Showing papers by "Ben-Gurion University of the Negev published in 2015"

Recommender Systems: Introduction and Challenges

Abstract: Recommender Systems (RSs) are software tools and techniques that provide suggestions for items that are most likely of interest to a particular user. In this introductory chapter, we briefly discuss basic RS ideas and concepts. Our main goal is to delineate, in a coherent and structured way, the chapters included in this handbook. Additionally, we aim to help the reader navigate the rich and detailed content that this handbook offers.

Temperature- and Component-Dependent Degradation of Perovskite Photovoltaic Materials under Concentrated Sunlight

Abstract: We report on accelerated degradation testing of MAPbX3 films (X = I or Br) by exposure to concentrated sunlight of 100 suns and show that the evolution of light absorption and the corresponding structural modifications are dependent on the type of halide ion and the exposure temperature. One hour of such exposure provides a photon dose equivalent to that of one sun exposure for 100 hours. The degradation in absorption of MAPbI3 films after exposure to 100 suns for 60 min at elevated sample temperature (∼45-55 °C), due to decomposition of the hybrid perovskite material, is documented. No degradation was observed after exposure to the same sunlight concentration but at a lower sample temperature (∼25 °C). No photobleaching or decomposition of MAPbBr3 films was observed after exposure to similar stress conditions (light intensity, dose, and temperatures). Our results indicate that the degradation is highly dependent on the hybrid perovskite composition and can be light- and thermally enhanced.

Facts and fictions about polymorphism.

Abstract: We present new facts about polymorphism based on (i) crystallographic data from the Cambridge Structural Database (CSD, a database built over 50 years of community effort), (ii) 229 solid form screens conducted at Hoffmann-La Roche and Eli Lilly and Company over the course of 8+ and 15+ years respectively and (iii) a dataset of 446 polymorphic crystals with energies and properties computed with modern DFT-d methods. We found that molecular flexibility or size has no correlation with the ability of a compound to be polymorphic. Chiral molecules, however, were found to be less prone to polymorphism than their achiral counterparts and compounds able to hydrogen bond exhibit only a slightly higher propensity to polymorphism than those which do not. Whilst the energy difference between polymorphs is usually less than 1 kcal mol(-1), conformational polymorphs are capable of differing by larger values (up to 2.5 kcal mol(-1) in our dataset). As overall statistics, we found that one in three compounds in the CSD are polymorphic whilst at least one in two compounds from the Roche and Lilly set display polymorphism with a higher estimate of up to three in four when compounds are screened intensively. Whilst the statistics provide some guidance of expectations, each compound constitutes a new challenge and prediction and realization of targeted polymorphism still remains a holy grail of materials sciences.

Emerging Optical Wireless Communications-Advances and Challenges

Abstract: New data services and applications are emerging continuously and enhancing the mobile broadband experience. The ability to cope with these varied and sophisticated services and applications will be a key success factor for the highly demanding future network infrastructure. One such technology that could help address the problem would be optical wireless communications (OWC), which presents a growing research interest in the last few years for indoor and outdoor applications. This paper is an overview of the OWC systems focusing on visible light communications, free space optics, transcutaneous OWC, underwater OWC, and optical scattering communications.

Exposure to polycyclic aromatic hydrocarbons with special focus on cancer

Abstract: Polycyclic aromatic hydrocarbons (PAHs) are a group of compounds consisting of two or more fused aromatic rings. Most of them are formed during incomplete combustion of organic materials such as wood and fossil fuels, petroleum products, and coal. The composition of PAH mixtures varies with the source and is also affected by selective weathering effects in the environment. PAHs are ubiquitous pollutants frequently found in a variety of environments such as fresh water and marine sediments, the atmosphere, and ice. Due to their widespread distribution, the environmental pollution due to PAHs has aroused global concern. Many PAHs and their epoxides are highly toxic, mutagenic and/or carcinogenic to microorganisms as well as to higher forms of life including humans. The main aim of this review is to provide contemporary information on PAH sources, route of exposure, worldwide emission rate, and adverse effects on humans, especially with reference to cancer.

Risk of Serious Infection With Biologic and Systemic Treatment of Psoriasis: Results From the Psoriasis Longitudinal Assessment and Registry (PSOLAR).

