Showing papers by "Bar-Ilan University published in 2013"

Processes and patterns of oceanic nutrient limitation

Abstract: Microbial activity is a fundamental component of oceanic nutrient cycles. Photosynthetic microbes, collectively termed phytoplankton, are responsible for the vast majority of primary production in marine waters. The availability of nutrients in the upper ocean frequently limits the activity and abundance of these organisms. Experimental data have revealed two broad regimes of phytoplankton nutrient limitation in the modern upper ocean. Nitrogen availability tends to limit productivity throughout much of the surface low-latitude ocean, where the supply of nutrients from the subsurface is relatively slow. In contrast, iron often limits productivity where subsurface nutrient supply is enhanced, including within the main oceanic upwelling regions of the Southern Ocean and the eastern equatorial Pacific. Phosphorus, vitamins and micronutrients other than iron may also (co-)limit marine phytoplankton. The spatial patterns and importance of co-limitation, however, remain unclear. Variability in the stoichiometries of nutrient supply and biological demand are key determinants of oceanic nutrient limitation. Deciphering the mechanisms that underpin this variability, and the consequences for marine microbes, will be a challenge. But such knowledge will be crucial for accurately predicting the consequences of ongoing anthropogenic perturbations to oceanic nutrient biogeochemistry.

Mg rechargeable batteries: an on-going challenge

Abstract: The first working Mg rechargeable battery prototypes were ready for presentation about 13 years ago after two breakthroughs. The first was the development of non-Grignard Mg complex electrolyte solutions with reasonably wide electrochemical windows in which Mg electrodes are fully reversible. The second breakthrough was attained by demonstrating high-rate Mg cathodes based on Chevrel phases. These prototypes could compete with lead–acid or Ni–Cd batteries in terms of energy density, very low self-discharge, a wide temperature range of operation, and an impressive prolonged cycle life. However, the energy density and rate capability of these Mg battery prototypes were not attractive enough to commercialize them. Since then we have seen gradual progress in the development of better electrolyte solutions, as well as suggestions of new cathodes. In this article we review the recent accumulated experience, understandings, new strategies and materials, in the continuous R&D process of non-aqueous Mg batteries. This paper provides a road-map of this field during the last decade.

Universal Dependency Annotation for Multilingual Parsing

Abstract: We present a new collection of treebanks with homogeneous syntactic dependency annotation for six languages: German, English, Swedish, Spanish, French and Korean. To show the usefulness of such a resource, we present a case study of crosslingual transfer parsing with more reliable evaluation than has been possible before. This ‘universal’ treebank is made freely available in order to facilitate research on multilingual dependency parsing. 1

Construction safety training using immersive virtual reality

Abstract: Construction workers’ ability to identify and assess risks is acquired through training and experience and is among the key factors that determine their behaviour and thus their safety. Yet researchers have questioned the effectiveness of conventional safety training. This research tested the hypotheses that safety training in a virtual reality (VR) construction site would be feasible and more effective, in terms of workers’ learning and recall in identifying and assessing construction safety risks, than would equivalent training using conventional methods. Sixty-six subjects were provided training in construction safety and their safety knowledge was tested prior to the training, immediately afterward, and one month later. Half of the subjects received traditional classroom training with visual aids; the other half were trained using a 3D immersive VR power-wall. Significant advantage was found for VR training for stone cladding work and for cast-in-situ concrete work, but not for general site safety. VR...

Mn-doped monolayer MoS 2 : An atomically thin dilute magnetic semiconductor

Abstract: We investigate the electronic and magnetic properties of Mn-doped monolayer MoS${}_{2}$ using a combination of first-principles density functional theory (DFT) calculations and Monte Carlo simulations. Mn dopants that are substitutionally inserted at Mo sites are shown to couple ferromagnetically via a double-exchange mechanism. This interaction is relatively short ranged, making percolation a key factor in controlling long-range magnetic order. The DFT results are parameterized using an empirical model to facilitate Monte Carlo studies of concentration- and temperature-dependent ordering in these systems, through which we obtain Curie temperatures in excess of room temperature for Mn doping in the range of 10--15$%$. Our studies demonstrate the potential for engineering a new class of atomically thin dilute magnetic semiconductors based on Mn-doped MoS${}_{2}$ monolayers.

The structural basis of antibody-antigen recognition.

