bluuebunny/crossref_metadata_2025 huggingface dataset:
A novel alternate anaplerotic pathway to the glyoxylate cycle in streptomycetes
Authors: Han L , Reynolds K A
Published: November 2016

ccr encoding crotonyl coenzyme A (CoA) reductase (CCR), which catalyzes the conversion of crotonyl-CoA to butyryl-CoA in the presence of NADPH, was previously cloned from Streptomyces collinus. We now report that a complete open reading frame, designated meaA, is located downstream from ccr. The predicted gene product showed 35% identity with methylmalonyl-CoA mutases from various sources. In addition, the predicted amino acid sequences of S. collinus ccr and meaA exhibit strong similarity to that of adhA (43% identity), a putative alcohol dehydrogenase gene, and meaA (62% identity) of Methylobacterium extorquens, respectively. Both adhA and meaA are involved in the assimilation of C1 and C2 compounds in an unknown pathway in the isocitrate lyase (ICL)-negative Methylobacterium. We have demonstrated that S. collinus can grow with acetate as its sole carbon source even though there is no detectable ICL, suggesting that in this organism ccr and meaA may also be involved in a pathway for the assimilation of C2 compounds. Previous studies with streptomycetes provided a precedent for a pathway that initiates with the condensation of two acetyl-CoA molecules to form butyryl-CoA, which is then transformed to succinyl-CoA with two separate CoB12-mediated rearrangements and a series of oxidations. The biological functions of ccr and meaA in this process were investigated by gene disruption. A ccr-blocked mutant showed no detectable crotonyl-CoA reductase activity and, compared to the wild-type strain, exhibited dramatically reduced growth when acetate was the sole carbon source. An meaA-blocked mutant also exhibited reduced growth on acetate. However, both methylmalonyl-CoA mutase and isobutyryl-CoA mutase, which catalyze the two CoB12-dependent rearrangements in this proposed pathway, were shown to be present in the meaA-blocked mutant. These results suggested that both ccr and meaA are involved in a novel pathway for the growth of S. collinus when acetate is its sole carbon source.
Cloning and mutational analysis of the gene for the stationary-phase inducible catalase (catC) from Pseudomonas putida
Authors: Miller C D , Kim Y C , Anderson A J
Published: November 2016

Pseudomonas putida, a bacterium that colonizes plant roots and enhances plant growth, produces three isozymes of catalase (A, B, and C) in stationary-phase cells. A catalase probe, generated by PCR analysis of P. putida genomic DNA with oligomers based on typical catalase sequences, hybridized to a genomic clone that expressed catalase C in Escherichia coli. The catC gene from this clone had a 2,133-bp open reading frame with a high level of identity to the stationary-phase-specific E. coli katE. Chromosomal mutants of P. putida deficient in catalase C, obtained by gene interruption with a luxAB-npt cassette, demonstrated enhanced catC transcription in stationary-phase cells and, upon exposure to phenol, in logarithmic-phase cells. The catalase C-deficient cells were not impaired in their ability to colonize roots of bean or wheat plants grown under sterile conditions.
Polymorphic Regulation of Outer Membrane Lipid A Composition
Authors: Bishop Russell E.
Published: November 2016

The importance of the polymorphic-phase behavior of lipid A structural variations in determining their endotoxic activities has been recognized previously, but any potential role for lipid A polymorphism in controlling outer membrane structure and function has been largely ignored until now. In a recent article in
mBio
[7(5):e01532-16, https://doi.org/10.1128/mBio.01532-16], Katherine E. Bonnington and Meta J. Kuehn of Duke University’s Department of Biochemistry make a compelling case for considering how the molecular shapes of the various lipid A structural subtypes found in the outer membrane contribute to the process of outer membrane vesicle (OMV) formation.
Life-threatening Wunderlich's syndrome with concurrent clopidogrel use
Authors: Kinnear Ned , Hennessey Derek Barrry , Douglass-Molloy Hannah , Jack Greg
Published: November 2016

Spontaneous non-traumatic renal haemorrhage, or Wunderlich's syndrome, is a rare but potentially life-threatening event. We present the case of a 63-year-old man on clopidogrel who became haemodynamically unstable as a result of this condition. Angioembolisation revealed the unusual finding of active bleeding from multiple distinct subsegmental renal vessels, for which haemostasis was successfully achieved by coil placement. The patient remains well and with near-normal renal function on follow-up.
The ghost of pandemics past: revisiting two centuries of influenza in Sweden
Authors: Holmberg Martin
Published: November 2016