Abstract: Importance The efficacy of treatment for psoriasis must be balanced against potential adverse events. Objective To determine the effect of treatment on the risk of serious infections in patients with psoriasis. Design, Setting, and Participants A multicenter, longitudinal, disease-based registry (Psoriasis Longitudinal Assessment and Registry [PSOLAR]) at dermatology centers. Participants were adult patients with psoriasis who were receiving or were eligible to receive conventional systemic or biologic agents. The registry opened on June 20, 2007, and data included herein were collected through August 23, 2013. Exposures Patients were prescribed psoriasis therapies as in standard clinical practice. Patients will be followed for up to 8 years. Data were collected and serious adverse events (including serious infections) were assessed at regular intervals. Main Outcomes and Measures Cohort characteristics are described based on evaluation at entry into the registry. The cumulative incidence rates of serious infections are reported across treatment cohorts, including ustekinumab, infliximab, adalimumab, etanercept, and nonbiologics (with or without methotrexate). A multivariate analysis using a Cox proportional hazards regression model was used to identify predictors of the time to the first serious infection using the nonmethotrexate/nonbiologics cohort as the reference. Results Data were analyzed from 11 466 patients with psoriasis (22 311 patient-years). Differences in patient characteristics were found between the biologics and nonmethotrexate/nonbiologics cohorts (eg, age, sex, body mass index, and disease characteristics), as well as among the individual biologic groups (eg, a higher prevalence of psoriatic arthritis in the infliximab cohort). The cumulative incidence rate of serious infections was 1.45 per 100 patient-years (n = 323) across treatment cohorts, and the rates were 0.83, 1.47, 1.97, and 2.49 per 100 patient-years in the ustekinumab, etanercept, adalimumab, and infliximab cohorts, respectively, and 1.05 and 1.28 per 100 patient-years in the nonmethotrexate/nonbiologics and methotrexate/nonbiologics cohorts, respectively. The most commonly reported types of serious infections across the registry were pneumonia and cellulitis. Increasing age, diabetes mellitus, smoking, significant infection history, infliximab exposure, and adalimumab exposure were each associated with an increased risk of serious infection. Conclusions and Relevance Results from PSOLAR suggest a higher risk of serious infections with adalimumab and infliximab compared with nonmethotrexate and nonbiologic therapies. No increased risk was observed with ustekinumab or etanercept. Trial Registration clinicaltrials.gov Identifier:NCT00508547

Self-Serving Justifications Doing Wrong and Feeling Moral

Abstract: Unethical behavior by “ordinary” people poses significant societal and personal challenges. We present a novel framework centered on the role of self-serving justification to build upon and advance the rapidly expanding research on intentional unethical behavior of people who value their morality highly. We propose that self-serving justifications emerging before and after people engage in intentional ethical violations mitigate the threat to the moral self, enabling them to do wrong while feeling moral. Pre-violation justifications lessen the anticipated threat to the moral self by redefining questionable behaviors as excusable. Post-violation justifications alleviate the experienced threat to the moral self through compensations that balance or lessen violations. We highlight the psychological mechanisms that prompt people to do wrong and feel moral, and suggest future research directions regarding the temporal dimension of self-serving justifications of ethical misconduct.

Adopting a spatially explicit perspective to study the mysterious fairy circles of Namibia

Abstract: The mysterious ‘fairy circles’ are vegetation-free discs that cover vast areas along the pro-Namib Desert. Despite 30 yr of research their origin remains unknown. Here we adopt a novel approach that focuses on analysis of the spatial patterns of fairy circles obtained from representative 25-ha aerial images of north-west Namibia. We use spatial point pattern analysis to quantify different features of their spatial structures and then critically inspect existing hypotheses with respect to their ability to generate the observed circle patterns. Our working hypothesis is that fairy circles are a self-organized vegetation pattern. Finally, we test if an existing partial-differential-equation model, that was designed to describe vegetation pattern formation, is able to reproduce the characteristic features of the observed fairy circle patterns. The model is based on key-processes in arid areas such as plant competition for water and local resource-biomass feedbacks. The fairy circles showed at all three study areas the same regular spatial distribution patterns, characterized by Voronoi cells with mostly six corners, negative correlations in their size up to a distance of 13 m, and remarkable homogeneity over large spatial scales. These results cast doubts on abiotic gas-leakage along geological lines or social insects as causal agents of their origin. However, our mathematical model was able to generate spatial patterns that agreed quantitatively in all of these features with the observed patterns. This supports the hypothesis that fairy circles are self-organized vegetation patterns that emerge from positive biomass-water feedbacks involving water transport by extended root systems and soil-water diffusion. Future research should search for mechanisms that explain how the different hypotheses can generate the patterns observed here and test the ability of self-organization to match the birth- and death dynamics of fairy circles and their regional patterns in the density and size with respect to environmental gradients.