Abstract: The function of antibodies (Abs) involves specific binding to antigens (Ags) and activation of other components of the immune system to fight pathogens The six hypervariable loops within the variable domains of Abs, commonly termed complementarity determining regions (CDRs), are widely assumed to be responsible for Ag recognition, while the constant domains are believed to mediate effector activation Recent studies and analyses of the growing number of available Ab structures, indicate that this clear functional separation between the two regions may be an oversimplification Some positions within the CDRs have been shown to never participate in Ag binding and some off-CDRs residues often contribute critically to the interaction with the Ag Moreover, there is now growing evidence for non-local and even allosteric effects in Ab-Ag interaction in which Ag binding affects the constant region and vice versa This review summarizes and discusses the structural basis of Ag recognition, elaborating on the contribution of different structural determinants of the Ab to Ag binding and recognition We discuss the CDRs, the different approaches for their identification and their relationship to the Ag interface We also review what is currently known about the contribution of non-CDRs regions to Ag recognition, namely the framework regions (FRs) and the constant domains The suggested mechanisms by which these regions contribute to Ag binding are discussed On the Ag side of the interaction, we discuss attempts to predict B-cell epitopes and the suggested idea to incorporate Ab information into B-cell epitope prediction schemes Beyond improving the understanding of immunity, characterization of the functional role of different parts of the Ab molecule may help in Ab engineering, design of CDR-derived peptides, and epitope prediction

Cyclophosphamide triggers follicle activation and "burnout"; AS101 prevents follicle loss and preserves fertility.

Abstract: Premature ovarian failure and infertility are major side effects of chemotherapy treatments in young cancer patients A more thorough understanding of the mechanism behind chemotherapy-induced follicle loss is necessary to develop new methods to preserve fertility in these patients We show that the alkylating agent cyclophosphamide (Cy) activates the growth of the quiescent primordial follicle population in mice, resulting in loss of ovarian reserve Despite the initial massive apoptosis observed in growing, though not in resting, follicles of Cy-treated mice, differential follicle counts demonstrated both a decrease in primordial follicles and an increase in early growing follicles Immunohistochemistry showed that granulosa cells were undergoing proliferation Analysis of the phosphatidylinositol 3-kinase signaling pathway demonstrated that Cy increased phosphorylation of proteins that stimulate follicle activation in the oocytes and granulosa cells Coadministration of an immunomodulator, AS101, reduced follicle activation, thereby increasing follicle reserve and rescuing fertility after Cy, and also increased the efficacy of Cy against breast cancer cell lines These findings suggest that the mechanism in Cy-induced loss of ovarian reserve is accelerated primordial follicle activation, which results in a “burnout” effect and follicle depletion By preventing this activation, AS101 shows potential as an ovarian-protective agent, which may be able to preserve fertility in female cancer patients

Recognizing Textual Entailment: Models and Applications

Abstract: In the last few years, a number of NLP researchers have developed and participated in the task of Recognizing Textual Entailment (RTE). This task encapsulates Natural Language Understanding capabilities within a very simple interface: recognizing when the meaning of a text snippet is contained in the meaning of a second piece of text. This simple abstraction of an exceedingly complex problem has broad appeal partly because it can be conceived also as a component in other NLP applications, from Machine Translation to Semantic Search to Information Extraction. It also avoids commitment to any specific meaning representation and reasoning framework, broadening its appeal within the research community. This level of abstraction also facilitates evaluation, a crucial component of any technological advancement program. This book explains the RTE task formulation adopted by the NLP research community, and gives a clear overview of research in this area. It draws out commonalities in this research, detailing the intuitions behind dominant approaches and their theoretical underpinnings. This book has been written with a wide audience in mind, but is intended to inform all readers about the state of the art in this fascinating field, to give a clear understanding of the principles underlying RTE research to date, and to highlight the short- and long-term research goals that will advance this technology.

Electrochemical and spectroscopic analysis of Mg2+ intercalation into thin film electrodes of layered oxides: V2O5 and MoO3.

