Showing papers by "Ben-Gurion University of the Negev published in 2010"

Ensemble-based classifiers

Abstract: The idea of ensemble methodology is to build a predictive model by integrating multiple models. It is well-known that ensemble methods can be used for improving prediction performance. Researchers from various disciplines such as statistics and AI considered the use of ensemble methodology. This paper, review existing ensemble techniques and can be served as a tutorial for practitioners who are interested in building ensemble based systems.

Suicide and suicide risk in lesbian, gay, bisexual, and transgender populations: review and recommendations.

Abstract: Despite strong indications of elevated risk of suicidal behavior in lesbian, gay, bisexual, and transgender people, limited attention has been given to research, interventions or suicide prevention programs targeting these populations. This article is a culmination of a three-year effort by an expert panel to address the need for better understanding of suicidal behavior and suicide risk in sexual minority populations, and stimulate the development of needed prevention strategies, interventions and policy changes. This article summarizes existing research findings, and makes recommendations for addressing knowledge gaps and applying current knowledge to relevant areas of suicide prevention practice.

Blood–brain barrier breakdown as a therapeutic target in traumatic brain injury

Abstract: Traumatic brain injury (TBI) is the leading cause of death in young adults and children. The treatment of TBI in the acute phase has improved substantially; however, the prevention and management of long-term complications remain a challenge. Blood-brain barrier (BBB) breakdown has often been documented in patients with TBI, but the role of such vascular pathology in neurological dysfunction has only recently been explored. Animal studies have demonstrated that BBB breakdown is involved in the initiation of transcriptional changes in the neurovascular network that ultimately lead to delayed neuronal dysfunction and degeneration. Brain imaging data have confirmed the high incidence of BBB breakdown in patients with TBI and suggest that such pathology could be used as a biomarker in the clinic and in drug trials. Here, we review the neurological consequences of TBI, focusing on the long-term complications of such injuries. We present the clinical evidence for involvement of BBB breakdown in TBI and examine the primary and secondary mechanisms that underlie such pathology. We go on to consider the consequences of BBB injury, before analyzing potential mechanisms linking vascular pathology to neuronal dysfunction and degeneration, and exploring possible targets for treatment. Finally, we highlight areas for future basic research and clinical studies into TBI.

NCLX is an essential component of mitochondrial Na+/Ca2+ exchange.

Abstract: Mitochondrial Ca(2+) efflux is linked to numerous cellular activities and pathophysiological processes. Although it is established that an Na(+)-dependent mechanism mediates mitochondrial Ca(2+) efflux, the molecular identity of this transporter has remained elusive. Here we show that the Na(+)/Ca(2+) exchanger NCLX is enriched in mitochondria, where it is localized to the cristae. Employing Ca(2+) and Na(+) fluorescent imaging, we demonstrate that mitochondrial Na(+)-dependent Ca(2+) efflux is enhanced upon overexpression of NCLX, is reduced by silencing of NCLX expression by siRNA, and is fully rescued by the concomitant expression of heterologous NCLX. NCLX-mediated mitochondrial Ca(2+) transport was inhibited, moreover, by CGP-37157 and exhibited Li(+) dependence, both hallmarks of mitochondrial Na(+)-dependent Ca(2+) efflux. Finally, NCLX-mediated mitochondrial Ca(2+) exchange is blocked in cells expressing a catalytically inactive NCLX mutant. Taken together, our results converge to the conclusion that NCLX is the long-sought mitochondrial Na(+)/Ca(2+) exchanger.

Radically rethinking agriculture for the 21st century.

Abstract: Population growth, arable land and fresh water limits, and climate change have profound implications for the ability of agriculture to meet this century’s demands for food, feed, fiber, and fuel while reducing the environmental impact of their production. Success depends on the acceptance and use of contemporary molecular techniques, as well as the increasing development of farming systems that use saline water and integrate nutrient flows.

