the non-Abelian plane waves in spacetimes in Kundt’s class. Reduction of the solutions to type N leads to generalized pp and Kundt waves. The geodesic equations are briefly discussed.
Regulatory Circuits That Enable Proliferation of the Fungus Candida albicans in a Mammalian Host

The human body harbors trillions of microorganisms—a rich and diverse microbiota that plays key roles in human health and disease. All three domains of life—eukaryotes, archaea, and bacteria—are represented in this large assembly of microbes. Among eukaryotes, fungi are particularly prominent residents of the human body. For example, 101 species belonging to 85 fungal genera have been found in the oral cavity of healthy people [1]. Similarly, . 200 fungal species (half of them novel or unnamed) representing at least 50 genera have been found in the murine gut [2]. By comparison, there are ,150 bacterial species (or phylotypes) inhabiting the mouths of healthy individuals [3] and ,500–1000 bacterial species in their intestines [4,5]. Although the methodologies differ, as do the classification schemes, it seems that the taxonomical diversity of the fungal component of the microbiota may not be so different from its bacterial counterpart, even though the latter has been much more heavily catalogued. With the exception of a handful of species, however, very little is known about the biology of the members of the human ‘‘mycobiome’’ (i.e., fungal microbiome) and even less about the interactions that they establish with the human host. In this review we focus on the most widely studied fungus that inhabits the human body, Candida albicans. Most, if not all, healthy adults carry this species asymptomatically in their gastrointestinal (GI) tract. Despite its status as a commensal microorganism, C. albicans is also a leading cause of mucosal disease in healthy hosts and systemic, life-threatening infections in individuals with debilitated immune systems, such as AIDS patients or people receiving chemotherapy. Not surprisingly, it is this ‘‘virulent’’ or ‘‘pathogenic’’ facet of C. albicans that has traditionally received the most attention from researchers. More recently, however, several laboratories have begun to explore the tactics that the fungus uses to proliferate in its more common niche, the mammalian gut. These studies have uncovered unexpected connections between the commensal and pathogenic lifestyles. We highlight some of these findings here.
The Role of Frizzled3 and Frizzled6 in Neural Tube Closure and in the Planar Polarity of Inner-Ear Sensory Hair Cells

In the mouse, Frizzled3 (Fz3) and Frizzled6 (Fz6) have been shown previously to control axonal growth and guidance in the CNS and hair patterning in the skin, respectively. Here, we report that Fz3 and Fz6 redundantly control neural tube closure and the planar orientation of hair bundles on a subset of auditory and vestibular sensory cells. In the inner ear, Fz3 and Fz6 proteins are localized to the lateral faces of sensory and supporting cells in all sensory epithelia in a pattern that correlates with the axis of planar polarity. Interestingly, the polarity of Fz6 localization with respect to the asymmetric position of the kinocilium is reversed between vestibular hair cells in the cristae of the semicircular canals and auditory hair cells in the organ of Corti. Vangl2, one of two mammalian homologs of the Drosophila planar cell polarity (PCP) gene van Gogh/Strabismus, is also required for correct hair bundle orientation on a subset of auditory sensory cells and on all vestibular sensory cells. In the inner ear of a Vangl2 mutant (Looptail; Lp), Fz3 and Fz6 proteins accumulate to normal levels but do not localize correctly at the cell surface. These results support the view that vertebrates and invertebrates use similar molecular mechanisms to control a wide variety of PCP-dependent developmental processes. This study also establishes the vestibular sensory epithelium as a tractable tissue for analyzing PCP, and it introduces the use of genetic mosaics for determining the absolute orientation of PCP proteins in mammals.
Predicting entrepreneurial intention across the university

Purpose The purpose of this paper is to quantify the relative importance of four key entrepreneurial characteristics identified in the literature (proactiveness, attitude to risk, innovativeness and self-efficacy) in predicting students’ entrepreneurial intention (EI) across a range of faculties offering different subjects at a UK higher education institution (HEI). This approach will help to identify whether there are variations across the faculties in the predictors of EI. This enables recommendations to be made with regard to the development of educational delivery and support to encourage and develop the specific predictors of EI within the different subject areas. Design/methodology/approach This research uses a 40-item questionnaire to obtain information on students’ demographics, entrepreneurial characteristics and EI, based on a five-point Likert-type scale. Principle component analysis, correlation analysis and multiple hierarchical regression analysis are used to analyse the data from 1,185 students to develop models which predict EI for each of the six faculties. Findings Individual models which predict EI are developed for each of the six faculties showing variations in the makeup of the predictors across faculties in the HEI. Attitude to risk was the strongest predictor in five of the six faculties and the second strongest predictor in the sixth. The differences, together with the implications, for educational approaches and pedagogy are considered. Originality/value This research breaks down the level of analysis of EI to the individual faculty level in order to investigate whether different entrepreneurial characteristics predict EI in different academic disciplines across a UK HEI. This enables entrepreneurship educational approaches to be considered at a faculty level rather than a one size fits all approach.
A Package Recommendation Framework for Trip Planning Activities