Hospital Incidence and Outcomes of the Acute Respiratory Distress Syndrome Using the Kigali Modification of the Berlin Definition

Abstract: Rationale: Estimates of the incidence of the acute respiratory distress syndrome (ARDS) in high- and middle-income countries vary from 10.1 to 86.2 per 100,000 person-years in the general population. The epidemiology of ARDS has not been reported for a low-income country at the level of the population, hospital, or intensive care unit (ICU). The Berlin definition may not allow identification of ARDS in resource-constrained settings.Objectives: To estimate the incidence and outcomes of ARDS at a Rwandan referral hospital using the Kigali modification of the Berlin definition: without requirement for positive end-expiratory pressure, hypoxia cutoff of SpO2/FiO2 less than or equal to 315, and bilateral opacities on lung ultrasound or chest radiograph.Methods: We screened every adult patient for hypoxia at a public referral hospital in Rwanda for 6 weeks. For every patient with hypoxia, we collected data on demographics and ARDS risk factors, performed lung ultrasonography, and evaluated chest radiography whe...

Swarming bacteria migrate by Lévy Walk

Abstract: Levy walks have been found in the motion of large animals such as birds and fish in search of sparsely and randomly distributed food. Here, Ariel et al. observe, by tracking long-duration trajectories of fluorescently labelled bacteria, similar walks in bacterial swarms for the first time.

Evaluating Recommender Systems

Abstract: Recommender systems are now popular both commercially and in the research community, where many approaches have been suggested for providing recommendations. In many cases a system designer that wishes to employ a recommendater system must choose between a set of candidate approaches. A first step towards selecting an appropriate algorithm is to decide which properties of the application to focus upon when making this choice. Indeed, recommender systems have a variety of properties that may affect user experience, such as accuracy, robustness, scalability, and so forth. In this paper we discuss how to compare recommenders based on a set of properties that are relevant for the application. We focus on comparative studies, where a few algorithms are compared using some evaluation metric, rather than absolute benchmarking of algorithms. We describe experimental settings appropriate for making choices between algorithms. We review three types of experiments, starting with an offline setting, where recommendation approaches are compared without user interaction, then reviewing user studies, where a small group of subjects experiment with the system and report on the experience, and finally describe large scale online experiments, where real user populations interact with the system. In each of these cases we describe types of questions that can be answered, and suggest protocols for experimentation. We also discuss how to draw trustworthy conclusions from the conducted experiments. We then review a large set of properties, and explain how to evaluate systems given relevant properties. We also survey a large set of evaluation metrics in the context of the property that they evaluate.

Longitudinal associations between depression, anxiety, pain, and pain-related disability in chronic pain patients.

Abstract: OBJECTIVE The current study sets out to examine the longitudinal relationship between pain, pain-related disability, and symptoms of depression and anxiety. The latter symptoms are highly prevalent in chronic pain and seriously impede functioning and quality of life. Nevertheless, the direction of the relationship involving these variables among individuals with chronic pain is still unclear. METHODS Four-hundred twenty-eight individuals with chronic pain (238 women, mean age 54.84 years, mean pain duration 85.21 months) treated at two pain clinics completed questionnaires regarding their pain (Short-Form McGill Pain Questionnaire), depression (Center for Epidemiological Studies-Depression Scale), state anxiety (State-Trait Anxiety Inventory), and pain-related disability (Pain Disability Index) at four time points, with an average of 5 months between measurements. Cross-lagged, structural equation modeling analyses were performed, enabling the examination of longitudinal associations between the variables. RESULTS Significant symptoms of both depression and anxiety were reported by more than half of the sample on all waves. A latent depression/anxiety variable longitudinally predicted pain (β = .27, p < .001) and pain-related disability (β = .38, p < .001). However, neither pain (β = .10, p = .126) nor pain-related disability (β = -.01, p = .790) predicted depression/anxiety. CONCLUSIONS Among adult patients with chronic pain treated at specialty pain clinics, high levels of depression and anxiety may worsen pain and pain-related disability.

Guidelines for the Care and Welfare of Cephalopods in Research -A consensus based on an initiative by CephRes, FELASA and the Boyd Group.