Abstract: Electrochemical, surface, and structural studies related to rechargeable Mg batteries were carried out with monolithic thin-film cathodes comprising layered V2O5 and MoO3. The reversible intercalation reactions of these electrodes with Mg ion in nonaqueous Mg salt solutions were explored using a variety of analytical tools. These included slow-scan rate cyclic voltammetry (SSCV), chrono-potentiometry (galvanostatic cycling), Raman and photoelectron spectroscopies, high-resolution microscopy, and XRD. The V2O5 electrodes exhibited reversible Mg-ion intercalation at capacities around 150-180 mAh g(-1) with 100% efficiency. A capacity of 220 mAh g(-1) at >95% efficiency was obtained with MoO3 electrodes. By applying the electrochemical driving force sufficiently slowly it was possible to measure the electrodes at equilibrium conditions and verify by spectroscopy, microscopy, and diffractometry that these electrodes undergo fully reversible structural changes upon Mg-ion insertion/deinsertion cycling.

The Challenge of Romantic Relationships in Emerging Adulthood Reconceptualization of the Field

Abstract: Although theories of romantic stage development suggest that youth in the period of emerging adulthood are fully capable of commitment to an intimate romantic relationship, recent research suggests that the relationships of many young people are quite different. Marriage and other forms of deep commitment are delayed while many youth engage in short-term casual encounters or in noncommitted relationships. In this article, we suggest that these data pose a challenge to stage theories that can be reconciled by considering the developmental life tasks that emerging adults must simultaneously resolve. We propose a transitional emerging adult romantic stage, coordinating romance and life plans, in which young people strive to integrate their career paths and life plans with those of a romantic partner. Resolution of this stage provides the grounding for long-term commitment to a life partner. This proposal is discussed within the perspective of life cycle and evolutionary life history theories.

Fast Translocation of Proteins through Solid State Nanopores

Abstract: Measurements on protein translocation through solid-state nanopores reveal anomalous (non-Smoluchowski) transport behavior, as evidenced by extremely low detected event rates; that is, the capture rates are orders of magnitude smaller than what is theoretically expected. Systematic experimental measurements of the event rate dependence on the diffusion constant are performed by translocating proteins ranging in size from 6 to 660 kDa. The discrepancy is observed to be significantly larger for smaller proteins, which move faster and have a lower signal-to-noise ratio. This is further confirmed by measuring the event rate dependence on the pore size and concentration for a large 540 kDa protein and a small 37 kDa protein, where only the large protein follows the expected behavior. We dismiss various possible causes for this phenomenon and conclude that it is due to a combination of the limited temporal resolution and low signal-to-noise ratio. A one-dimensional first-passage time-distribution model supports...

Leadership, Creative Problem-Solving Capacity, and Creative Performance: The Importance of Knowledge Sharing

Abstract: This article presents two studies that examine whether leader supportive behaviors facilitate knowledge sharing and employee creative problem-solving capacity, thereby enhancing creative performance. The findings from both studies indicate that leader supportive behaviors are directly and indirectly related, through both internal and external knowledge sharing, to employee creative problem-solving capacity. In addition, creative problem solving was related to the two dimensions of creative performance—fluency and originality. However, a test of the mediation model indicated that creative problem solving only mediated the relationship between internal knowledge sharing creative performance and originality. These findings highlight the complex process by which leaders facilitate both internal and external knowledge sharing and employee creative problem-solving capacity, thereby improving employee creative performance.

A Simple Proof of the A2 Conjecture

Abstract: We give a simple proof of the A2 conjecture proved recently by T. Hytonen. Our proof avoids completely the notion of the Haar shift operator, and it is based only on the “local mean oscillation decomposition”. Also our proof yields a simple proof of the “two-weight conjecture” as well.

Temporal-Spatial Interaction between Reactive Oxygen Species and Abscisic Acid Regulates Rapid Systemic Acclimation in Plants

Abstract: Being sessile organisms, plants evolved sophisticated acclimation mechanisms to cope with abiotic challenges in their environment. These are activated at the initial site of exposure to stress, as well as in systemic tissues that have not been subjected to stress (termed systemic acquired acclimation [SAA]). Although SAA is thought to play a key role in plant survival during stress, little is known about the signaling mechanisms underlying it. Here, we report that SAA in plants requires at least two different signals: an autopropagating wave of reactive oxygen species (ROS) that rapidly spreads from the initial site of exposure to the entire plant and a stress-specific signal that conveys abiotic stress specificity. We further demonstrate that SAA is stress specific and that a temporal–spatial interaction between ROS and abscisic acid regulates rapid SAA to heat stress in plants. In addition, we demonstrate that the rapid ROS signal is associated with the propagation of electric signals in Arabidopsis thaliana. Our findings unravel some of the basic signaling mechanisms underlying SAA in plants and reveal that signaling events and transcriptome and metabolome reprogramming of systemic tissues in response to abiotic stress occur at a much faster rate than previously envisioned.