Previous influenza pandemics are usually invoked in pandemic preparedness planning without a thorough analysis of the events surrounding them, what has been called the ‘configuration’ of epidemics. Historic pandemics are instead used to contrast them to the novelty of the coming imagined plague or as fear of a ghost-like repetition of the past. This view of pandemics is guided by a biomedical framework that is ahistorical and reductionist. The meaning of ‘pandemic’ influenza is in fact highly ambiguous in its partitioning of pandemic and seasonal influenza. The past 200 years of influenza epidemics in Sweden are examined with a special focus on key social structures—households, schools, transportations and the military. These are shown to have influenced the progression of influenza pandemics. Prevailing beliefs around influenza pandemics have also profoundly influenced intervention strategies. Measuring long-term trends in pandemic severity is problematic because pandemics are non-linear events where the conditions surrounding them constantly change. However, in a linearised view, the Spanish flu can be seen to represent a historical turning point and the H1N1 2009 pandemic not as an outlier, but following a 100-year trend of decreasing severity. Integrating seasonal and pandemic influenza, and adopting an ecosocial stance can deepen our understanding and bring the ghost-like pandemic past to life.
A Low Phase Noise LC Quadrature VCO Using Impulse Shaping Based on Gaussian Pulse Generator
Authors: Khatti Naser , Dousti Massoud
Published: November 2016

This paper presents a new tail current-shaping technique to improve the phase noise of an LC quadrature VCO (LC-QVCO) based on Gaussian pulse generator (GPG). The GPG makes a narrow pulse from oscillator sinusoidal output and injects it back to gates of tail transistors to reduce the root-mean-square (RMS) value of impulse sensitivity function (ISF) and to improve phase noise. It will be shown that by utilizing a GPG, total phase noise improvement will be as high as 6[Formula: see text]dB. The proposed circuit was designed and simulated by ADS simulator using 0.18[Formula: see text][Formula: see text]m TSMC RF CMOS design kit. The phase noise's at 3[Formula: see text]MHz frequency offset and carrier frequencies of 2.43[Formula: see text]GHz and 2.6[Formula: see text]GHz are –141[Formula: see text]dBc/Hz and –135[Formula: see text]dBc/Hz, respectively, while the total power consumption is 14[Formula: see text]mW under 1.8[Formula: see text]V supply voltage. Tuning range is from 2.43[Formula: see text]GHz to 2.6[Formula: see text]GHz. The figure of merit (FOM) values for the proposed LC-QVCO at 3[Formula: see text]MHz frequency offset are –187.6[Formula: see text]dBc/Hz and –182.3[Formula: see text]dBc/Hz for 2.43[Formula: see text]GHz and 2.6[Formula: see text]GHz carrier frequencies, respectively.
Large time behavior of solutions to the compressible Navier–Stokes equations in an infinite layer under slip boundary condition
Authors: Aihaiti Abulizi , Enomoto Shota , Kagei Yoshiyuki
Published: November 2016

This paper is concerned with large time behavior of solutions to the compressible Navier–Stokes equations in an infinite layer of [Formula: see text] under slip boundary condition. It is shown that if the initial data is sufficiently small, the global solution uniquely exists and the large time behavior of the solution is described by a superposition of one-dimensional diffusion waves.
EXPERIMENTAL INVESTIGATIONS ON THE INTERACTIONS BETWEEN LIQUIDS AND STRUCTURES TO PASSIVELY CONTROL THE SURFACE-DRIVEN CAPILLARY FLOW IN MICROFLUIDIC LAB-ON-A-CHIP SYSTEMS TO SEPARATE THE MICROPARTICLES FOR BIOENGINEERING APPLICATIONS
Authors: MUKHOPADHYAY SUBHADEEP
Published: November 2016

