Showing papers by "University of Haifa published in 2017"

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication

Abstract: Wheat (Triticum spp.) is one of the founder crops that likely drove the Neolithic transition to sedentary agrarian societies in the Fertile Crescent more than 10,000 years ago. Identifying genetic modifications underlying wheat's domestication requires knowledge about the genome of its allo-tetraploid progenitor, wild emmer (T. turgidum ssp. dicoccoides). We report a 10.1-gigabase assembly of the 14 chromosomes of wild tetraploid wheat, as well as analyses of gene content, genome architecture, and genetic diversity. With this fully assembled polyploid wheat genome, we identified the causal mutations in Brittle Rachis 1 (TtBtr1) genes controlling shattering, a key domestication trait. A study of genomic diversity among wild and domesticated accessions revealed genomic regions bearing the signature of selection under domestication. This reference assembly will serve as a resource for accelerating the genome-assisted improvement of modern wheat varieties.

Seaweed production: overview of the global state of exploitation, farming and emerging research activity

Abstract: The use of seaweeds has a long history, as does the cultivation of a select and relatively small group of species. This review presents several aspects of seaweed production, such as an update on t...

A Research Synthesis of the Associations between Socioeconomic Background, Inequality, School Climate, and Academic Achievement.

Abstract: Educational researchers and practitioners assert that supportive school and classroom climates can positively influence the academic outcomes of students, thus potentially reducing academic achieve

Health literacy in childhood and youth: a systematic review of definitions and models

Abstract: Children and young people constitute a core target group for health literacy research and practice: during childhood and youth, fundamental cognitive, physical and emotional development processes take place and health-related behaviours and skills develop. However, there is limited knowledge and academic consensus regarding the abilities and knowledge a child or young person should possess for making sound health decisions. The research presented in this review addresses this gap by providing an overview and synthesis of current understandings of health literacy in childhood and youth. Furthermore, the authors aim to understand to what extent available models capture the unique needs and characteristics of children and young people. Six databases were systematically searched with relevant search terms in English and German. Of the n = 1492 publications identified, N = 1021 entered the abstract screening and N = 340 full-texts were screened for eligibility. A total of 30 articles, which defined or conceptualized generic health literacy for a target population of 18 years or younger, were selected for a four-step inductive content analysis. The systematic review of the literature identified 12 definitions and 21 models that have been specifically developed for children and young people. In the literature, health literacy in children and young people is described as comprising variable sets of key dimensions, each appearing as a cluster of related abilities, skills, commitments, and knowledge that enable a person to approach health information competently and effectively and to derive at health-promoting decisions and actions. Identified definitions and models are very heterogeneous, depicting health literacy as multidimensional, complex construct. Moreover, health literacy is conceptualized as an action competence, with a strong focus on personal attributes, while also recognising its interrelatedness with social and contextual determinants. Life phase specificities are mainly considered from a cognitive and developmental perspective, leaving children’s and young people’s specific needs, vulnerabilities, and social structures poorly incorporated within most models. While a critical number of definitions and models were identified for youth or secondary school students, similar findings are lacking for children under the age of ten or within a primary school context.

Deep convolutional neural networks for Raman spectrum recognition: a unified solution.

Abstract: Machine learning methods have found many applications in Raman spectroscopy, especially for the identification of chemical species. However, almost all of these methods require non-trivial preprocessing such as baseline correction and/or PCA as an essential step. Here we describe our unified solution for the identification of chemical species in which a convolutional neural network is trained to automatically identify substances according to their Raman spectrum without the need for preprocessing. We evaluated our approach using the RRUFF spectral database, comprising mineral sample data. Superior classification performance is demonstrated compared with other frequently used machine learning algorithms including the popular support vector machine method.

Amorphous calcium carbonate particles form coral skeletons.

