Miracle-dz/UniFAR-FTUs huggingface dataset:
Scalable Recommendation with Hierarchical Poisson Factorization

We develop hierarchical Poisson matrix factorization (HPF), a novel method for providing users with high quality recommendations based on implicit feedback, such as views, clicks, or purchases. In contrast to existing recommendation models, HPF has a number of desirable properties. First, we show that HPF more accurately captures the long-tailed user activity found in most consumption data by explicitly considering the fact that users have finite attention budgets. This leads to better estimates of users' latent preferences, and therefore superior recommendations, compared to competing methods. Second, HPF learns these latent factors by only explicitly considering positive examples, eliminating the often costly step of generating artificial negative examples when fitting to implicit data. Third, HPF is more than just one method— it is the simplest in a class of probabilistic models with these properties, and can easily be extended to include more complex structure and assumptions. We develop a variational algorithm for approximate posterior inference for HPF that scales up to large data sets, and we demonstrate its performance on a wide variety of real-world recommendation problems—users rating movies, listening to songs, reading scientific papers, and reading news articles.
Differential Expression of Iron Acquisition Genes by Brucella melitensis and Brucella canis during Macrophage Infection

Brucella spp. cause chronic zoonotic disease often affecting individuals and animals in impoverished economic or public health conditions; however, these bacteria do not have obvious virulence factors. Restriction of iron availability to pathogens is an effective strategy of host defense. For brucellae, virulence depends on the ability to survive and replicate within the host cell where iron is an essential nutrient for the growth and survival of both mammalian and bacterial cells. Iron is a particularly scarce nutrient for bacteria with an intracellular lifestyle. Brucella melitensis and Brucella canis share ∼99% of their genomes but differ in intracellular lifestyles. To identify differences, gene transcription of these two pathogens was examined during infection of murine macrophages and compared to broth grown bacteria. Transcriptome analysis of B. melitensis and B. canis revealed differences of genes involved in iron transport. Gene transcription of the TonB, enterobactin, and ferric anguibactin transport systems was increased in B. canis but not B. melitensis during infection of macrophages. The data suggest differences in iron requirements that may contribute to differences observed in the lifestyles of these closely related pathogens. The initial importance of iron for B. canis but not for B. melitensis helps elucidate differing intracellular survival strategies for two closely related bacteria and provides insight for controlling these pathogens.
Evolving research trends in bioinformatics

The cross-disciplinary nature of bioinformatics entails co-evolution with other biomedical disciplines, whereby some bioinformatics applications become popular in certain disciplines and, in turn, these disciplines influence the focus of future bioinformatics development efforts. We observe here that the growth of computational approaches within various biomedical disciplines is not merely a reflection of a general extended usage of computers and the Internet, but due to the production of useful bioinformatics databases and methods for the rest of the biomedical scientific community. We have used the abstracts stored both in the MEDLINE database of biomedical literature and in NIH-funded project grants, to quantify two effects. First, we examine the biomedical literature as a whole and find that the use of computational methods has become increasingly prevalent across biomedical disciplines over the past three decades, while use of databases and the Internet have been rapidly increasing over the past decade. Second, we study the recent trends in the use of bioinformatics topics. We observe that molecular sequence databases are a widely adopted contribution in biomedicine from the field of bioinformatics, and that microarray analysis is one of the major new topics engaged by the bioinformatics community. Via this analysis, we were able to identify areas of rapid growth in the use of informatics to aid in curriculum planning, development of computational infrastructure and strategies for workforce education and funding.
Aortopexy as treatment for tracheo-bronchomalacia in children: An 18-year single-center experience*

