Miracle-dz/UniFAR-FTUs huggingface dataset:
Using Entropy Estimates for DAG-Based Ontologies

Motivation: Entropy measurements on hierarchical structures have been used in methods for information retrieval and natural language modeling. Here we explore its application to semantic similarity. By finding shared ontology terms, semantic similarity can be established between annotated genes. A common procedure for establishing semantic similarity is to calculate the descriptiveness (information content) of ontology terms and use these values to determine the similarity of annotations. Most often information content is calculated for an ontology term by analyzing its frequency in an annotation corpus. The inherent problems in using these values to model functional similarity motivates our work. Summary: We present a novel calculation for establishing the entropy of a DAG-based ontology, which can be used in an alternative method for establishing the information content of its terms. We also compare our IC metric to two others using semantic and sequence similarity.
ON THE DIRICHLET PROBLEMS FOR SYMMETRIC FUNCTION EQUATIONS OF THE EIGENVALUES OF THE COMPLEX HESSIAN

Also Γk is symmetric in λ = (λ1, · · · , λn), which means that if λ = (λ1, · · · , λn) ∈ Γk, then λ̃ = (λi1 , · · · , λin) ∈ Γk where (i1, i2, · · · , in) is any permutation of 1, 2, · · · , n. We say that u is plurisubharmonic in D if λ(H(u)(z)) ∈ Γn, for all z ∈ D; we say that u is subharmonic in D if λ(H(u)(z)) ∈ Γ1 for all z ∈ D. We will let Γ be a convex cone which is symmetric in λ ∈ Γ, with vertex 0 so that Γn ⊆ Γ ⊆ Γ1. Let M(n,Γ) be subset of all n × n hermitian matices H over C so that λ(H) ∈ Γ where λ(H) is a vector in IR being formed by all eigenvalues of H. We will consider more general symmetric function than the kth symmetric function σ on M(n,Γ). Let D be a bounded domain in C with smooth boundary ∂D. We say that a real-valued function u is Γ-subharmonic if λ(H(u)(z)) ∈ Γ for all z ∈ D. we will consider the Dirichlet problem for a functional equation:
A new approach to evaluating novel recommendations

This paper presents two methods, named Item- and User-centric, to evaluate the quality of novel recommendations. The former method focuses on analyzing the item-based recommendation network. The aim is to detect whether the network topology has any pathology that hinders novel recommendations. The latter, user-centric evaluation, aims at measuring users' perceived quality of novel, previously unknown, recommendations. The results of the experiments, done in the music recommendation context, show that last.fm social recommender, based on collaborative filtering, is prone to popularity bias. This has direct consequences on the topology of the item-based recommendation network. Pure audio content-based methods (CB) are not affected by popularity. However, a user-centric experiment done with 288 subjects shows that even though a social-based approach recommends less novel items than our CB, users' perceived quality is better than those recommended by a pure CB method.
Tirilazad Mesylate Does Not Improve Early Cerebral Metabolic Recovery Following Compression Ischemia in Dogs

Background and Purpose: Tirilazad mesylate (U74006F) has been reported to improve recovery following cerebral ischemia. We conducted a randomized blinded study to determine if the drug would improve immediate metabolic recovery after complete cerebral compression ischemia. Methods: Mongrel dogs were anesthetized with pentobarbital and fentanyl and treated with either vehicle (citrate buffer, n=8) or tirilazad (1.5 mg/kg i.v. plus 0.18 mg/kg/hr, n=8). Normothermic complete cerebral compression ischemia was produced for 12 minutes by lateral ventricular fluid infusion to raise intracranial pressure above systolic arterial pressure. Cerebral high‐energy phosphate concentrations and intracellular pH were measured by phosphorus magnetic resonance spectroscopy. Cerebral blood flow was measured with radiolabeled microspheres, and oxygen consumption was calculated from sagittal sinus blood samples. Somatosensory evoked potentials were measured throughout the experiment. Results: During ischemia, both groups demonstrated complete loss of high‐energy phosphates and a fall in intracellular pH (vehicle, 5.76±0.23; tirilazad, 5.79±0.26; mean±SEM). At 180 minutes of reperfusion, there were no differences between groups in recovery of intracellular pH (vehicle, 6.89±0.07; tirilazad, 6.88±0.18), phosphocreatine concentration (vehicle, 89±16%; tirilazad, 94±24% of baseline value), oxygen consumption (vehicle, 2.6±0.2 ml/min/100 g; tirilazad, 1.8±0.5 ml/min/100 g), or somatosensory evoked potential amplitude (vehicle, 11±6%; tirilazad, 7±4% of baseline value). Forebrain blood flow fell below baseline levels at 180 minutes of reperfusion in the tirilazad‐treated animals but not in the vehicle‐treated dogs (vehicle, 28±4 ml/min/100 g; tirilazad, 18±5 ml/min/100 g). Conclusions: We conclude that tirilazad pretreatment does not improve immediate metabolic recovery 3 hours following 12 minutes of normothermic complete ischemia produced by cerebral compression. (Stroke 1992;23:1479‐1486)
Socioeconomic differences in children’s television viewing trajectory: A population-based prospective cohort study