Abstract: Do corals form their skeletons by precipitation from solution or by attachment of amorphous precursor particles as observed in other minerals and biominerals? The classical model assumes precipitation in contrast with observed "vital effects," that is, deviations from elemental and isotopic compositions at thermodynamic equilibrium. Here, we show direct spectromicroscopy evidence in Stylophora pistillata corals that two amorphous precursors exist, one hydrated and one anhydrous amorphous calcium carbonate (ACC); that these are formed in the tissue as 400-nm particles; and that they attach to the surface of coral skeletons, remain amorphous for hours, and finally, crystallize into aragonite (CaCO3). We show in both coral and synthetic aragonite spherulites that crystal growth by attachment of ACC particles is more than 100 times faster than ion-by-ion growth from solution. Fast growth provides a distinct physiological advantage to corals in the rigors of the reef, a crowded and fiercely competitive ecosystem. Corals are affected by warming-induced bleaching and postmortem dissolution, but the finding here that ACC particles are formed inside tissue may make coral skeleton formation less susceptible to ocean acidification than previously assumed. If this is how other corals form their skeletons, perhaps this is how a few corals survived past CO2 increases, such as the Paleocene-Eocene Thermal Maximum that occurred 56 Mya.

Analysis of Microbiome Data in the Presence of Excess Zeros.

Abstract: Motivation: An important feature of microbiome count data is the presence of a large number of zeros. A common strategy to handle these excess zeros is to add a small number called pseudo-count (e.g., 1). Other strategies include using various probability models to model the excess zero counts. Although adding a pseudo-count is simple and widely used, as demonstrated in this paper, it is not ideal. On the other hand, methods that model excess zeros using a probability model often make an implicit assumption that all zeros can be explained by a common probability models. As described in this article, this is not always recommended as there are potentially three types/sources of zeros in a microbiome data. The purpose of this paper is to develop a simple methodology to identify and accomodate three different types of zeros and to test hypotheses regarding the relative abundance of taxa in two or more experimental groups. Another major contribution of this paper is to perform constrained (directional or ordered) inference when there are more than two ordered experimental groups (e.g., subjects ordered by diet or age groups or environmental exposure groups). As far as we know this is the first paper that addresses such problems in the analysis of microbiome data. Results: Using extensive simulation studies, we demonstrate that the proposed methodology not only controls the false discovery rate at a desired level of significance while competing well in terms of power with DESeq2, a popular procedure derived from RNASeq literature. As expected, the method using pseudo-counts tends to be very conservative and the classical t-test that ignores the underlying simplex structure in the data has an inflated FDR.

Is the alliance really therapeutic? Revisiting this question in light of recent methodological advances.

Abstract: The therapeutic value of alliance is a contested supposition. Although many theorists and researchers believe that alliance is therapeutic in itself, others see it as a byproduct of effective treatment or as a common nonspecific factor enabling the truly effective ingredients of treatment to work. For many years, the debate was confined mainly to the domain of theory, and no studies were available to confirm which of these approaches is correct. The only empirical evidence that existed was studies showing a correlation between alliance and outcome, and advocates of the above conflicting opinions used the same correlation to prove the validity of their position. Over the last few years, however, a revolution has taken place in alliance research, which brings this theoretical debate into the realm of the empirical. Several recent alliance studies have applied advanced methodologies to achieve this aim. Based on an integration of these studies, the present article proposes a new model for understanding the potential therapeutic role of alliance as sufficient to induce change by itself. The model stresses the importance of differentiating between patients' general tendencies to form satisfying relationships with others, which affect also the relationship with the therapist ("trait-like" component of alliance), and the process of the development of changes in such tendencies through interaction with the therapist ("state-like" component of alliance). The former enables treatment to be effective; the latter makes alliance therapeutic. Based on the literature, this article attempts to determine which of these components is the predictor of treatment outcome. (PsycINFO Database Record

Efficacy of Cannabis-Based Medicines for Pain Management: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.