Use of NDVI and Land Surface Temperature for Drought Assessment: Merits and Limitations

Abstract: A large number of water- and climate-related applications, such as drought monitoring, are based on spaceborne-derived relationships between land surface temperature (LST) and the normalized difference vegetation index (NDVI). The majority of these applications rely on the existence of a negative slope between the two variables, as identified in site- and time-specific studies. The current paper investigates the generality of the LST–NDVI relationship over a wide range of moisture and climatic/radiation regimes encountered over the North American continent (up to 60°N) during the summer growing season (April–September). Information on LST and NDVI was obtained from long-term (21 years) datasets acquired with the Advanced Very High Resolution Radiometer (AVHRR). It was found that when water is the limiting factor for vegetation growth (the typical situation for low latitudes of the study area and during the midseason), the LST–NDVI correlation is negative. However, when energy is the limiting fact...

Starvation physiology: reviewing the different strategies animals use to survive a common challenge.

Abstract: All animals face the possibility of limitations in food resources that could ultimately lead to starvation-induced mortality. The primary goal of this review is to characterize the various physiological strategies that allow different animals to survive starvation. The ancillary goals of this work are to identify areas in which investigations of starvation can be improved and to discuss recent advances and emerging directions in starvation research. The ubiquity of food limitation among animals, inconsistent terminology associated with starvation and fasting, and rationale for scientific investigations into starvation are discussed. Similarities and differences with regard to carbohydrate, lipid, and protein metabolism during starvation are also examined in a comparative context. Examples from the literature are used to underscore areas in which reporting and statistical practices, particularly those involved with starvation-induced changes in body composition and starvation-induced hypometabolism can be improved. The review concludes by highlighting several recent advances and promising research directions in starvation physiology. Because the hundreds of studies reviewed here vary so widely in their experimental designs and treatments, formal comparisons of starvation responses among studies and taxa are generally precluded; nevertheless, it is my aim to provide a starting point from which we may develop novel approaches, tools, and hypotheses to facilitate meaningful investigations into the physiology of starvation in animals.

Temperature Dependence of the Nitrogen-Vacancy Magnetic Resonance in Diamond

Abstract: The temperature dependence of the magnetic-resonance spectra of nitrogen-vacancy (NV-) ensembles in the range of 280-330 K was studied. Four samples prepared under different conditions were analyzed with NV- concentrations ranging from 10 ppb to 15 ppm. For all samples, the axial zero-field splitting (ZFS) parameter D was found to vary significantly with temperature, T, as dD/dT=-74.2(7) kHz/K. The transverse ZFS parameter E was nonzero (between 4 and 11 MHz) in all samples, and exhibited a temperature dependence of dE/(EdT)=-1.4(3)x10{-4} K-1. The results might be accounted for by considering local thermal expansion. The temperature dependence of the ZFS parameters presents a significant challenge for diamond magnetometers and may ultimately limit their bandwidth and sensitivity.

Theta*: any-angle path planning on grids

Abstract: Grids with blocked and unblocked cells are often used to represent terrain in robotics and video games. However, paths formed by grid edges can be longer than true shortest paths in the terrain since their headings are artificially constrained. We present two new correct and complete anyangle path-planning algorithms that avoid this shortcoming. Basic Theta* and Angle-Propagation Theta* are both variants of A* that propagate information along grid edges without constraining paths to grid edges. Basic Theta* is simple to understand and implement, fast and finds short paths. However, it is not guaranteed to find true shortest paths. Angle-Propagation Theta* achieves a better worst-case complexity per vertex expansion than Basic Theta* by propagating angle ranges when it expands vertices, but is more complex, not as fast and finds slightly longer paths. We refer to Basic Theta* and Angle-Propagation Theta* collectively as Theta*. Theta* has unique properties, which we analyze in detail. We show experimentally that it finds shorter paths than both A* with post-smoothed paths and Field D* (the only other version of A* we know of that propagates information along grid edges without constraining paths to grid edges) with a runtime comparable to that of A* on grids. Finally, we extend Theta* to grids that contain unblocked cells with non-uniformtraversal costs and introduce variants of Theta* which provide different tradeoffs between path length and runtime.