We aimed to evaluate the association between family socioeconomic status and repeatedly measured child television viewing time from early childhood to the school period. We analyzed data on 3,561 Dutch children from the Generation R Study, a population-based study in the Netherlands. Parent-reported television viewing time for children aged 2, 3, 4, 6 and 9 years were collected by questionnaires sent from April 2004 until January 2015. Odds ratios of watching television ≥1 hour/day at each age were calculated for children of mothers with low, mid-low, mid-high and high (reference group) education and children from low, middle and high (reference group) income households. A generalized logistic mixed model was used to assess the association between family socioeconomic status and child television viewing time trajectory. The percentage of children watching television ≥1 hour/day increased from age 2 to 9 years for all children (24.2%-85.0% for children of low-educated mothers; 4.7%-61.4% for children of high-educated mothers; 17.2%-74.9% for children from low income households; 6.2%-65.1% for children from high income households). Independent socioeconomic effect in child television viewing time was found for maternal educational level. The interaction between net household income and child age in longitudinal analyses was significant (p = 0.01), indicating that the television viewing time trajectories were different in household income subgroups. However the interaction between maternal educational level and child age was not significant (p = 0.19). Inverse socioeconomic gradients in child television viewing time were found from the preschool period to the late school period. The educational differences between the various educational subgroups remained stable with increasing age, but the differences between household income groups changed over time. Intervention developers and healthcare practitioners need to raise awareness among non-highly educated parents that the socioeconomic gradient in television viewing time has a tracking effect starting from preschool age.
Linking biomechanics and ecology through predator–prey interactions: flight performance of dragonflies and their prey

SUMMARY Aerial predation is a highly complex, three-dimensional flight behavior that affects the individual fitness and population dynamics of both predator and prey. Most studies of predation adopt either an ecological approach in which capture or survival rates are quantified, or a biomechanical approach in which the physical interaction is studied in detail. In the present study, we show that combining these two approaches provides insight into the interaction between hunting dragonflies (Libellula cyanea) and their prey (Drosophila melanogaster) that neither type of study can provide on its own. We performed >2500 predation trials on nine dragonflies housed in an outdoor artificial habitat to identify sources of variability in capture success, and analyzed simultaneous predator–prey flight kinematics from 50 high-speed videos. The ecological approach revealed that capture success is affected by light intensity in some individuals but that prey density explains most of the variability in success rate. The biomechanical approach revealed that fruit flies rarely respond to approaching dragonflies with evasive maneuvers, and are rarely successful when they do. However, flies perform random turns during flight, whose characteristics differ between individuals, and these routine, erratic turns are responsible for more failed predation attempts than evasive maneuvers. By combining the two approaches, we were able to determine that the flies pursued by dragonflies when prey density is low fly more erratically, and that dragonflies are less successful at capturing them. This highlights the importance of considering the behavior of both participants, as well as their biomechanics and ecology, in developing a more integrative understanding of organismal interactions.
Change for the Better ? Linking the Mechanisms of Deliberative Opinion Change to Normative Theory

The case for institutional deliberative reform does not go through unless we assume that it changes opinions via mechanisms congruent with normative theories of deliberation. Yet little research addresses this assumption head-on. I bridge deliberative theory and practice by making explicit several causal claims implicit in the theory literature, and then testing them in three policy domains. I use hierarchical statistical techniques to more adequately model the intrinsic dependence of deliberative data, and include social network effects to test interpersonal paths of influence. The results provide substantial, though qualified, support for several of deliberative theory’s claims.
Opportunistic intestinal protozoal infections in immunocompromised children.

