Parallel vs. Sequential Belief Propagation Decoding of LDPC Codes over GF(q) and Markov Sources

A sequential updating scheme (SUS) for belief propagation (BP) decoding of LDPC codes over Galois fields, $GF(q)$, and correlated Markov sources is proposed, and compared with the standard parallel updating scheme (PUS). A thorough experimental study of various transmission settings indicates that the convergence rate, in iterations, of the BP algorithm (and subsequently its complexity) for the SUS is about one half of that for the PUS, independent of the finite field size $q$. Moreover, this 1/2 factor appears regardless of the correlations of the source and the channel's noise model, while the error correction performance remains unchanged. These results may imply on the 'universality' of the one half convergence speed-up of SUS decoding

A new strategic framework for water-related health research

The aim of this study was to compile a new strategic framework to guide the funding and management of research in waterrelated human health in South Africa. This framework had to identify the research areas of highest need in the country and provide an effective, yet simple, tool for the management of research projects. A review of current water-related human health research was first undertaken. Using this review as background document, input was solicited from key people in Government, water boards, metro councils, science councils and universities. As part of the study, the country’s research support infrastructure for water-related health research was investigated. The framework was finalised at a stakeholder workshop. A structure of Thrust Areas, with Programmes under each Thrust Area, was suggested for research management and funding. A matrix system of research thrusts versus impacts/risks, interventions and governance was further constructed to assist in the identification of research gaps, rendering the framework a very useful tool in the funding and management of water-related human health research.Keywords: water, public health, research needs, research managemen

Coupling ideality of free electrons with photonic integrated waveguides

Recently, integrated photonics has brought new capabilities to electron microscopy and been used to demonstrate efficient electron phase modulation and electron-photon correlations. Here, we quantitatively analyze the interaction strength between a free electron and a photonic integrated circuit with a heterogeneous structure. We adopt a dissipative QED treatment and show that with proper electron beam positioning and waveguide geometry, one can achieve near-unity coupling ideality to a well-defined spatial-temporal waveguide mode. Furthermore, we show that the frequency and waveform of the coupled mode can be tailored to the application. These features show that photonic integrated waveguides are a promising platform for free-electron quantum optics with applications like high-fidelity electron-photon entanglement, heralded single-electron and photon state synthesis

An N-Terminal Extension to UBA5 Adenylation Domain Boosts UFM1 Activation: Isoform-Specific Differences in Ubiquitin-like Protein Activation

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.Modification of proteins by the ubiquitin-like protein, UFM1, requires activation of UFM1 by the E1-activating enzyme, UBA5. In humans, UBA5 possesses two isoforms, each comprising an adenylation domain, but only one containing an N-terminal extension. Currently, the role of the N-terminal extension in UFM1 activation is not clear. Here we provide structural and biochemical data on UBA5 N-terminal extension to understand its contribution to UFM1 activation. The crystal structures of the UBA5 long isoform bound to ATP with and without UFM1 show that the N-terminus not only is directly involved in ATP binding but also affects how the adenylation domain interacts with ATP. Surprisingly, in the presence of the N-terminus, UBA5 no longer retains the 1:2 ratio of ATP to UBA5, but rather this becomes a 1:1 ratio. Accordingly, the N-terminus significantly increases the affinity of ATP to UBA5. Finally, the N-terminus, although not directly involved in the E2 binding, stimulates transfer of UFM1 from UBA5 to the E2, UFC1.Marie Curie Career Integration GrantIsrael Science FoundationIsraeli Cancer Associatio

Scalar-mediated ttˉt\bar t forward-backward asymmetry

A large forward-backward asymmetry in $t\bar t$ production, for large invariant mass of the $t\bar t$ system, has been recently observed by the CDF collaboration. Among the scalar mediated mechanisms that can explain such a large asymmetry, only the t-channel exchange of a color-singlet weak-doublet scalar is consistent with both differential and integrated $t\bar t$ cross section measurements. Constraints from flavor changing processes dictate a very specific structure for the Yukawa couplings of such a new scalar. No sizable deviation in the differential or integrated $t\bar t$ production cross section is expected at the LHC.Comment: 22 pages, 1 figure and 2 tables. v2: Corrected Eqs.(50,51,74), adapted Fig.1, Tab.1 and relevant discussions. Extended discussion of top decay and single to