Abstract: This paper is the result of an international initiative and is a first attempt to develop guidelines for the care and welfare of cephalopods (i.e. nautilus, cuttlefish, squid and octopus) following the inclusion of this Class of ∼700 known living invertebrate species in Directive 2010/63/EU. It aims to provide information for investigators, animal care committees, facility managers and animal care staff which will assist in improving both the care given to cephalopods, and the manner in which experimental procedures are carried out. Topics covered include: implications of the Directive for cephalopod research; project application requirements and the authorisation process; the application of the 3Rs principles; the need for harm-benefit assessment and severity classification. Guidelines and species-specific requirements are provided on: i. supply, capture and transport; ii. environmental characteristics and design of facilities (e.g. water quality control, lighting requirements, vibration/noise sensitivity); iii. accommodation and care (including tank design), animal handling, feeding and environmental enrichment; iv. assessment of health and welfare (e.g. monitoring biomarkers, physical and behavioural signs); v. approaches to severity assessment; vi. disease (causes, prevention and treatment); vii. scientific procedures, general anaesthesia and analgesia, methods of humane killing and confirmation of death. Sections covering risk assessment for operators and education and training requirements for carers, researchers and veterinarians are also included. Detailed aspects of care and welfare requirements for the main laboratory species currently used are summarised in Appendices. Knowledge gaps are highlighted to prompt research to enhance the evidence base for future revision of these guidelines.

Function Secret Sharing

Abstract: Motivated by the goal of securely searching and updating distributed data, we introduce and study the notion of function secret sharing (FSS). This new notion is a natural generalization of distributed point functions (DPF), a primitive that was recently introduced by Gilboa and Ishai (Eurocrypt 2014). Given a positive integer \(p\ge 2\) and a class \(\mathcal F\) of functions \(f:\{0,1\}^n\rightarrow \mathbb G\), where \(\mathbb G\) is an Abelian group, a \(p\)-party FSS scheme for \(\mathcal F\) allows one to split each \(f\in \mathcal F\) into \(p\) succinctly described functions \(f_i:\{0,1\}^n\rightarrow \mathbb G\), \(1\le i\le p\), such that: (1) \(\sum _{i=1}^p f_i=f\), and (2) any strict subset of the \(f_i\) hides \(f\). Thus, an FSS for \(\mathcal F\) can be thought of as method for succinctly performing an “additive secret sharing” of functions from \(\mathcal F\). The original definition of DPF coincides with a two-party FSS for the class of point functions, namely the class of functions that have a nonzero output on at most one input.

How Mitochondrial Dynamism Orchestrates Mitophagy

Abstract: Mitochondria are highly dynamic, except in adult cardiomyocytes. Yet, the fission and fusion-promoting proteins that mediate mitochondrial dynamism are highly expressed in, and essential to the normal functioning of, hearts. Here, we review accumulating evidence supporting important roles for mitochondrial fission and fusion in cardiac mitochondrial quality control, focusing on the PTEN-induced putative kinase 1–Parkin mitophagy pathway. Based in part on recent findings from in vivo mouse models in which mitofusin-mediated mitochondrial fusion or dynamin-related protein 1–mediated mitochondrial fission was conditionally interrupted in cardiac myocytes, we propose several new concepts that may provide insight into the cardiac mitochondrial dynamism–mitophagy interactome.

A recurrent de novo mutation in KCNC1 causes progressive myoclonus epilepsy

Abstract: Progressive myoclonus epilepsies (PMEs) are a group of rare, inherited disorders manifesting with action myoclonus, tonic-clonic seizures and ataxia. We sequenced the exomes of 84 unrelated individuals with PME of unknown cause and molecularly solved 26 cases (31%). Remarkably, a recurrent de novo mutation, c.959G>A (p.Arg320His), in KCNC1 was identified as a new major cause for PME. Eleven unrelated exome-sequenced (13%) and two affected individuals in a secondary cohort (7%) had this mutation. KCNC1 encodes KV3.1, a subunit of the KV3 voltage-gated potassium ion channels, which are major determinants of high-frequency neuronal firing. Functional analysis of the Arg320His mutant channel showed a dominant-negative loss-of-function effect. Ten cases had pathogenic mutations in known PME-associated genes (NEU1, NHLRC1, AFG3L2, EPM2A, CLN6 and SERPINI1). Identification of mutations in PRNP, SACS and TBC1D24 expand their phenotypic spectra to PME. These findings provide insights into the molecular genetic basis of PME and show the role of de novo mutations in this disease entity.

In situ low-relief landscape formation as a result of river network disruption.