The International Urban Energy Balance Models Comparison Project: First Results from Phase 1

Abstract: A large number of urban surface energy balance models now exist with different assumptions about the important features of the surface and exchange processes that need to be incorporated To date, no comparison of these models has been conducted; in contrast, models for natural surfaces have been compared extensively as part of the Project for Intercomparison of Land-surface Parameterization Schemes Here, the methods and first results from an extensive international comparison of 33 models are presented The aim of the comparison overall is to understand the complexity required to model energy and water exchanges in urban areas The degree of complexity included in the models is outlined and impacts on model performance are discussed During the comparison there have been significant developments in the models with resulting improvements in performance (root-mean-square error falling by up to two-thirds) Evaluation is based on a dataset containing net all-wave radiation, sensible heat, and latent heat flux observations for an industrial area in Vancouver, British Columbia, Canada The aim of the comparison is twofold: to identify those modeling approaches that minimize the errors in the simulated fluxes of the urban energy balance and to determine the degree of model complexity required for accurate simulations There is evidence that some classes of models perform better for individual fluxes but no model performs best or worst for all fluxes In general, the simpler models perform as well as the more complex models based on all statistical measures Generally the schemes have best overall capability to model net all-wave radiation and least capability to model latent heat flux

Nestedness versus modularity in ecological networks: two sides of the same coin?

Abstract: 1. Understanding the structure of ecological networks is a crucial task for interpreting community and ecosystem responses to global change. 2. Despite the recent interest in this subject, almost all studies have focused exclusively on one specific network property. The question remains as to what extent different network properties are related and how understanding this relationship can advance our comprehension of the mechanisms behind these patterns. 3. Here, we analysed the relationship between nestedness and modularity, two frequently studied network properties, for a large data set of 95 ecological communities including both plant-animal mutualistic and host-parasite networks. 4. We found that the correlation between nestedness and modularity for a population of random matrices generated from the real communities decreases significantly in magnitude and sign with increasing connectance independent of the network type. At low connectivities, networks that are highly nested also tend to be highly modular; the reverse happens at high connectivities. 5. The above result is qualitatively robust when different null models are used to infer network structure, but, at a finer scale, quantitative differences exist. We observed an important interaction between the network structure pattern and the null model used to detect it. 6. A better understanding of the relationship between nestedness and modularity is important given their potential implications on the dynamics and stability of ecological communities.

Google Android: A Comprehensive Security Assessment

Abstract: This research provides a security assessment of the Android framework-Google's software stack for mobile devices. The authors identify high-risk threats to the framework and suggest several security solutions for mitigating them.

Flat combining and the synchronization-parallelism tradeoff

Abstract: Traditional data structure designs, whether lock-based or lock-free, provide parallelism via fine grained synchronization among threads.We introduce a new synchronization paradigm based on coarse locking, which we call flat combining. The cost of synchronization in flat combining is so low, that having a single thread holding a lock perform the combined access requests of all others, delivers, up to a certain non-negligible concurrency level, better performance than the most effective parallel finely synchronized implementations. We use flat-combining to devise, among other structures, new linearizable stack, queue, and priority queue algorithms that greatly outperform all prior algorithms.

Metformin Use and Mortality Among Patients With Diabetes and Atherothrombosis

Abstract: Results: The mortality rates were 6.3% (95% confidence interval[CI],5.2%-7.4%)withmetforminand9.8%8.4%11.2%)withoutmetformin;theadjustedhazardratio(HR) was0.76(0.65-0.89;P.001).Associationwithlowermortalitywasconsistentamongsubgroups,noticeablyinpatients withahistoryofcongestiveheartfailure(HR,0.69;95%CI, 0.54-0.90;P=.006),patientsolderthan65years(0.77;0.620.95;P=.02),andpatientswithanestimatedcreatinineclearanceof30to60mL/min/1.73m 2 (0.64;95%CI,0.48-0.86; P=.003)(toconvertcreatinineclearancetomL/s/m 2 ,multiply by 0.0167). Conclusions: Metformin use may decrease mortality among patients with diabetes when used as a means of secondary prevention, including subsets of patients in whom metformin use is not now recommended. Metformin use should be tested prospectively in this population to confirm its effect on survival. Arch Intern Med. 2010;170(21):1892-1899