Abstract: BACKGROUND The management of chronic pain is a complex challenge worldwide. Cannabis-based medicines (CBMs) have proven to be efficient in reducing chronic pain, although the topic remains highly controversial in this field. OBJECTIVES This study's aim is to conduct a conclusive review and meta-analysis, which incorporates all randomized controlled trials (RCTs) in order to update clinicians' and researchers' knowledge regarding the efficacy and adverse events (AEs) of CBMs for chronic and postoperative pain treatment. STUDY DESIGN A systematic review and meta-analysis. METHODS An electronic search was conducted using Medline/Pubmed and Google Scholar with the use of Medical Subject Heading (MeSH) terms on all literature published up to July 2015. A follow-up manual search was conducted and included a complete cross-check of the relevant studies. The included studies were RCTs which compared the analgesic effects of CBMs to placebo. Hedges's g scores were calculated for each of the studies. A study quality assessment was performed utilizing the Jadad scale. A meta-analysis was performed utilizing random-effects models and heterogeneity between studies was statistically computed using I² statistic and tau² test. RESULTS The results of 43 RCTs (a total of 2,437 patients) were included in this review, of which 24 RCTs (a total of 1,334 patients) were eligible for meta-analysis. This analysis showed limited evidence showing more pain reduction in chronic pain -0.61 (-0.78 to -0.43, P < 0.0001), especially by inhalation -0.93 (-1.51 to -0.35, P = 0.001) compared to placebo. Moreover, even though this review consisted of some RCTs that showed a clinically significant improvement with a decrease of pain scores of 2 points or more, 30% or 50% or more, the majority of the studies did not show an effect. Consequently, although the primary analysis showed that the results were favorable to CBMs over placebo, the clinical significance of these findings is uncertain. The most prominent AEs were related to the central nervous and the gastrointestinal (GI) systems. LIMITATIONS Publication limitation could have been present due to the inclusion of English-only published studies. Additionally, the included studies were extremely heterogeneous. Only 7 studies reported on the patients' history of prior consumption of CBMs. Furthermore, since cannabinoids are surrounded by considerable controversy in the media and society, cannabinoids have marked effects, so that inadequate blinding of the placebo could constitute an important source of limitation in these types of studies. CONCLUSIONS The current systematic review suggests that CBMs might be effective for chronic pain treatment, based on limited evidence, primarily for neuropathic pain (NP) patients. Additionally, GI AEs occurred more frequently when CBMs were administered via oral/oromucosal routes than by inhalation.Key words: Cannabis, CBMs, chronic pain, postoperative pain, review, meta-analysis.

The sponge microbiome project

Abstract: Marine sponges (phylum Porifera) are a diverse, phylogenetically deep-branching clade known for forming intimate partnerships with complex communities of microorganisms. To date, 16S rRNA gene sequencing studies have largely utilised different extraction and amplification methodologies to target the microbial communities of a limited number of sponge species, severely limiting comparative analyses of sponge microbial diversity and structure. Here, we provide an extensive and standardised dataset that will facilitate sponge microbiome comparisons across large spatial, temporal, and environmental scales. Samples from marine sponges (n = 3569 specimens), seawater (n = 370), marine sediments (n = 65) and other environments (n = 29) were collected from different locations across the globe. This dataset incorporates at least 268 different sponge species, including several yet unidentified taxa. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA using standardised procedures. Raw sequences (total of 1.1 billion sequences) were processed and clustered with (i) a standard protocol using QIIME closed-reference picking resulting in 39 543 operational taxonomic units (OTU) at 97% sequence identity, (ii) a de novo clustering using Mothur resulting in 518 246 OTUs, and (iii) a new high-resolution Deblur protocol resulting in 83 908 unique bacterial sequences. Abundance tables, representative sequences, taxonomic classifications, and metadata are provided. This dataset represents a comprehensive resource of sponge-associated microbial communities based on 16S rRNA gene sequences that can be used to address overarching hypotheses regarding host-associated prokaryotes, including host specificity, convergent evolution, environmental drivers of microbiome structure, and the sponge-associated rare biosphere.