Abstract: The relict landscapes of southeast Tibet are being formed in situ as a result of river drainage reorganization that renders rivers unable to balance tectonic uplift, so these landscapes may not provide an unaltered record of past geomorphic conditions. High elevation, low relief surfaces or 'relict landscapes' are generally thought to be uplifted, old landscapes that preserve past tectonic and environmental conditions. Rong Yang et al. have tested current models of landscape evolution using digital topographic analysis of so-called relict landscapes in southeast Tibet and Yunnan province, China — dramatic scenery boasting up to 3 km of relief encompassing the gorges of the Yangtze, Mekong and Salween rivers. They find that the region may not provide an unaltered record of past geomorphic conditions. Rather, these landscapes form in situ as a result of river drainage reorganization that renders rivers unable to balance tectonic uplift. Landscapes on Earth retain a record of the tectonic, environmental and climatic history under which they formed. Landscapes tend towards an equilibrium in which rivers attain a stable grade that balances the tectonic production of elevation and with hillslopes that attain a gradient steep enough to transport material to river channels. Equilibrium low-relief surfaces are typically found at low elevations, graded to sea level. However, there are many examples of high-elevation, low-relief surfaces, often referred to as relict landscapes1,2, or as elevated peneplains3. These do not grade to sea level and are typically interpreted as uplifted old landscapes, preserving former, more moderate tectonic conditions4. Here we test this model of landscape evolution through digital topographic analysis of a set of purportedly relict landscapes on the southeastern margin of the Tibetan Plateau, one of the most geographically complex, climatically varied and biologically diverse regions of the world. We find that, in contrast to theory, the purported surfaces are not consistent with progressive establishment of a new, steeper, river grade, and therefore they cannot necessarily be interpreted as a remnant of an old, low relief surface. We propose an alternative model, supported by numerical experiments, in which tectonic deformation has disrupted the regional river network, leaving remnants of it isolated and starved of drainage area and thus unable to balance tectonic uplift. The implication is that the state of low relief with low erosion rate is developing in situ, rather than preserving past erosional conditions.

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

Abstract: We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na(+)] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

Long-Term Exposure to Fine Particulate Matter, Residential Proximity to Major Roads and Measures of Brain Structure

Abstract: Background and Purpose—Long-term exposure to ambient air pollution is associated with cerebrovascular disease and cognitive impairment, but whether it is related to structural changes in the brain is not clear. We examined the associations between residential long-term exposure to ambient air pollution and markers of brain aging using magnetic resonance imaging. Methods—Framingham Offspring Study participants who attended the seventh examination were at least 60 years old and free of dementia and stroke were included. We evaluated associations between exposures (fine particulate matter [PM2.5] and residential proximity to major roadways) and measures of total cerebral brain volume, hippocampal volume, white matter hyperintensity volume (log-transformed and extensive white matter hyperintensity volume for age), and covert brain infarcts. Models were adjusted for age, clinical covariates, indicators of socioeconomic position, and temporal trends. Results—A 2-μg/m3 increase in PM2.5 was associated with −0.32...

Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA

Abstract: We introduce an extended version of oxDNA, a coarse-grained model of DNA designed to capture the thermodynamic, structural and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves, and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures such as DNA origami which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na$^+$]=0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

Completely Organic Multilayer Thin Film with Thermoelectric Power Factor Rivaling Inorganic Tellurides

Abstract: Composed exclusively of organic components, polyaniline (PANi), graphene, and double-walled nanotubes (DWNTs) are alternately deposited from aqueous solutions using a layer-by-layer assembly. The 40 quadlayer thin film (470 nm thick) exhibits electrical conductivity of 1.08 × 10(5) S m(-1) and a Seebeck coefficient of 130 μV K(-1) , producing a thermoelectric power factor of 1825 μW m(-1) K(-2) .

Polymeric Nanoparticles for Nonviral Gene Therapy Extend Brain Tumor Survival in Vivo

Abstract: Biodegradable polymeric nanoparticles have the potential to be safer alternatives to viruses for gene delivery; however, their use has been limited by poor efficacy in vivo. In this work, we synthesize and characterize polymeric gene delivery nanoparticles and evaluate their efficacy for DNA delivery of herpes simplex virus type I thymidine kinase (HSVtk) combined with the prodrug ganciclovir (GCV) in a malignant glioma model. We investigated polymer structure for gene delivery in two rat glioma cell lines, 9L and F98, to discover nanoparticle formulations more effective than the leading commercial reagent Lipofectamine 2000. The lead polymer structure, poly(1,4-butanediol diacrylate-co-4-amino-1-butanol) end-modified with 1-(3-aminopropyl)-4-methylpiperazine, is a poly(β-amino ester) (PBAE) and formed nanoparticles with HSVtk DNA that were 138 ± 4 nm in size and 13 ± 1 mV in zeta potential. These nanoparticles containing HSVtk DNA showed 100% cancer cell killing in vitro in the two glioma cell lines when...