Hundred immunocompromised children and 100 house contact controls were chosen. Patients included: 52 nephrotic syndrome children receiving corticosteroids for more than one month (age 5.28 +/- 2.32 years), 14 protein-calorie malnutrition (PCM) patients (8 cases of marasmus aged 6 +/- 2.27 months and 6 cases of marasmic kwashiorkor aged 1.39 +/- 0.88 years) and 34 lymphomas patients (22 cases of Hodgkin's disease and 12 cases of non-Hodgkin's lymphoma; age 4.5 +/- 3.54 years). Examination of concentrated stool was done using iodine stain of fresh mounts and modified Ziehl-Neelsen (cold acid-fast) to fixed smears. T-cell subsets were counted after staining with mouse monoclonal antibodies against CD4 and CD8 labeled with fluorescein. Both nephrotic syndrome and lymphomas groups showed affection of cellular immunity in the form of significant decrease in T-helper and H/S ratio and significant increase in suppressor T-cell subsets. Giardia lamblia, Entamoeba histolytica, Cryptosporidium parvum and Blastocystis hominis were the most frequent in patients group and were significantly more prevalent among patients than controls. No significant difference in the prevalence of Entamoeba coli and Chylomastix mesnili between the two groups. C. parvum infection were strictly confined to groups with T-cell subsets abnormalities i.e. nephrotic syndrome and lymphomas groups.
Population Genetics of Rare Variants and Complex Diseases

Objectives: Identifying drivers of complex traits from the noisy signals of genetic variation obtained from high-throughput genome sequencing technologies is a central challenge faced by human geneticists today. We hypothesize that the variants involved in complex diseases are likely to exhibit non-neutral evolutionary signatures. Uncovering the evolutionary history of all variants is therefore of intrinsic interest for complex disease research. However, doing so necessitates the simultaneous elucidation of the targets of natural selection and population-specific demographic history. Methods: Here we characterize the action of natural selection operating across complex disease categories, and use population genetic simulations to evaluate the expected patterns of genetic variation in large samples. We focus on populations that have experienced historical bottlenecks followed by explosive growth (consistent with many human populations), and describe the differences between evolutionarily deleterious mutations and those that are neutral. Results: Genes associated with several complex disease categories exhibit stronger signatures of purifying selection than non-disease genes. In addition, loci identified through genome-wide association studies of complex traits also exhibit signatures consistent with being in regions recurrently targeted by purifying selection. Through simulations, we show that population bottlenecks and rapid growth enable deleterious rare variants to persist at low frequencies just as long as neutral variants, but low-frequency and common variants tend to be much younger than neutral variants. This has resulted in a large proportion of modern-day rare alleles that have a deleterious effect on function and that potentially contribute to disease susceptibility. Conclusions: The key question for sequencing-based association studies of complex traits is how to distinguish between deleterious and benign genetic variation. We used population genetic simulations to uncover patterns of genetic variation that distinguish these two categories, especially derived allele age, thereby providing inroads into novel methods for characterizing rare genetic variation driving complex diseases.
Structural Insights into the Human Metapneumovirus Glycoprotein Ectodomain

ABSTRACT Human metapneumovirus is a major cause of respiratory tract infections worldwide. Previous reports have shown that the viral attachment glycoprotein (G) modulates innate and adaptive immune responses, leading to incomplete immunity and promoting reinfection. Using bioinformatics analyses, static light scattering, and small-angle X-ray scattering, we show that the extracellular region of G behaves as a heavily glycosylated, intrinsically disordered polymer. We discuss potential implications of these findings for the modulation of immune responses by G.
Feminist, Queer, Crip by Alison Kafer (review)