Differential release of chromatin-bound IL-1α discriminates between necrotic and apoptotic cell death by the ability to induce sterile inflammation

Abstract: IL-1α, like IL-1β, possesses multiple inflammatory and immune properties. However, unlike IL-1β, the cytokine is present intracellularly in healthy tissues and is not actively secreted. Rather, IL-1α translocates to the nucleus and participates in transcription. Here we show that intracellular IL-1α is a chromatin-associated cytokine and highly dynamic in the nucleus of living cells. During apoptosis, IL-1α concentrates in dense nuclear foci, which markedly reduces its mobile nature. In apoptotic cells, IL-1α is retained within the chromatin fraction and is not released along with the cytoplasmic contents. To simulate the in vivo inflammatory response to cells undergoing different mechanisms of death, lysates of cells were embedded in Matrigel plugs and implanted into mice. Lysates from cells undergoing necrosis recruited cells of the myeloid lineage into the Matrigel, whereas lysates of necrotic cells lacking IL-1α failed to recruit an infiltrate. In contrast, lysates of cells undergoing apoptotic death were inactive. Cells infiltrating the Matrigel were due to low concentrations (20–50 pg) of the IL-1α precursor containing the receptor interacting C-terminal, whereas the N-terminal propiece containing the nuclear localization site failed to do so. When normal keratinocytes were subjected to hypoxia, the constitutive IL-1α precursor was released into the supernatant. Thus, after an ischemic event, the IL-1α precursor is released by hypoxic cells and incites an inflammatory response by recruiting myeloid cells into the area. Tissues surrounding the necrotic site also sustain damage from the myeloid cells. Nuclear trafficking and differential release during necrosis vs. apoptosis demonstrate that inflammation by IL-1α is tightly controlled.

Attachment-based family therapy for adolescents with suicidal ideation: a randomized controlled trial.

Abstract: Objective To evaluate whether Attachment-Based Family Therapy (ABFT) is more effective than Enhanced Usual Care (EUC) for reducing suicidal ideation and depressive symptoms in adolescents. Method This was a randomized controlled trial of suicidal adolescents between the ages of 12 and 17, identified in primary care and emergency departments. Of 341 adolescents screened, 66 (70% African American) entered the study for 3 months of treatment. Assessment occurred at baseline, 6 weeks, 12 weeks, and 24 weeks. ABFT consisted of individual and family meetings, and EUC consisted of a facilitated referral to other providers. All participants received weekly monitoring and access to a 24-hour crisis phone. Trajectory of change and clinical recovery were measured for suicidal ideation and depressive symptoms. Results Using intent to treat, patients in ABFT demonstrated significantly greater rates of change on self-reported suicidal ideation at post-treatment evaluation, and benefits were maintained at follow-up, with a strong overall effect size (ES = 0.97). Between-group differences were similar on clinician ratings. Significantly more patients in ABFT met criteria for clinical recovery on suicidal ideation post-treatment (87%; 95% confidence interval [CI] = 74.6–99.6) than patients in EUC (51.7%; 95% CI=32.4–54.32). Benefits were maintained at follow-up (ABFT, 70%; 95% CI=52.6–87.4; EUC 34.6%; 95% CI=15.6–54.2; odds ratio=4.41). Patterns of depressive symptoms over time were similar, as were results for a subsample of adolescents with diagnosed depression. Retention in ABFT was higher than in EUC (mean = 9.7 versus 2.9). Conclusions ABFT is more efficacious than EUC in reducing suicidal ideation and depressive symptoms in adolescents. Additional research is warranted to confirm treatment efficacy and to test the proposed mechanism of change (the Family Safety Net Study). Clinical Trial Registry Information: Preventing Youth Suicide in Primary Care: A Family Model, URL: http://www.clinicaltrials.gov, unique identifier: NCT00604097.