In this research paper, total 246 individual microfluidic devices have been fabricated by maskless lithography, hot embossing lithography and direct bonding technique. The effect of surface area to volume ratio on the surface-driven capillary flow of different liquids has been experimentally investigated in these microfluidic devices fabricated by polymethylmethacrylate (PMMA). Also, the individual effects of liquid viscosity and surface wettability on the surface-driven capillary flow of different liquids are experimentally investigated. The polystyrene particles of 10[Formula: see text][Formula: see text]m diameters have been separated from the aqueous microparticle suspensions in the microfluidic lab-on-a-chip systems with 100% separation efficiency. Also, the polystyrene particles of 5[Formula: see text][Formula: see text]m diameters have been separated from a different set of aqueous microparticle suspensions in the microfluidic lab-on-a-chip systems with 100% separation efficiency. The individual designs of the microfluidic lab-on-a-chip systems are a novel approach in this research paper. The effect of surface area to volume ratio on the separation time is experimentally investigated as another novel approach of this research paper.
Almost complex manifolds with non-degenerate torsion
Authors: Bozzetti Cristina , Medori Costantino
Published: November 2016

We show that almost complex manifolds [Formula: see text] of real dimension 4 for which the image of the Nijenhuis tensor forms a non-integrable bundle, called torsion bundle, admit a [Formula: see text]-structure locally, that is, a double absolute parallelism. In this way, the problem of equivalence for such almost complex manifolds can be solved; moreover, the classification of locally homogeneous manifold [Formula: see text] is explicitly given when the Lie algebra of its infinitesimal automorphisms is non-solvable (indeed reductive). It is also shown that the group of the automorphisms of [Formula: see text] is a Lie group of dimension less than or equal to 4, whose isotropy subgroup has at most two elements, and that there are not non-constant holomorphic functions on [Formula: see text].
Characterization of ergodic rational functions on the set of 2-adic units
Authors: Memić Nacima
Published: November 2016

We give an explicit characterization of ergodicity of rational functions on the set of units of the [Formula: see text]-adic group by means of the coefficients in their nominators and denominators. Although rational functions are not ergodic on the set of p-adic numbers, this was proved by Diao and Silva, we study their ergodicity on the 2-adic unit sphere if they only contain integer coefficients. The first results of this paper provide isometricity tests of polynomials and rational functions on the set of 2-adic units with 2-adic integer coefficients. Then, follow results on ergodicity tests on general isometric functions, then on rational functions on the set of 2-adic units with 2-adic integer coefficients.
Degeneration of Hodge structures over Picard modular surfaces
Authors: Ancona Giuseppe
Published: November 2016

We study variations of Hodge structures over a Picard modular surface, and compute the weights and types of their degenerations through the cusps of the Baily–Borel compactification. These computations are one of the key inputs which allow Wildeshaus [On the interior motive of certain Shimura varieties: the case of Picard surfaces, Manuscripta Math. 148(3) (2015) 351–377] to construct motives associated with Picard modular forms.
Locally indecomposable Galois representations with full residual image
Authors: Sharma Devika
Published: November 2016

We consider certain [Formula: see text]-ordinary non-CM Hida families with full residual Galois representation and give mild conditions under which every arithmetic point in these families is locally indecomposable when [Formula: see text]. The proof uses methods from deformation theory and mostly works for any odd prime [Formula: see text], but ultimately relies on the existence of a weight [Formula: see text] form in an auxiliary family which is available only for [Formula: see text]. We end by giving several non-trivial examples of [Formula: see text]-ordinary non-CM locally indecomposable modular forms of small level with full residual Galois representation.
On the density of cyclotomic lattices constructed from codes
Authors: Moustrou Philippe
Published: November 2016

Recently, Venkatesh improved the best known lower bound for lattice sphere packings by a factor [Formula: see text] for infinitely many dimensions [Formula: see text]. Here, we prove an effective version of this result, in the sense that we exhibit, for the same set of dimensions, finite families of lattices containing a lattice reaching this bound. Our construction uses codes over cyclotomic fields, lifted to lattices via Construction A. We also prove a similar result for families of symplectic lattices.
Periods of iterated rational functions
Authors: Burnette Charles , Schmutz Eric
Published: November 2016

If [Formula: see text] is a polynomial of degree [Formula: see text] in [Formula: see text], let [Formula: see text] be the number of cycles of length [Formula: see text] in the directed graph on [Formula: see text] with edges [Formula: see text] For random polynomials, the numbers [Formula: see text] have asymptotic behavior resembling that for the cycle lengths of random functions [Formula: see text] However random polynomials differ from random functions in important ways. For example, given the set of cyclic (periodic) points, it is not necessarily true that all permutations of those cyclic points are equally likely to occur as the restriction of [Formula: see text]. This, and the limitations of Lagrange interpolation, together complicate research on [Formula: see text] the ultimate period of [Formula: see text] under compositional iteration. We prove a lower bound for the average value of [Formula: see text]: if [Formula: see text], but [Formula: see text], then the expected value of [Formula: see text] is [Formula: see text] where the sum is over all [Formula: see text] polynomials of degree [Formula: see text] in [Formula: see text]. Similar results are proved for rational functions.
An induced real quaternion spherical ensemble of random matrices
Authors: Mays Anthony , Ponsaing Anita
Published: November 2016