In myriad cultural sites, the sexual pleasures and politics of disabled bodies have been avoided, disciplined, or discouraged. Highlighting the pervasive desexualization of disability, queer/crip activists have criticized the alignment of heteronormativity with “compulsory able-bodiedness,” politicized pain, valued diverse embodiments, and reveled in the spatial and embodied pleasures of new crip “sexual geographies. ” However, access to sex isn’t just a question of pleasure or personhood. It is also a critical question of futurity, according to Alison Kafer’s Feminist, Queer, Crip. A defiant claiming of crip futures, Feminist, Queer, Crip makes theoretical contributions to a dizzying array of fields, including feminist theory, environmental studies, queer theory, transgender studies, disability studies, and bioethics. Mining a diverse archive that includes inspirational billboards, newspapers, websites, literature, and cultural theory, Kafer argues that disability is often discursively constructed as an apolitical obstacle to futurity, which is usually imagined in terms of reproductive capacity, sexual intimacy, development, progress, or utopianism. Her first four chapters form a quartet that assess how images of disability, often under the guise of inclusion, are deployed in service to moralizing commonsense visions of “the good life. ” Kafer intervenes into wellestablished queer scholarship on temporality by positioning “crip time” in opposition to a future-oriented “curative imaginary,” her term for a broad cultural disposition that only imagines disability in terms of medical intervention and eventual elimination. Rather than imagining disability as “no future,” to use Lee Edelman’s phrase, Kafer strives for “accessible futures” that consider disability as a unique and valuable orientation to temporality. For instance, her first chapter poses many temporal questions, including how chronic illness alters normative timelines, how aging as a temporal experience overlaps with disability, or how aspects of queer temporality, such as Judith Halberstam’s “eccentric economic practices” or “imaginative life schedules,” also encompass crip experiences of time. ((( BOOK REVIEW
The Stability of Low-Rank Matrix Reconstruction: A Constrained Singular Value View

The stability of low-rank matrix reconstruction with respect to noise is investigated in this paper. The <formula formulatype="inline"><tex Notation="TeX">$\ell _{\ast}$</tex></formula>-constrained minimal singular value (<formula formulatype="inline"> <tex Notation="TeX">$\ell _{\ast}$</tex></formula>-CMSV) of the measurement operator is shown to determine the recovery performance of nuclear norm minimization-based algorithms. Compared with the stability results using the matrix restricted isometry constant, the performance bounds established using <formula formulatype="inline"><tex Notation="TeX">$\ell _{\ast}$</tex></formula>-CMSV are more concise, and their derivations are less complex. Isotropic and subgaussian measurement operators are shown to have <formula formulatype="inline"><tex Notation="TeX">$\ell _{\ast}$</tex></formula>-CMSVs bounded away from zero with high probability, as long as the number of measurements is relatively large. The <formula formulatype="inline"> <tex Notation="TeX">$\ell _{\ast}$</tex></formula>-CMSV for correlated Gaussian operators are also analyzed and used to illustrate the advantage of <formula formulatype="inline"><tex Notation="TeX">$\ell _{\ast}$</tex></formula>-CMSV compared with the matrix restricted isometry constant. We also provide a fixed point characterization of <formula formulatype="inline"><tex Notation="TeX">$\ell _{\ast}$</tex></formula>-CMSV that is potentially useful for its computation.
MP-Collaborator: A Mobile Collaboration Tool in Pervasive Environment

In modern organizations, the communication between collaborators is essential to improve productivity. There is a need for mobile collaboration tools that allow efficient collaboration among staff in organization which may be located in different geographical areas and time zones. Mobile and pervasive computing provides easy and convenient access to information, enabling effective collaboration. This paper describes a context and location-aware mobile application, called MP-Collaborator, created to improve and optimize the communication between collaborators in any organization. MP Collaborator draws information from location, user status and Pocket Outlook Calendar to create a user availability profile, which is published to any other user in the network. Based on availability status, the user can be reached using a simple phone call or a message. Through the opportunistic use of available mobile technologies MP-Collaborator provides a simple but critical service - user presence service. The proposed solution is validated both in terms of features and communication through a series of experiments on real devices through Wi-Fi network.
Prophylactic thrombolysis by thrombin-activated latent prourokinase targeted to PECAM-1 in the pulmonary vasculature.