Classical recommender systems provide users with ranked lists of recommendations, where each one consists of a single item. However, these ranked lists are not suitable for applications such as trip planning, which deal with heterogeneous items. In this paper, we focus on the problem of recommending a set of packages to the user, where each package is constituted with a set of different Points of Interest that may constitute a tour. Given a collection of POIs, our goal is to recommend the most interesting packages for the user, where each package satisfies the budget constraints. We formally define the problem and we present a novel composite recommendation system, inspired from composite retrieval. Experimental evaluation of our proposed system, using a real-world dataset demonstrates its quality and its ability to improve both diversity and relevance of recommendations.
Contribution to a theory of database reverse engineering

Both a general framework and specific techniques for file and database reverse engineering (recovering its conceptual schema) are proposed. The framework relies on a process/product model that matches formal as well as empirical design procedures. Based on the analysis of database design processes, two major phases are defined, i.e., data structure extraction and data structure conceptualization. For each of them, a set of activities is proposed. Most of these activities can be described as transformation and integration of specifications. <<ETX>>
SPARTA: Scalable Per-Address RouTing Architecture ∗

Modern data centers demand network features that current network designs struggle to meet. For example, layer-2 Ethernet networks provide the ﬂexibility and ease of conﬁguration that network operators want, but they scale poorly and make poor use of available bandwidth. Layer-3 IP networks can provide better scalability and bandwidth, but are less ﬂexible and are more difﬁcult to conﬁgure and manage.
Characterizing Algebraic Invariants by Differential Radical Invariants (CMU-CS-13-129)

We prove that any invariant algebraic set of a given polynomial vector field can be algebraically represented by one polynomial and a finite set of its successive Lie derivatives. This so-called differential radical characterization relies on a sound abstraction of the reachable set of solutions by the smallest variety that contains it. The characterization leads to a differential radical invariant proof rule that is sound and complete, which implies that invariance of algebraic equations over real-closed fields is decidable. Furthermore, the problem of generating invariant varieties is shown to be as hard as minimizing the rank of a symbolic matrix, and is therefore NP-hard. We investigate symbolic linear algebra tools based on Gaussian elimination to efficiently automate the generation. The approach can, e.g., generate nontrivial algebraic invariant equations capturing the airplane behavior during take-off or landing in longitudinal motion.
Randomized, controlled trial of behavior therapy for families of adolescents with insulin-dependent diabetes mellitus.

OBJECTIVE To describe the short-term results of a controlled trial of Behavioral Family Systems Therapy (BFST) for families of adolescents with diabetes. METHODS We randomized 119 families of adolescents with diabetes to 3 months' treatment with either BFST, an education and support Group (ES), or current therapy (CT). Family relationships, psychological adjustment to diabetes, treatment adherence and diabetic control were assessed at baseline, after 3 months of treatment (reported here), and 6 and 12 months later. RESULTS Compared with CT and ES, BFST yielded more improvement in parent-adolescent relations and reduced diabetes-specific conflict. Effects on psychological adjustment to diabetes and diabetic control were less robust and depended on the adolescent's age and gender. There were no effects on treatment adherence. CONCLUSIONS BFST yielded some improvement in parent-adolescent relationships; its effects on diabetes outcomes depended on the adolescent's age and gender. Factors mediating the effectiveness of BFST must be clarified.
A Review of Student Modeling Techniques in Intelligent Tutoring Systems

In this paper, we survey techniques used in intelligent tutoring systems (ITSs) to model student knowledge. The three techniques that we review in detail are knowledge tracing, performance factor analysis, and matrix factorization. We also briefly cover other techniques that have been used. This review is meant to be a repository of knowledge for those who want to integrate these techniques into serious games. It is also meant to increase awareness and interest as to the techniques available that can be integrated into serious games.
Leo Finkle: The Embodiment of Spiritual Rebirth in “The Magic Barrel”

Leo Finkle, the protagonist in Jewish American author Bernard Malamud’s famous short story “The Magic Barrel”, is a representative embodiment of universal spiritual rebirth, especial for the Jewish people who have suffered a lot in their specific history and culture. In his writing, Astro (1977) once remarks, “Malamud often uses a prison motif to evoke any place or circumstance which restricts man’s freedom of development”. The severity of his characters’ suffering is a necessity — only great affliction can bring out their hidden spiritual force and their understanding of their own capacity for dignity and compassion. Leo Finkle, realizing his own dignity and his responsibility to others, comes out of his isolated zone and steps out to achieve his own spiritual rebirth. Based on psychoanalysis, this paper attempts to address inward struggles of Leo Finkle, an epitome of all humankind, and explore how he achieves his spiritual rebirth when he is confronted with conflicting reality, through which, we can also have a profound understanding of Malamud’s humanist care not only for Jewish people, but also for all human beings, that is to say, his concern about universal humanities such as mercy, redemption, spiritual rebirth so on and so forth. In this way, we may pay more attention to Jewish people and other marginalized social groups in today’s society.
Finding Unusual Medical Time-Series Subsequences: Algorithms and Applications

In this work, we introduce the new problem of finding time series discords. Time series discords are subsequences of longer time series that are maximally different to all the rest of the time series subsequences. They thus capture the sense of the most unusual subsequence within a time series. While discords have many uses for data mining, they are particularly attractive as anomaly detectors because they only require one intuitive parameter (the length of the subsequence), unlike most anomaly detection algorithms that typically require many parameters. While the brute force algorithm to discover time series discords is quadratic in the length of the time series, we show a simple algorithm that is three to four orders of magnitude faster than brute force, while guaranteed to produce identical results. We evaluate our work with a comprehensive set of experiments on electrocardiograms and other medical datasets
Apathy symptom profile and behavioral associations in frontotemporal dementia vs dementia of Alzheimer type.