Objectives: To define the factors influencing the outcome of aortopexy as management of tracheo-bronchomalacia. Design: A retrospective, single-center, observational, cohort study. Settings: Surgical services in a tertiary care hospital. Patients: One hundred five children who underwent an aortopexy for tracheo-bronchomalacia between 1990 and 2008. Interventions: None. Measurements and Main Results: Comorbidity (categorized into three groups), surgical approach, and location of malacia were reviewed and analyzed in relation to mortality, need for a second intervention, complications, time to extubation after surgery, intensive care unit stay, and clinical improvement. Median age at surgery was 24 wks (1 wk–541 wks). Two surgical approaches were used: median sternotomy (n = 46) and left anterior parasternal (n = 59). Long-term (>2 yrs) follow-up was available for 73 patients (median = 7.0 yrs [2–18 yrs]); 73% were asymptomatic, 18% had minor symptoms, and 9% needed either ventilation or tracheostomy. The overall mortality rate was 9%, of which one-third was airway-related. Multivariable analysis revealed that major comorbidities were a significant risk factor both for mortality and the need for further procedures (re-do surgery, tracheostomy, internal stents) in contrast to surgical approach and involvement of the bronchus. Intensive care unit stay and days of ventilation after surgery were also significantly higher in patients with major comorbidities. Conclusions: Aortopexy proved to be an effective treatment for most cases of tracheo-bronchomalacia, but major comorbidity was associated with an adverse outcome. Our data suggest that aortopexy should be considered in most cases of severe tracheo-bronchomalacia.
Mitochondrial DNA Variants Mediate Energy Production and Expression Levels for CFH, C3 and EFEMP1 Genes: Implications for Age-Related Macular Degeneration

Background Mitochondrial dysfunction is associated with the development and progression of age-related macular degeneration (AMD). Recent studies using populations from the United States and Australia have demonstrated that AMD is associated with mitochondrial (mt) DNA haplogroups (as defined by combinations of mtDNA polymorphisms) that represent Northern European Caucasians. The aim of this study was to use the cytoplasmic hybrid (cybrid) model to investigate the molecular and biological functional consequences that occur when comparing the mtDNA H haplogroup (protective for AMD) versus J haplogroup (high risk for AMD). Methodology/Principal Findings Cybrids were created by introducing mitochondria from individuals with either H or J haplogroups into a human retinal epithelial cell line (ARPE-19) that was devoid of mitochondrial DNA (Rho0). In cybrid lines, all of the cells carry the same nuclear genes but vary in mtDNA content. The J cybrids had significantly lower levels of ATP and reactive oxygen/nitrogen species production, but increased lactate levels and rates of growth. Q-PCR analyses showed J cybrids had decreased expressions for CFH, C3, and EFEMP1 genes, high risk genes for AMD, and higher expression for MYO7A, a gene associated with retinal degeneration in Usher type IB syndrome. The H and J cybrids also have comparatively altered expression of nuclear genes involved in pathways for cell signaling, inflammation, and metabolism. Conclusion/Significance Our findings demonstrate that mtDNA haplogroup variants mediate not only energy production and cell growth, but also cell signaling for major molecular pathways. These data support the hypothesis that mtDNA variants play important roles in numerous cellular functions and disease processes, including AMD.
Fidelity-Naturalness Evaluation of Single Image Super Resolution

We study the problem of evaluating super resolution methods. Traditional evaluation methods usually judge the quality of super resolved images based on a single measure of their difference with the original high resolution images. In this paper, we proposed to use both fidelity (the difference with original images) and naturalness (human visual perception of super resolved images) for evaluation. For fidelity evaluation, a new metric is proposed to solve the bias problem of traditional evaluation. For naturalness evaluation, we let humans label preference of super resolution results using pair-wise comparison, and test the correlation between human labeling results and image quality assessment metrics' outputs. Experimental results show that our fidelity-naturalness method is better than the traditional evaluation method for super resolution methods, which could help future research on single-image super resolution.
Decreased Levels of Circulating IL17-Producing CD161+CCR6+ T Cells Are Associated with Graft-versus-Host Disease after Allogeneic Stem Cell Transplantation