Dominating clasp of the financial sector revealed by partial correlation analysis of the stock market.

Abstract: What are the dominant stocks which drive the correlations present among stocks traded in a stock market? Can a correlation analysis provide an answer to this question? In the past, correlation based networks have been proposed as a tool to uncover the underlying backbone of the market. Correlation based networks represent the stocks and their relationships, which are then investigated using different network theory methodologies. Here we introduce a new concept to tackle the above question—the partial correlation network. Partial correlation is a measure of how the correlation between two variables, e.g., stock returns, is affected by a third variable. By using it we define a proxy of stock influence, which is then used to construct partial correlation networks. The empirical part of this study is performed on a specific financial system, namely the set of 300 highly capitalized stocks traded at the New York Stock Exchange, in the time period 2001–2003. By constructing the partial correlation network, unlike the case of standard correlation based networks, we find that stocks belonging to the financial sector and, in particular, to the investment services sub-sector, are the most influential stocks affecting the correlation profile of the system. Using a moving window analysis, we find that the strong influence of the financial stocks is conserved across time for the investigated trading period. Our findings shed a new light on the underlying mechanisms and driving forces controlling the correlation profile observed in a financial market.

Narrative research: Time for a paradigm.

Abstract: As a result of the popularization of the narrative idea and the considerable diversity existing among narrative studies, a rather “all included” conception has arisen, in which the framework of narrative inquiry has been significantly blurred. For narrative inquiry to persist as a unique mode of investigation into human nature, a complementary dialogue is required that aims at outlining its core, alongside the emphasis given in the literature on diversity as its hallmark. As a possible reference point for this debate, recognizing the narrative paradigm that has crystallized since the “narrative turn” is suggested. The narrative paradigm is discussed in light of six major dimensions — ontology, epistemology, methodology, inquiry aim, inquirer posture and participant/narrator posture — indicating that it coincides with other interpretive paradigms in certain aspects yet proffers a unique philosophical infrastructure that gives rise to particular methodological principles and methods. Considering the narrative paradigm as the essence of narrative inquiry asserts that the latter is not confined to a methodology, as often implied. Rather it constitutes a full-fledged research Weltanschauung that intimately connects the “hows” of investigation to the “whats”, namely premises about the nature of reality and our relationships with it.

Association of Serotype with Risk of Death Due to Pneumococcal Pneumonia: A Meta-Analysis

Abstract: Streptococcus pneumoniae, or pneumococcus, is an important cause of pneumonia, meningitis, otitis media, and septicemia and is associated with significant morbidity and mortality worldwide. There are 92 known pneumococcal serotypes, and each produces a unique polysaccharide capsule that protects the bacterium against host immune effectors [1]. Serotype affects many aspects of pneumococcal epidemiology. The rank orders of serotypes found in nasopharyngeal carriage [2] and invasive disease [3, 4] are similar worldwide with a few exceptions. Likewise, the invasiveness of a serotype, or the frequency with which it causes invasive disease per carriage episode, is a stable property [5]. There is an inverse relationship between the carriage prevalence of a serotype and its invasiveness [5] and between disease severity and invasiveness [6]. The outcome of a case of invasive pneumococcal disease (IPD) can be affected both by bacterial factors, such as serotype, and by host characteristics, such as old age, very young age, low socioeconomic status, quality of care, alcoholism, immunodeficiency, and other underlying conditions[7–10]. Some studies have found that even after controlling for relevant host factors, certain serotypes are independently associated with more severe outcomes [11–13]. Likewise, experimental studies in mice have shown that serotypes differ in their ability to cause severe disease [14], and strains with larger capsules are more virulent in animals than strains of the same serotype with smaller capsules [15, 16]. It was long ago noted that differences in polysaccharide production between types 1, 2, and 3 correlated with the case-fatality ratios (CFR) for these serotypes in humans [7, 17]. While a number of studies have investigated the relationship between serotype and disease outcome, they differ in the kinds of clinical syndromes included, the age of the populations studied, and the covariates included when deriving effect estimates. As a result, published studies differ in the magnitude and direction of effect estimates for certain serotypes, and these studies have not previously been compared to determine whether stable patterns of virulence exist. We performed a systematic review and meta-analysis of IPD outcome by serotype to evaluate the stability of these estimates between studies. We found that clinical outcome in bacteremic pneumonia, like carriage prevalence and invasiveness, is a stable serotype-associated property, and we hypothesize about the biological reasons for these patterns.