A recombinant prodrug, single-chain urokinase-type plasminogen activator (scuPA) fused to an anti-PECAM-1 antibody single-chain variable fragment (anti-PECAM scFv/scuPA) targets endothelium and augments thrombolysis in the pulmonary vasculature. (1) To avoid premature activation and inactivation and to limit systemic toxicity, we replaced the native plasmin activation site in scFv/low-molecular-weight (lmw)-scuPA with a thrombin activation site, generating anti-PECAM scFv/uPA-T that (1) is latent and activated by thrombin instead of plasmin; (2) binds to PECAM-1; (3) does not consume plasma fibrinogen; (4) accumulates in mouse lungs after intravenous injection; and (5) resists PA inhibitor PAI-1 until activated by thrombin. In mouse models of pulmonary thrombosis caused by thromboplastin and ischemia-reperfusion (I/R), scFv/uPA-T provided more potent thromboprophylaxis and greater lung protection than plasmin-sensitive scFv/uPA. Endothelium-targeted thromboprophylaxis triggered by a prothrombotic enzyme illustrates a novel approach to time- and site-specific regulation of proteolytic reactions that can be modulated for therapeutic benefit.
Clinical Scenario of the Metabolic Syndrome

The term metabolic syndrome (MeS) refers to a cluster of associated symptoms composed of impaired fasting glucose, abdominal obesity, hypertension, and dyslipidemia. MeS is associated with an increased risk of cardiovascular and diabetes-associated morbidity and mortality. The increased amount of visceral fat together with a chronic inflammatory state predisposes to the development of arteriosclerosis. Furthermore, insulin resistance (IR) and dyslipidemia are associated with fatty liver disease. In addition, MeS is linked to non-cardiovascular diseases such as cancer as well as psychiatric or endocrine disorders. Here, we discuss the clinical impact of MeS in cardiovascular and non-cardiovascular diseases to highlight the importance of prevention, early diagnosis, and multifactorial treatment of high-risk individuals.
Data center energy cost minimization: A spatio-temporal scheduling approach

Cloud computing is supported by an infrastructure known as Internet data center (IDC). As cloud computing thrives, the energy consumption and cost for IDCs are exploding. There is growing interest in energy cost minimization for IDCs in deregulated electricity markets. In this paper we study how to leverage both geographic and temporal variation of energy price to minimize energy cost for distributed IDCs. To this end, we propose a novel spatio-temporal load balancing approach. Using reallife electricity price and workload traces, extensive evaluations demonstrate that the proposed spatio-temporal load balancing approach significantly reduces energy cost for distributed IDCs.
The Faces of Televisual Media : Teaching, Violence, Selling To Children

Contents: Preface. Part I: Setting the Stage and Context. B.M. Young, Introduction. T. Tarpley, The Future of Televisual Media. Part II: Instructional/Educational Televisual Media. R. Moss, A Short History of the Window on the World. V. Crane, M. Chen, Content Development of Children's Media. J.H. Lee, A.C. Huston, Educational Televisual Media Effects. J.K. Asamen, G.L. Berry, The Multicultural Worldview of Children Through the Lens of Television. S.M. Fisch, Challenges for the Future of Educational Media. Part III: Entertainment Televisual Media. J.P. Murray, The Violent Face of Television: Research and Discussion. E. Scharrer, G. Comstock, Entertainment Televisual Media: Content Patterns and Themes. J.A. Bryant, J. Bryant, Effects of Entertainment Televisual Media on Children. L.R. Huesmann, M.M. Skoric, Regulating Media Violence: Why, How, and by Whom? P. Vorderer, U. Ritterfeld, Children's Future Programming and Media Use Between Entertainment and Education. Part IV: Selling Televisual Media. M.D. Johnson, B.M. Young, Advertising History of Televisual Media. D. Kunkel, M. McIlrath, Message Content in Advertising to Children. S.L. Smith, C. Atkin, Television Advertising and Children: Examining the Intended and Unintended Effects. B.M. Young, Issues and Politics of Televisual Advertising and Children. S.L. Calvert, Future Faces of Selling to Children. Part V: At Closing Curtain. E.L. Palmer, Realities and Challenges in the Rapidly Changing Televisual Media Landscape.