Deep Convolutional Neural Networks for Raman Spectrum Recognition: A Unified Solution

Abstract: Machine learning methods have found many applications in Raman spectroscopy, especially for the identification of chemical species. However, almost all of these methods require non-trivial preprocessing such as baseline correction and/or PCA as an essential step. Here we describe our unified solution for the identification of chemical species in which a convolutional neural network is trained to automatically identify substances according to their Raman spectrum without the need of ad-hoc preprocessing steps. We evaluated our approach using the RRUFF spectral database, comprising mineral sample data. Superior classification performance is demonstrated compared with other frequently used machine learning algorithms including the popular support vector machine.

The Mediterranean dietary pattern as the diet of choice for non-alcoholic fatty liver disease: Evidence and plausible mechanisms.

Abstract: Non-alcoholic fatty liver disease (NAFLD) has become a major global health burden, leading to increased risk for cirrhosis, hepatocellular carcinoma, type-2 diabetes and cardiovascular disease. Lifestyle intervention aiming at weight reduction is the most established treatment. However, changing the dietary composition even without weight loss can also reduce steatosis and improve metabolic alterations as insulin resistance and lipid profile. The Mediterranean diet (MD) pattern has been proposed as appropriate for this goal, and was recommended as the diet of choice for the treatment of NAFLD by the EASL-EASD-EASO Clinical Practice Guidelines. The MD has an established superiority in long term weight reduction over low fat diet, but it improves metabolic status and steatosis even without it. However, the effect on liver inflammation and fibrosis was tested only in few observational studies with positive results. Furthermore, considering the strong association between NAFLD and diabetes and CVD, the MD has a highly established advantage in prevention of these diseases, demonstrated in randomized clinical trials. The individual components of the MD such as olive oil, fish, nuts, whole grains, fruits, and vegetables, have been shown to beneficially effect or negatively correlate with NAFLD, while consumption of components that characterize a Western dietary pattern as soft drinks, fructose, meat and saturated fatty acids have been shown to have detrimental association with NAFLD. In this review we will cover the epidemiological evidence and the plausible molecular mechanisms by which the MD as a whole and each of its components can be of benefit in NAFLD.

Avian egg shape: Form, function, and evolution

Abstract: Avian egg shape is generally explained as an adaptation to life history, yet we currently lack a global synthesis of how egg-shape differences arise and evolve. Here, we apply morphometric, mechanistic, and macroevolutionary analyses to the egg shapes of 1400 bird species. We characterize egg-shape diversity in terms of two biologically relevant variables, asymmetry and ellipticity, allowing us to quantify the observed morphologies in a two-dimensional morphospace. We then propose a simple mechanical model that explains the observed egg-shape diversity based on geometric and material properties of the egg membrane. Finally, using phylogenetic models, we show that egg shape correlates with flight ability on broad taxonomic scales, suggesting that adaptations for flight may have been critical drivers of egg-shape variation in birds.

Air-light estimation using haze-lines

Abstract: Outdoor images taken in bad weather conditions, such as haze and fog, look faded and have reduced contrast. Recently there has been great success in single image dehazing, i.e., improving the visibility and restoring the colors from a single image. A crucial step in these methods is the calculation of the air-light color, the color of an area of the image with no objects in line-of-sight. We propose a new method for calculating the air-light. The method relies on the haze-lines prior that was recently introduced. This prior is based on the observation that the pixel values of a hazy image can be modeled as lines in RGB space that intersect at the air-light. We use Hough transform in RGB space to vote for the location of the air-light. We evaluate the proposed method on an existing dataset of real world images, as well as some synthetic and other real images. Our method performs on-par with current state-of-the-art techniques and is more computationally efficient.