IL-1 family nomenclature

Abstract: To the Editor: Newly cloned interleukin 1 (IL-1) family members1–3 were originally given an IL-1 family (IL-1F) designation4, but as functions have now been elucidated for several of these5,6, we propose that each now be assigned an individual interleukin designation. IL-1F6, IL-1F8 and IL-1F9 are encoded by distinct genes but use the same receptor complex (IL-1Rrp2 and AcP), are proinflammatory and deliver nearly identical signals7–12. We propose these be designated IL-36α, IL-36β and IL-36γ, respectively. IL-1F5 also binds to IL-1Rrp2 but antagonizes those cytokines in a manner analogous to that used by IL-1Ra to antagonize IL-1α and IL-1β7–9. We propose that IL-1F5 be renamed IL-36Ra (for ‘receptor antagonist’). In the IL-1 nomenclature, IL-1Ra is used for the natural product, whereas IL-1ra is used for the recombinant product; therefore, IL-36Ra is appropriate for natural IL-1F5. IL-1F7 produces anti-inflammatory effects by suppressing innate immune responses; it does this by decreasing the production of inflammatory cytokines induced by Toll-like receptor agonists as well as that of IL-1 and tumor necrosis factor13,14. We propose this IL-1 family member be renamed IL-37. IL-1F7 has various splice forms1,2,15,16, of which IL-1F7b is the most studied. We propose that IL-1F7a, IL-1F7b and so on be renamed IL-37a, IL-37b and so on. The one remaining IL-1 family member, for which no function has yet been demonstrated, is IL-1F10; however, as evidence of its properties remains limited, we suggest that it retain its IL-1F designation until a function is clearly identified, although it might be prudent to reserve the designation IL-38 for this eventuality.

miRNA malfunction causes spinal motor neuron disease

Abstract: Defective RNA metabolism is an emerging mechanism involved in ALS pathogenesis and possibly in other neurodegenerative disorders. Here, we show that microRNA (miRNA) activity is essential for long-term survival of postmitotic spinal motor neurons (SMNs) in vivo. Thus, mice that do not process miRNA in SMNs exhibit hallmarks of spinal muscular atrophy (SMA), including sclerosis of the spinal cord ventral horns, aberrant end plate architecture, and myofiber atrophy with signs of denervation. Furthermore, a neurofilament heavy subunit previously implicated in motor neuron degeneration is specifically up-regulated in miRNA-deficient SMNs. We demonstrate that the heavy neurofilament subunit is a target of miR-9, a miRNA that is specifically down-regulated in a genetic model of SMA. These data provide evidence for miRNA function in SMN diseases and emphasize the potential role of miR-9–based regulatory mechanisms in adult neurons and neurodegenerative states.

Coordination Capacity

Abstract: We develop elements of a theory of cooperation and coordination in networks. Rather than considering a communication network as a means of distributing information, or of reconstructing random processes at remote nodes, we ask what dependence can be established among the nodes given the communication constraints. Specifically, in a network with communication rates {Ri,j} between the nodes, we ask what is the set of all achievable joint distributions p(x1, ..., xm) of actions at the nodes of the network. Several networks are solved, including arbitrarily large cascade networks. Distributed cooperation can be the solution to many problems such as distributed games, distributed control, and establishing mutual information bounds on the influence of one part of a physical system on another.