BACKGROUND Apathy is a common and significant problem in patients with dementia, regardless of its cause. Observations about frontosubcortical circuit syndromes indicate that apathy may have affective, behavioral, or cognitive manifestations. OBJECTIVES To explore whether the apathy manifested in frontotemporal dementia (FTD), with its predominantly anterior brain neuropathologic features, differs from the apathy in dementia of Alzheimer type (DAT), with its predominantly hippocampal- and temporoparietal-based neuropathologic features, and to determine whether other behavioral disturbances reported in frontosubcortical circuit syndromes correlate with apathy. DESIGN Analyses included individual items within Neuropsychiatric Inventory subscale items. Items of the apathy/indifference subscale were designated by consensus as affective (lacking in emotions), behavioral (inactive, chores abandoned), or cognitive (no interest in the activities of others). Proportions of correlated nonapathy Neuropsychiatric Inventory items were calculated. SETTING Several neurology specialty clinics contributed to our data set. PARTICIPANTS A total of 92 participants with FTD and 457 with DAT. MAIN OUTCOME MEASURES The Neuropsychiatric Inventory was analyzed. RESULTS Apathy was more prevalent in patients with FTD than in those with DAT, but when present, the specific apathy symptoms associated with both types of dementia were rarely restricted to 1 of the 3 domains of apathy. Dysphoria concurrent with apathy was unique to the DAT group and negatively correlated in the FTD group. Participants with affective apathy more frequently copresented with an orbital frontosubcortical syndrome in FTD (impulsivity and compulsions). Affective apathy also copresented with uncooperative agitation, anger, and physical agitation in both types of dementia. CONCLUSIONS Apathy is common in patients with FTD and DAT, although it is more common in those with FTD. When present, it usually involves changes in affect, behavior, and cognition. It is associated with behaviors that have previously been shown to affect patient safety, independence, and quality of life.
Proteomic Profile of Reversible Protein Oxidation Using PROP, Purification of Reversibly Oxidized Proteins

Signal transduction pathways that are modulated by thiol oxidation events are beginning to be uncovered, but these discoveries are limited by the availability of relatively few analytical methods to examine protein oxidation compared to other signaling events such as protein phosphorylation. We report here the coupling of PROP, a method to purify reversibly oxidized proteins, with the proteomic identification of the purified mixture using mass spectrometry. A gene ontology (GO), KEGG enrichment and Wikipathways analysis of the identified proteins indicated a significant enrichment in proteins associated with both translation and mRNA splicing. This methodology also enabled the identification of some of the specific cysteine residue targets within identified proteins that are reversibly oxidized by hydrogen peroxide treatment of intact cells. From these identifications, we determined a potential consensus sequence motif associated with oxidized cysteine residues. Furthermore, because we identified proteins and specific sites of oxidation from both abundant proteins and from far less abundant signaling proteins (e.g. hepatoma derived growth factor, prostaglandin E synthase 3), the results suggest that the PROP procedure was efficient. Thus, this PROP-proteomics methodology offers a sensitive means to identify biologically relevant redox signaling events that occur within intact cells.
Adrenal hormones suppress cell division in the adult rat dentate gyrus

The rat dentate gyrus is unusual among mammalian brain regions in that it shows cell birth well into adulthood. During development, dentate gyrus cell birth is regulated by adrenal steroids. However, it is presently unknown whether cell division in the adult is also mediated by these same factors. In order to determine whether this is the case, we combined adrenalectomy, with or without corticosterone (CORT) replacement, and 3H-thymidine autoradiography, Nissl staining, and immunohistochemistry for the glial cell markers vimentin and glial fibrillary acidic protein (GFAP) as well as for the neuronal marker neuron-specific enolase. Removal of circulating adrenal steroids resulted in a greater density of both GFAP-immunoreactive and vimentin- immunoreactive cells compared to sham-operated animals; CORT replacement prevented increases in both of these cell types. The increase in the density of vimentin-immunoreactive cells probably resulted from an increase in the birth of these cells, as adrenalectomized rats showed greater numbers of 3H-thymidine-labeled vimentin-positive cells compared to sham rats. In contrast, no changes in the number of 3H-thymidine-labeled GFAP-positive cells were observed with adrenalectomy, indicating that the increase in this cell type probably does not involve cell birth. In addition, the density of 3H- thymidine-labeled cells that were not immunoreactive for either glial cell marker and that showed neuronal characteristics was dramatically increased with adrenalectomy. These results suggest that adrenal hormones normally suppress the birth of both glia and neurons in the adult rat dentate gyrus.