No Bot Expects the DeepCAPTCHA! Introducing Immutable Adversarial Examples, With Applications to CAPTCHA Generation

Abstract: Recent advances in deep learning (DL) allow for solving complex AI problems that used to be considered very hard. While this progress has advanced many fields, it is considered to be bad news for Completely Automated Public Turing tests to tell Computers and Humans Apart (CAPTCHAs), the security of which rests on the hardness of some learning problems. In this paper, we introduce DeepCAPTCHA, a new and secure CAPTCHA scheme based on adversarial examples , an inherit limitation of the current DL networks. These adversarial examples are constructed inputs, either synthesized from scratch or computed by adding a small and specific perturbation called adversarial noise to correctly classified items, causing the targeted DL network to misclassify them. We show that plain adversarial noise is insufficient to achieve secure CAPTCHA schemes, which leads us to introduce immutable adversarial noise —an adversarial noise that is resistant to removal attempts. In this paper, we implement a proof of concept system, and its analysis shows that the scheme offers high security and good usability compared with the best previously existing CAPTCHAs.

Interannual thermohaline (1979–2014) and nutrient (2002–2014) dynamics in the Levantine surface and intermediate water masses, SE Mediterranean Sea

Abstract: In this study a > 30 years dataset of 1382 CTD casts in the Levantine Basin (LB) was analyzed to examine the thermohaline trends of the Surface (~ 0–50 m) and Intermediate (~ 150–350 m) Water masses (LSW, LIW). In addition, a 13 years (2002–2014) dataset of 3 deep water stations (> 1000 m) in the eastern Levantine Basin (Haifa Section cruises) that were visited 2–3 times annually was used to explore the relations between the physical and nutrient properties in the LIW. Over the past 30 years the LSW and LIW masses displayed positive long-term trends in salinity of + 0.008 ± 0.006 and + 0.005 ± 0.003 year − 1 , respectively, and temperature of + 0.12 ± 0.07 and + 0.03 ± 0.02 °C year − 1 , respectively. Decadal variations in salinity and temperature were superimposed on all long-term trends. Throughout the period 2002–2014 nutrient levels in the LIW core and corresponding integrated values of chlorophyll a also varied in nearly opposite phase with temperature and salinity. Furthermore, these variations occurred with a similar decadal periodicity, but with shifted phase with those observed in the Southern Adriatic and North Ionian Seas in the same water mass. The latter were considered to be caused by decadal reversals in the North Ionian Gyre, i.e. Bimodal Oscillation System (BiOS). These results indicate that the thermohaline flux variations attributed to the BiOS mechanism have a significant impact in magnitude on the available nutrients and the dynamics of the eastern basin primary productivity. These results should be taken into consideration in assessing the relative contribution of external nutrient loads in comparison to those attributed to variations in thermohaline fluxes and in the assessment of long-term and interannual primary productivity (chlorophyll a and nutrients) trends in the LB.

Evolutionary Conservation of ABA Signaling for Stomatal Closure

Abstract: Abscisic acid (ABA)-driven stomatal regulation reportedly evolved after the divergence of ferns, during the early evolution of seed plants approximately 360 million years ago. This hypothesis is based on the observation that the stomata of certain fern species are unresponsive to ABA, but exhibit passive hydraulic control. However, ABA-induced stomatal closure was detected in some mosses and lycophytes. Here, we observed that a number of ABA signaling and membrane transporter protein families diversified over the evolutionary history of land plants. The aquatic ferns Azolla filiculoides and Salvinia cucullata have representatives of 23 families of proteins orthologous to those of Arabidopsis (Arabidopsis thaliana) and all other land plant species studied. Phylogenetic analysis of the key ABA signaling proteins indicates an evolutionarily conserved stomatal response to ABA. Moreover, comparative transcriptomic analysis has identified a suite of ABA-responsive genes that differentially expressed in a terrestrial fern species, Polystichum proliferum. These genes encode proteins associated with ABA biosynthesis, transport, reception, transcription, signaling, and ion and sugar transport, which fit the general ABA signaling pathway constructed from Arabidopsis and Hordeum vulgare. The retention of these key ABA-responsive genes could have had a profound effect on the adaptation of ferns to dry conditions. Furthermore, stomatal assays have shown the primary evidence for ABA-induced closure of stomata in two terrestrial fern species P. proliferum and Nephrolepis exaltata. In summary, we report, to our knowledge, new molecular and physiological evidence for the presence of active stomatal control in ferns.