The C-type lectin-like receptor CD161 is a well-established marker for human IL17-producing T cells, which have been implicated to contribute to the development of graft-versus-host disease (GVHD) after allogeneic stem cell transplantation (allo-SCT). In this study, we analyzed CD161+ T cell recovery, their functional properties and association with GVHD occurrence in allo-SCT recipients. While CD161+CD4+ T cells steadily recovered, CD161hiCD8+ T cell numbers declined during tapering of Cyclosporine A (CsA), which can be explained by their initial growth advantage over CD161neg/lowCD8+ T cells due to ABCB1-mediated CsA efflux. Interestingly, occurrence of acute and chronic GVHD was significantly correlated with decreased levels of circulating CD161+CD4+ as well as CD161hiCD8+ T cells. In addition, these subsets from transplanted patients secreted high levels of IFNγ and IL17. Moreover, we found that CCR6 co-expression by CD161+ T cells mediated specific migration towards CCL20, which was expressed in GVHD biopsies. Finally, we demonstrated that CCR6+ T cells indeed were present in these CCL20+ GVHD-affected tissues. In conclusion, we showed that functional CD161+CCR6+ co-expressing T cells disappear from the circulation and home to GVHD-affected tissue sites. These findings support the hypothesis that CCR6+CD161-expressing T cells may be involved in the immune pathology of GVHD following their CCL20-dependent recruitment into affected tissues.
Spectral Regularization Algorithms for Learning Large Incomplete Matrices

We use convex relaxation techniques to provide a sequence of regularized low-rank solutions for large-scale matrix completion problems. Using the nuclear norm as a regularizer, we provide a simple and very efficient convex algorithm for minimizing the reconstruction error subject to a bound on the nuclear norm. Our algorithm Soft-Impute iteratively replaces the missing elements with those obtained from a soft-thresholded SVD. With warm starts this allows us to efficiently compute an entire regularization path of solutions on a grid of values of the regularization parameter. The computationally intensive part of our algorithm is in computing a low-rank SVD of a dense matrix. Exploiting the problem structure, we show that the task can be performed with a complexity linear in the matrix dimensions. Our semidefinite-programming algorithm is readily scalable to large matrices: for example it can obtain a rank-80 approximation of a 10(6) × 10(6) incomplete matrix with 10(5) observed entries in 2.5 hours, and can fit a rank 40 approximation to the full Netflix training set in 6.6 hours. Our methods show very good performance both in training and test error when compared to other competitive state-of-the art techniques.
Effects of E-beam treatment on the interfacial and mechanical properties of henequen/polypropylene composites

In the present study, chopped henequen natural fibers without and with surface modification by electron beam (E-beam) treatment were incorporated into a polypropylene matrix. Prior to composite fabrication, a bundle of raw henequen fibers were treated at various E-beam intensities from 10 kGy to 500 kGy. The effect of E-beam intensity on the interfacial, mechanical and thermal properties of randomly oriented henequen/polypropylene composites with the fiber contents of 40 vol% was investigated focusing on the interfacial shear strength, flexural and tensile properties, dynamic mechanical properties, thermal stability, and fracture behavior. Each characteristic of the material strongly depended on the E-beam intensity irradiated, showing an increasing or decreasing effect. The present study demonstrates that henequen fiber surfaces can be modified successfully with an appropriate dosage of electron beam and use of a low E-beam intensity of 10 kGy results in the improvement of the interfacial properties, flexural properties, tensile properties, dynamic mechanical properties and thermal stability of henequen/polypropylene composites.
Mechanochemical modeling of wound healing: Multiphysics finite element simulations