We study the induced spherical ensemble of non-Hermitian matrices with real quaternion entries (considering each quaternion as a [Formula: see text] complex matrix). We define the ensemble by the matrix probability distribution function that is proportional to [Formula: see text] These matrices can also be constructed via a procedure called ‘inducing’, using a product of a Wishart matrix (with parameters [Formula: see text]) and a rectangular Ginibre matrix of size [Formula: see text]. The inducing procedure imposes a repulsion of eigenvalues from [Formula: see text] and [Formula: see text] in the complex plane with the effect that in the limit of large matrix dimension, they lie in an annulus whose inner and outer radii depend on the relative size of [Formula: see text], [Formula: see text] and [Formula: see text]. By using functional differentiation of a generalized partition function, we make use of skew-orthogonal polynomials to find expressions for the eigenvalue [Formula: see text]-point correlation functions, and in particular the eigenvalue density (given by [Formula: see text]). We find the scaled limits of the density in the bulk (away from the real line) as well as near the inner and outer annular radii, in the four regimes corresponding to large or small values of [Formula: see text] and [Formula: see text]. After a stereographic projection, the density is uniform on a spherical annulus, except for a depletion of eigenvalues on a great circle corresponding to the real axis (as expected for a real quaternion ensemble). We also form a conjecture for the behavior of the density near the real line based on analogous results in the [Formula: see text] and [Formula: see text] ensembles; we support our conjecture with data from Monte Carlo simulations of a large number of matrices drawn from the [Formula: see text] induced spherical ensemble. This ensemble is a quaternionic analog of a model of a one-component charged plasma on a sphere, with soft wall boundary conditions.
Sound and precise analysis of parallel programs through schedule specialization
Authors: Wu Jingyue , Tang Yang , Hu Gang , Cui Heming , Yang Junfeng
Published: November 2016

Parallel programs are known to be difficult to analyze. A key reason is that they typically have an enormous number of execution interleavings, or
schedules
. Static analysis over all schedules requires over-approximations, resulting in poor precision; dynamic analysis rarely covers more than a tiny fraction of all schedules. We propose an approach called
schedule specialization
to analyze a parallel program over only a small set of schedules for precision, and then enforce these schedules at runtime for soundness of the static analysis results. We build a schedule specialization framework for C/C++ multithreaded programs that use Pthreads. Our framework avoids the need to modify every analysis to be schedule-aware by specializing a program into a simpler program based on a schedule, so that the resultant program can be analyzed with stock analyses for improved precision. Moreover, our framework provides a precise
schedule-aware
def-use analysis on memory locations, enabling us to build three highly precise analyses: an alias analyzer, a data-race detector, and a path slicer. Evaluation on 17 programs, including 2 real-world programs and 15 popular benchmarks, shows that analyses using our framework reduced may-aliases by 61.9%, false race reports by 69%, and path slices by 48.7%; and detected 7 unknown bugs in well-checked programs.
Dynamic synthesis for relaxed memory models
Authors: Liu Feng , Nedev Nayden , Prisadnikov Nedyalko , Vechev Martin , Yahav Eran
Published: November 2016

Modern architectures implement relaxed memory models which may reorder memory operations or execute them non-atomically. Special instructions called memory fences are provided, allowing control of this behavior.

To implement a concurrent algorithm for a modern architecture, the programmer is forced to manually reason about subtle relaxed behaviors and figure out ways to control these behaviors by adding fences to the program. Not only is this process time consuming and error-prone, but it has to be repeated every time the implementation is ported to a different architecture.

In this paper, we present the first scalable framework for handling real-world concurrent algorithms running on relaxed architectures. Given a concurrent C program, a safety specification, and a description of the memory model, our framework tests the program on the memory model to expose violations of the specification, and synthesizes a set of necessary ordering constraints that prevent these violations. The ordering constraints are then realized as additional fences in the program.