Methods for scalar-on-function regression

Abstract: Recent years have seen an explosion of activity in the field of functional data analysis (FDA), in which curves, spectra, images, etc. are considered as basic functional data units. A central problem in FDA is how to fit regression models with scalar responses and functional data points as predictors. We review some of the main approaches to this problem, categorizing the basic model types as linear, nonlinear and nonparametric. We discuss publicly available software packages, and illustrate some of the procedures by application to a functional magnetic resonance imaging dataset.

Recovery and serious mental illness: a review of current clinical and research paradigms and future directions.

Abstract: Introduction: Recovery from serious mental illness has historically not been considered a likely or even possible outcome. However, a range of evidence suggests the courses of SMI are heterogeneous...

The Association between Imaging Parameters of the Paraspinal Muscles, Spinal Degeneration, and Low Back Pain.

Abstract: This narrative review investigated imaging parameters of the paraspinal muscles and their association with spinal degenerative features and low back pain (LBP) found in the literature. Three principal signs of muscle degeneration were detected on imaging: decreased muscle size, decreased radiographic density, and increased fat deposits. Men have a higher density of paraspinal muscles than women, younger individuals have a higher density than older ones, and lean individuals have a higher density than those with an increased body mass index. Fatty infiltration appears to be a late stage of muscular degeneration and can be measured noninvasively by an MRI scan. Fatty infiltration in the lumbar multifidus is common in adults and is strongly associated with LBP, especially in women, independent of body composition. Fatty infiltration develops in areas where most degenerative changes are found. MR spectroscopy studies have corroborated that the lumbar multifidus in LBP subjects has a significantly higher fat content than asymptomatic controls. There is a strong need for establishing uniform methods of evaluating normal parameters and degenerative changes of the paraspinal muscles. Additional imaging studies are needed to improve the understanding of the association and causal relationships between LBP, spinal degeneration, and changes in the paraspinal muscles.

Polymyxin monotherapy or in combination against carbapenem-resistant bacteria: systematic review and meta-analysis

Abstract: Objectives The objective of this study was to summarize available data on polymyxin-based combination therapy or monotherapy for carbapenem-resistant Gram-negative bacteria. Methods This is a systematic review. We included observational studies and randomized controlled trials (RCTs) comparing polymyxin monotherapy versus polymyxin-based combination therapy in adult patients with infections caused by carbapenem-resistant or carbapenemase-producing Gram-negative bacteria. Only named antibiotic regimens were included. The primary outcome was 30 day mortality. Unadjusted OR (uOR) and adjusted OR where available with 95% CI were pooled in random-effects meta-analyses. Results Twenty-two studies including 28 comparisons were included. Polymyxin monotherapy was associated with a uOR of 1.58 (95% CI = 1.03-2.42) for mortality compared with polymyxin/carbapenem combination therapy (seven observational studies, 537 patients), without heterogeneity. Subgrouping studies to serious and critical risk of bias resulted in uORs of 0.94 (95% CI = 0.42-2.09) and 1.94 (95% CI = 1.17-3.23), respectively. Mortality was significantly higher with polymyxin monotherapy compared with combination therapy with tigecycline, aminoglycosides or fosfomycin (potentially double-coverage regimens): uOR of 1.57 (95% CI = 1.06-2.32) overall (10 observational studies and 1 RCT, 585 patients, no heterogeneity) and uOR of 2.09 (95% CI = 1.21-3.6) for Klebsiella pneumoniae bacteraemia (7 observational studies, 285 patients, no heterogeneity); very low quality evidence. Two RCTs and one observational study assessing rifampicin/colistin combination therapy for Acinetobacter baumannii infections showed no difference in mortality compared with colistin monotherapy; moderate quality evidence. Conclusions The significant association observed in observational studies between polymyxin monotherapy and mortality cannot be taken as proof of combination therapy effects due to the low quality of the evidence. The only three RCTs to date show no effect of rifampicin/colistin or fosfomycin/colistin on mortality for Acinetobacter infections.