Angiogenesis consists of the growth of new blood vessels from the pre-existing vasculature. This phenomenon takes place in several biological processes, including wound healing. In this work, we present a mathematical model of angiogenesis applied to skin wound healing. The developed model includes biological (capillaries and fibroblasts), chemical (oxygen and angiogenic growth factor concentrations) and mechanical factors (cell traction forces and extracellular matrix deformation) that influence the evolution of the healing process. A novelty from previous works, apart from the coupling of angiogenesis and wound contraction, is the more realistic modelling of skin as a hyperelastic material. Large deformations are addressed using an updated Lagrangian approach. The coupled non-linear model is solved with the finite element method, and the process is studied over two wound geometries (circular and elliptical) of the same area. The results indicate that the elliptical wound vascularizes two days earlier than the circular wound but that they experience a similar contraction level, reducing its size by 25 %. C. Valero · E. Javierre · J. M. García-Aznar · M. J. Gómez-Benito Multiscale in Mechanical and Biological Engineering (M2BE), Aragón Institute of Engineering Research (I3A), University of Zaragoza, Campus Río Ebro, 50018 Zaragoza, Spain e-mail: claraval@unizar.es J. M. García-Aznar e-mail: jmgaraz@unizar.es M. J. Gómez-Benito e-mail: gomezmj@unizar.es E. Javierre (B) Centro Universitario de la Defensa, Academia General Militar, Ctra. Huesca s/n, 50090 Zaragoza, Spain e-mail: etelvina.javierre@unizar.es
Leukemic cell growth in SCID mice as a predictor of relapse in high-risk B-lineage acute lymphoblastic leukemia.

Mice with severe combined immunodeficiency (SCID) provide a model system to examine the in vivo homing, engraftment, and growth patterns of normal and malignant human hematopoietic cells. The relation between leukemic cell growth in this model and the treatment outcome in patients from whom cells were derived has not been established. Leukemic cells from 42 children with newly diagnosed high-risk B-lineage acute lymphoblastic leukemia were inoculated intravenously into CB.17 SCID mice. Mice were killed at 12 weeks or when they became moribund as a result of disseminated leukemia. All mice were necropsied and subjected to a series of laboratory studies to assess their burden of human leukemic cells. Twenty-three patients whose leukemic cells caused histopathologically detectable leukemia in SCID mice had a significantly higher relapse rate than the 19 patients whose leukemic cells did not (estimated 5-year event-free survival: 29.5% v 94.7%; 95% confidence intervals, 11.2% to 50.7% v 68.1% to 99.2%; P < .0001 by log-rank test). The occurrence of overt leukemia in SCID mice was was a highly significant predictor of patient relapse. The estimated instantaneous risk of relapse for patients whose leukemic cells caused overt leukemia in SCID mice was 21.5-fold greater than that for the remaining patients. Thus, growth of human leukemic cells in SCID mice is a strong and independent predictor of relapse in patients with newly diagnosed high-risk B-lineage acute lymphoblastic leukemia.
Psychotic Symptoms in Frontotemporal Dementia: Prevalence and Review

Background/Aims: Although most patients with frontotemporal dementia (FTD) present with neuropsychiatric symptoms, the frequency of psychotic symptoms is unclear. This study aims to determine the prevalence of psychotic symptoms in a large cohort of well-diagnosed and followed FTD patients compared to age-matched patients with Alzheimer’s disease (AD) and to further review the literature on psychosis in FTD. Methods: Delusions, hallucinations and paranoia were evaluated among 86 patients who met consensus criteria for FTD, had frontotemporal changes on functional neuroimaging and were followed for 2 years. They were compared to 23 patients with early-onset AD on a caregiver-administered psychiatric questionnaire. Results: Among the FTD patients, only 2 (2.3%) had delusions, 1 of whom had paranoid ideation; no FTD patient had hallucinations. This was significantly less than the AD patients, 4 (17.4%) of whom had delusions and paranoia. Other investigations fail to establish a significant association of psychosis with FTD. Conclusions: These findings, and a literature review, indicate that psychotic symptoms are rare in FTD, possibly due to limited temporal-limbic involvement in this disorder.
Post-Intoxication Inhibition of Botulinum Neurotoxin Serotype A within Neurons by Small-Molecule, Non-Peptidic Inhibitors