We implemented our approach in a tool called DFence based on LLVM and used it to infer fences in a number of concurrent algorithms. Using DFence, we perform the first in-depth study of the interaction between fences in real-world concurrent C programs, correctness criteria such as sequential consistency and linearizability, and memory models such as TSO and PSO, yielding many interesting observations. We believe that this is the first tool that can handle programs at the scale and complexity of a lock-free memory allocator.
Multicore acceleration of priority-based schedulers for concurrency bug detection
Authors: Nagarakatte Santosh , Burckhardt Sebastian , Martin Milo M.K. , Musuvathi Madanlal
Published: November 2016

Testing multithreaded programs is difficult as threads can interleave in a nondeterministic fashion. Untested interleavings can cause failures, but testing all interleavings is infeasible. Many interleaving exploration strategies for bug detection have been proposed, but their relative effectiveness and performance remains unclear as they often lack publicly available implementations and have not been evaluated using common benchmarks. We describe NeedlePoint, an open-source framework that allows selection and comparison of a wide range of interleaving exploration policies for bug detection proposed by prior work.

Our experience with NeedlePoint indicates that priority-based probabilistic concurrency testing (the PCT algorithm) finds bugs quickly, but it runs only one thread at a time, which destroys parallelism by serializing executions. To address this problem we propose a parallel version of the PCT algorithm~(PPCT). We show that the new algorithm outperforms the original by a factor of 5x when testing parallel programs on an eight-core machine. We formally prove that parallel PCT provides the same probabilistic coverage guarantees as PCT. Moreover, PPCT is the first algorithm that runs multiple threads while providing coverage guarantees.
Views
Authors: Dinsdale-Young Thomas , Birkedal Lars , Gardner Philippa , Parkinson Matthew , Yang Hongseok
Published: November 2016

Compositional abstractions underly many reasoning principles for concurrent programs: the concurrent environment is abstracted in order to reason about a thread in isolation; and these abstractions are composed to reason about a program consisting of many threads. For instance, separation logic uses formulae that describe part of the state, abstracting the rest; when two threads use disjoint state, their specifications can be composed with the separating conjunction. Type systems abstract the state to the types of variables; threads may be composed when they agree on the types of shared variables.

In this paper, we present the "Concurrent Views Framework", a metatheory of concurrent reasoning principles. The theory is parameterised by an abstraction of state with a notion of composition, which we call views. The metatheory is remarkably simple, but highly applicable: the rely-guarantee method, concurrent separation logic, concurrent abstract predicates, type systems for recursive references and for unique pointers, and even an adaptation of the Owicki-Gries method can all be seen as instances of the Concurrent Views Framework. Moreover, our metatheory proves each of these systems is sound without requiring induction on the operational semantics.
Optimizing data structures in high-level programs
Authors: Rompf Tiark , Sujeeth Arvind K. , Amin Nada , Brown Kevin J. , Jovanovic Vojin , Lee HyoukJoong , Jonnalagedda Manohar , Olukotun Kunle , Odersky Martin
Published: November 2016

High level data structures are a cornerstone of modern programming and at the same time stand in the way of compiler optimizations. In order to reason about user- or library-defined data structures compilers need to be extensible. Common mechanisms to extend compilers fall into two categories. Frontend macros, staging or partial evaluation systems can be used to programmatically remove abstraction and specialize programs before they enter the compiler. Alternatively, some compilers allow extending the internal workings by adding new transformation passes at different points in the compile chain or adding new intermediate representation (IR) types. None of these mechanisms alone is sufficient to handle the challenges posed by high level data structures. This paper shows a novel way to combine them to yield benefits that are greater than the sum of the parts.

Instead of using staging merely as a front end, we implement internal compiler passes using staging as well. These internal passes delegate back to program execution to construct the transformed IR. Staging is known to simplify program generation, and in the same way it can simplify program transformation. Defining a transformation as a staged IR interpreter is simpler than implementing a low-level IR to IR transformer. With custom IR nodes, many optimizations that are expressed as rewritings from IR nodes to staged program fragments can be combined into a single pass, mitigating phase ordering problems. Speculative rewriting can preserve optimistic assumptions around loops.