CP violation Beyond the MSSM: Baryogenesis and Electric Dipole Moments

We study electroweak baryogenesis and electric dipole moments in the presence of the two leading-order, non-renormalizable operators in the Higgs sector of the MSSM. Significant qualitative and quantitative differences from MSSM baryogenesis arise due to the presence of new CP-violating phases and to the relaxation of constraints on the supersymmetric spectrum (in particular, both stops can be light). We find: (1) spontaneous baryogenesis, driven by a change in the phase of the Higgs vevs across the bubble wall, becomes possible; (2) the top and stop CP-violating sources can become effective; (3) baryogenesis is viable in larger parts of parameter space, alleviating the well-known fine-tuning associated with MSSM baryogenesis. Nevertheless, electric dipole moments should be measured if experimental sensitivities are improved by about one order of magnitude.Comment: 33 pages, 6 figure

2:1 for Naturalness at the LHC?

A large enhancement of a factor of 1.5 - 2 in Higgs production and decay in the diphoton channel, with little deviation in the ZZ channel, can only plausibly arise from a loop of new charged particles with large couplings to the Higgs. We show that, allowing only new fermions with marginal interactions at the weak scale, the required Yukawa couplings for a factor of 2 enhancement are so large that the Higgs quartic coupling is pushed to large negative values in the UV, triggering an unacceptable vacuum instability far beneath the 10 TeV scale. An enhancement by a factor of 1.5 can be accommodated if the charged fermions are lighter than 150 GeV, within reach of discovery in almost all cases in the 8 TeV run at the LHC, and in even the most difficult cases at 14 TeV. Thus if the diphoton enhancement survives further scrutiny, and no charged fermions beneath 150 GeV are found, there must be new bosons far beneath the 10 TeV scale. This would unambiguously rule out a large class of fine-tuned theories for physics beyond the Standard Model, including split SUSY and many of its variants, and provide strong circumstantial evidence for a natural theory of electroweak symmetry breaking at the TeV scale. Alternately, theories with only a single fine-tuned Higgs and new fermions at the weak scale, with no additional scalars or gauge bosons up to a cutoff much larger than the 10 TeV scale, unambiguously predict that the hints for a large diphoton enhancement in the current data will disappear.Comment: 18 pages, 6 figures; typos corrected and references adde

The Natural Variation of a Neural Code

The way information is represented by sequences of action potentials of spiking neurons is determined by the input each neuron receives, but also by its biophysics, and the specifics of the circuit in which it is embedded. Even the “code” of identified neurons can vary considerably from individual to individual. Here we compared the neural codes of the identified H1 neuron in the visual systems of two families of flies, blow flies and flesh flies, and explored the effect of the sensory environment that the flies were exposed to during development on the H1 code. We found that the two families differed considerably in the temporal structure of the code, its content and energetic efficiency, as well as the temporal delay of neural response. The differences in the environmental conditions during the flies' development had no significant effect. Our results may thus reflect an instance of a family-specific design of the neural code. They may also suggest that individual variability in information processing by this specific neuron, in terms of both form and content, is regulated genetically

Alu Exonization Events Reveal Features Required for Precise Recognition of Exons by the Splicing Machinery

Despite decades of research, the question of how the mRNA splicing machinery precisely identifies short exonic islands within the vast intronic oceans remains to a large extent obscure. In this study, we analyzed Alu exonization events, aiming to understand the requirements for correct selection of exons. Comparison of exonizing Alus to their non-exonizing counterparts is informative because Alus in these two groups have retained high sequence similarity but are perceived differently by the splicing machinery. We identified and characterized numerous features used by the splicing machinery to discriminate between Alu exons and their non-exonizing counterparts. Of these, the most novel is secondary structure: Alu exons in general and their 5′ splice sites (5′ss) in particular are characterized by decreased stability of local secondary structures with respect to their non-exonizing counterparts. We detected numerous further differences between Alu exons and their non-exonizing counterparts, among others in terms of exon–intron architecture and strength of splicing signals, enhancers, and silencers. Support vector machine analysis revealed that these features allow a high level of discrimination (AUC = 0.91) between exonizing and non-exonizing Alus. Moreover, the computationally derived probabilities of exonization significantly correlated with the biological inclusion level of the Alu exons, and the model could also be extended to general datasets of constitutive and alternative exons. This indicates that the features detected and explored in this study provide the basis not only for precise exon selection but also for the fine-tuned regulation thereof, manifested in cases of alternative splicing