IL-27 acts on DCs to suppress the T cell response and autoimmunity by inducing expression of the immunoregulatory molecule CD39

Abstract: Dendritic cells (DCs) control the balance between effector T cells and regulatory T cells in vivo. Hence, the study of DCs might identify mechanisms of disease pathogenesis and guide new therapeutic approaches for disorders mediated by the immune system. We found that interleukin 27 (IL-27) signaling in mouse DCs limited the generation of effector cells of the TH1 and TH17 subsets of helper T cells and the development of experimental autoimmune encephalomyelitis (EAE). The effects of IL-27 were mediated at least in part through induction of the immunoregulatory molecule CD39 in DCs. IL-27-induced CD39 decreased the extracellular concentration of ATP and downregulated nucleotide-dependent activation of the NLRP3 inflammasome. Finally, therapeutic vaccination with IL-27-conditioned DCs suppressed established relapsing-remitting EAE. Thus, IL-27 signaling in DCs limited pathogenic T cell responses and the development of autoimmunity.

The extreme vulnerability of interdependent spatially embedded networks

Abstract: Networks of networks are vulnerable: a failure in one sub-network can bring the rest crashing down. Previous simulations have suggested that randomly positioned networks might offer some limited robustness under certain circumstances. Analysis now shows, however, that real-world interdependent networks, where nodes are positioned according to geographical constraints, might not be so resilient.

Fast approximation algorithms for the diameter and radius of sparse graphs

Abstract: The diameter and the radius of a graph are fundamental topological parameters that have many important practical applications in real world networks. The fastest combinatorial algorithm for both parameters works by solving the all-pairs shortest paths problem (APSP) and has a running time of ~O(mn) in m-edge, n-node graphs. In a seminal paper, Aingworth, Chekuri, Indyk and Motwani [SODA'96 and SICOMP'99] presented an algorithm that computes in ~O(m√ n + n2) time an estimate D for the diameter D, such that ⌊ 2/3 D ⌋ ≤ ^D ≤ D. Their paper spawned a long line of research on approximate APSP. For the specific problem of diameter approximation, however, no improvement has been achieved in over 15 years.Our paper presents the first improvement over the diameter approximation algorithm of Aingworth et. al, producing an algorithm with the same estimate but with an expected running time of ~O(m√ n). We thus show that for all sparse enough graphs, the diameter can be 3/2-approximated in o(n2) time. Our algorithm is obtained using a surprisingly simple method of neighborhood depth estimation that is strong enough to also approximate, in the same running time, the radius and more generally, all of the eccentricities, i.e. for every node the distance to its furthest node.We also provide strong evidence that our diameter approximation result may be hard to improve. We show that if for some constant e>0 there is an O(m2-e) time (3/2-e)-approximation algorithm for the diameter of undirected unweighted graphs, then there is an O*( (2-δ)n) time algorithm for CNF-SAT on n variables for constant δ>0, and the strong exponential time hypothesis of [Impagliazzo, Paturi, Zane JCSS'01] is false.Motivated by this negative result, we give several improved diameter approximation algorithms for special cases. We show for instance that for unweighted graphs of constant diameter D not divisible by 3, there is an O(m2-e) time algorithm that gives a (3/2-e) approximation for constant e>0. This is interesting since the diameter approximation problem is hardest to solve for small D.

Oxytocin enhances brain function in children with autism

Abstract: Following intranasal administration of oxytocin (OT), we measured, via functional MRI, changes in brain activity during judgments of socially (Eyes) and nonsocially (Vehicles) meaningful pictures in 17 children with high-functioning autism spectrum disorder (ASD). OT increased activity in the striatum, the middle frontal gyrus, the medial prefrontal cortex, the right orbitofrontal cortex, and the left superior temporal sulcus. In the striatum, nucleus accumbens, left posterior superior temporal sulcus, and left premotor cortex, OT increased activity during social judgments and decreased activity during nonsocial judgments. Changes in salivary OT concentrations from baseline to 30 min postadministration were positively associated with increased activity in the right amygdala and orbitofrontal cortex during social vs. nonsocial judgments. OT may thus selectively have an impact on salience and hedonic evaluations of socially meaningful stimuli in children with ASD, and thereby facilitate social attunement. These findings further the development of a neurophysiological systems-level understanding of mechanisms by which OT may enhance social functioning in children with ASD.