Botulinum neurotoxins (BoNTs) comprise seven distinct serotypes that inhibit the release of neurotransmitter across neuromuscular junctions, resulting in potentially fatal flaccid paralysis. BoNT serotype A (BoNT/A), which targets synaptosomal-associated protein of 25kDa (SNAP-25), is particularly long-lived within neurons and requires a longer time for recovery of neuromuscular function. There are currently no treatments available to counteract BoNT/A after it has entered the neuronal cytosol. In this study, we examined the ability of small molecule non-peptidic inhibitors (SMNPIs) to prevent SNAP-25 cleavage post-intoxication of neurons. The progressive cleavage of SNAP-25 observed over 5 h following 1 h BoNT/A intoxication was prevented by addition of SMNPIs. In contrast, anti-BoNT/A neutralizing antibodies that strongly inhibited SNAP-25 cleavage when added during intoxication were completely ineffective when added post-intoxication. Although Bafilomycin A1, which blocks entry of BoNT/A into the cytosol by preventing endosomal acidification, inhibited SNAP-25 cleavage post-intoxication, the degree of inhibition was significantly reduced versus addition both during and after intoxication. Post-intoxication application of SMNPIs, on the other hand, was nearly as effective as application both during and after intoxication. Taken together, the results indicate that competitive SMNPIs of BoNT/A light chain can be effective within neurons post-intoxication.
Identification and Functional Analysis of Delta-9 Desaturase, a Key Enzyme in PUFA Synthesis, Isolated from the Oleaginous Diatom Fistulifera

Oleaginous microalgae are one of the promising resource of nonedible biodiesel fuel (BDF) feed stock alternatives. Now a challenge task is the decrease of the long-chain polyunsaturated fatty acids (PUFAs) content affecting on the BDF oxidative stability by using gene manipulation techniques. However, only the limited knowledge has been available concerning the fatty acid and PUFA synthesis pathways in microalgae. Especially, the function of Δ9 desaturase, which is a key enzyme in PUFA synthesis pathway, has not been determined in diatom. In this study, 4 Δ9 desaturase genes (fD9desA, fD9desB, fD9desC and fD9desD) from the oleaginous diatom Fistulifera were newly isolated and functionally characterized. The putative Δ9 acyl-CoA desaturases in the endoplasmic reticulum (ER) showed 3 histidine clusters that are well-conserved motifs in the typical Δ9 desaturase. Furthermore, the function of these Δ9 desaturases was confirmed in the Saccharomyces cerevisiae ole1 gene deletion mutant (Δole1). All the putative Δ9 acyl-CoA desaturases showed Δ9 desaturation activity for C16∶0 fatty acids; fD9desA and fD9desB also showed desaturation activity for C18∶0 fatty acids. This study represents the first functional analysis of Δ9 desaturases from oleaginous microalgae and from diatoms as the first enzyme to introduce a double bond in saturated fatty acids during PUFA synthesis. The findings will provide beneficial insights into applying metabolic engineering processes to suppressing PUFA synthesis in this oleaginous microalgal strain.
A Geometric Preferential Attachment Model of Networks

We study a random graph Gn that combines certain aspects of geometric random graphs and preferential attachment graphs. The vertices of Gn are n sequentially generated points x 1, x 2, . , x n chosen uniformly at random from the unit sphere in ℝ3. After generating xt , we randomly connect that point to m points from those points in x 1, x 2, . , xt -1 that are within distance r of xt . Neighbors are chosen with probability proportional to their current degree, and a parameter a biases the choice towards self loops. We show that if m is sufficiently large, if r ≥ ln n/n 1/2-β for some constant β, and if α > 2, then with high probabilty (whp) at time n the number of vertices of degree k follows a power law with exponent α + 1. Unlike the preferential attachment graph, this geometric preferential attachment graph has small separators, similar to experimental observations of [Blandford et al. 03]. We further show that if m ≥ K ln n, for K sufficiently large, then Gn is connected and has diameter O(ln n/r) whp.
State-space solution to a minimum-entropy ℋ1-optimal control problem with a nested information constraint

State-space formulas are derived for the minimum-entropy ℋ∞ controller when the plant and controller are constrained to be block-lower-triangular. Such a controller exists if and only if: the corresponding unstructured problem has a solution, a certain pair of coupled algebraic Riccati equations admits a mutually stabilizing fixed point, and a pair of spectral radius conditions is met. The controller's observer-based structure is also discussed, and a simple numerical approach for solving the coupled Riccati equations is presented.