Imaging currents in HgTe quantum wells in the quantum spin Hall regime

Abstract: The quantum spin Hall (QSH) state is a state of matter characterized by a non-trivial topology of its band structure, and associated conducting edge channels 1‐5 . The QSH state was predicted 6 and experimentally demonstrated 7 to be realized in HgTe quantum wells. The existence of the edge channels has been inferred from local and non-local transport measurements in sufficiently small devices 7‐9 . Here we directly confirm the existence of the edge channels by imaging the magnetic fields produced by current flowing in large Hall bars made from HgTe quantum wells. These images distinguish between current that passes through each edge and the bulk. On tuning the bulk conductivity by gating or raising the temperature, we observe a regime in which the edge channels clearly coexist with the conducting bulk, providing input to the question of how ballistic transport may be limited in the edge channels. Our results represent a versatile method for characterization of new QSH materials systems 10‐13 . Like an ordinary insulator, the QSH state has a bulk energy gap, but the QSH state supports within the gap a pair of counter-propagating spin-polarized edge modes 15 . The QSH state is predicted in HgTe/(Hg,Cd)Te quantum wells thicker than a critical thickness of 6.3nm, whereas thinner quantum wells should beordinaryinsulators 6,7 .Theedgemodesaretheoreticallyprotected against backscattering by their orthogonal spin states 1416 , and therefore should have a quantized conductance of e 2 =h, where e is

More efficient oblivious transfer and extensions for faster secure computation

Abstract: Protocols for secure computation enable parties to compute a joint function on their private inputs without revealing anything but the result. A foundation for secure computation is oblivious transfer (OT), which traditionally requires expensive public key cryptography. A more efficient way to perform many OTs is to extend a small number of base OTs using OT extensions based on symmetric cryptography.In this work we present optimizations and efficient implementations of OT and OT extensions in the semi-honest model. We propose a novel OT protocol with security in the standard model and improve OT extensions with respect to communication complexity, computation complexity, and scalability. We also provide specific optimizations of OT extensions that are tailored to the secure computation protocols of Yao and Goldreich-Micali-Wigderson and reduce the communication complexity even further. We experimentally verify the efficiency gains of our protocols and optimizations. By applying our implementation to current secure computation frameworks, we can securely compute a Levenshtein distance circuit with 1.29 billion AND gates at a rate of 1.2 million AND gates per second. Moreover, we demonstrate the importance of correctly implementing OT within secure computation protocols by presenting an attack on the FastGC framework.

Role of Thermal Heating on the Voltage Induced Insulator-Metal Transition in VO 2

Abstract: We show that the main mechanism for the dc voltage or dc current induced insulator-metal transition in vanadium dioxide VO(2) is due to local Joule heating and not a purely electronic effect. This "tour de force" experiment was accomplished by using the fluorescence spectra of rare-earth doped micron sized particles as local temperature sensors. As the insulator-metal transition is induced by a dc voltage or dc current, the local temperature reaches the transition temperature indicating that Joule heating plays a predominant role. This has critical implications for the understanding of the dc voltage or dc current induced insulator-metal transition and has a direct impact on applications which use dc voltage or dc current to externally drive the transition.

Coverage and adoption of altmetrics sources in the bibliometric community

Abstract: Altmetrics, indices based on social media platforms and tools, have recently emerged as alternative means of measuring scholarly impact. Such indices assume that scholars in fact populate online social environments, and interact with scholarly products there. We tested this assumption by examining the use and coverage of social media environments amongst a sample of bibliometricians. As expected, coverage varied: 82% of articles published by sampled bibliometricians were included in Mendeley libraries, while only 28% were included in CiteULike. Mendeley bookmarking was moderately correlated (.45) with Scopus citation. Over half of respondents asserted that social media tools were affecting their professional lives, although uptake of online tools varied widely. 68% of those surveyed had LinkedIn accounts, while this http URL, Mendeley, and ResearchGate each claimed a fifth of respondents. Nearly half of those responding had Twitter accounts, which they used both personally and professionally. Surveyed bibliometricians had mixed opinions on altmetrics' potential; 72% valued download counts, while a third saw potential in tracking articles' influence in blogs, Wikipedia, reference managers, and social media. Altogether, these findings suggest that some online tools are seeing substantial use by bibliometricians, and that they present a potentially valuable source of impact data.