We demonstrate several powerful program optimizations using this architecture that are particularly geared towards data structures: a novel loop fusion and deforestation algorithm, array of struct to struct of array conversion, object flattening and code generation for heterogeneous parallel devices. We validate our approach using several non trivial case studies that exhibit order of magnitude speedups in experiments.
Subjective auxiliary state for coarse-grained concurrency
Authors: Ley-Wild Ruy , Nanevski Aleksandar
Published: November 2016

From Owicki-Gries' Resource Invariants and Jones' Rely/Guarantee to modern variants based on Separation Logic, axiomatic logics for concurrency require auxiliary state to explicitly relate the effect of all threads to the global invariant on the shared resource. Unfortunately, auxiliary state gives the proof of an individual thread access to the auxiliaries of all other threads. This makes proofs sensitive to the global context, which prevents local reasoning and compositionality.

To tame this historical difficulty of auxiliary state, we propose subjective auxiliary state, whereby each thread is verified using a self view (i.e., the thread's effect on the shared resource) and an other view (i.e., the collective effect of all the other threads). Subjectivity generalizes auxiliary state from stacks and heaps to user-chosen partial commutative monoids, which can eliminate the dependence on the global thread structure.

We employ subjectivity to formulate Subjective Concurrent Separation Logic as a combination of subjective auxiliary state and Concurrent Separation Logic. The logic yields simple, compositional proofs of coarse-grained concurrent programs that use auxiliary state, and scales to support higher-order recursive procedures that can themselves fork new threads. We prove the soundness of the logic with a novel denotational semantics of action trees and a definition of safety using rely/guarantee transitions over a large subjective footprint. We have mechanized the denotational semantics, logic, metatheory, and a number of examples by a shallow embedding in Coq.
Constant Rate PCPs for Circuit-SAT with Sublinear Query Complexity
Authors: Ben-Sasson Eli , Kaplan Yohay , Kopparty Swastik , Meir Or , Stichtenoth Henning
Published: November 2016

The PCP theorem [Arora et al. 1998; Arora and Safra 1998] says that every NP-proof can be encoded to another proof, namely, a probabilistically checkable proof (PCP), which can be tested by a verifier that queries only a small part of the PCP. A natural question is how large is the blow-up incurred by this encoding, that is, how long is the PCP compared to the original NP-proof? The state-of-the-art work of Ben-Sasson and Sudan [2008] and Dinur [2007] shows that one can encode proofs of length
n
by PCPs of length
n
· poly log
n
that can be verified using a constant number of queries. In this work, we show that if the query complexity is relaxed to
n
ε
, then one can construct PCPs of length
O
(
n
) for circuit-SAT, and PCPs of length
O
(
t
log
t
) for any language in NTIME(
t
).

More specifically, for any ε > 0, we present (nonuniform) probabilistically checkable proofs (PCPs) of length 2

O
(1/ε)

·
n
that can be checked using
n
ε
queries for circuit-SAT instances of size
n
. Our PCPs have perfect completeness and constant soundness. This is the first constant-rate PCP construction that achieves constant soundness with nontrivial query complexity (
o
(
n
)).

Our proof replaces the low-degree polynomials in algebraic PCP constructions with tensors of transitive algebraic geometry (AG) codes. We show that the automorphisms of an AG code can be used to simulate the role of affine transformations that are crucial in earlier high-rate algebraic PCP constructions. Using this observation, we conclude that any asymptotically good family of transitive AG codes over a constant-sized alphabet leads to a family of constant-rate PCPs with polynomially small query complexity. Such codes are constructed in the appendix to this article for the first time for every message length, building on an earlier construction for infinitely many message lengths by Stichtenoth [2006].
Joins via Geometric Resolutions
Authors: Khamis Mahmoud Abo , Ngo Hung Q. , Ré Christopher , Rudra Atri
Published: November 2016

We present a simple geometric framework for the relational join. Using this framework, we design an algorithm that achieves the fractional hypertree-width bound, which generalizes classical and recent worst-case algorithmic results on computing joins. In addition, we use our framework and the same algorithm to show a series of what are colloquially known as beyond worst-case results. The framework allows us to prove results for data stored in BTrees, multidimensional data structures, and even multiple indices per table. A key idea in our framework is formalizing the inference one does with an index as a type of geometric resolution, transforming the algorithmic problem of computing joins to a geometric problem. Our notion of geometric resolution can be viewed as a geometric analog of logical resolution. In addition to the geometry and logic connections, our algorithm can also be thought of as backtracking search with memoization.
Deterministic (Δ + 1)-Coloring in Sublinear (in Δ) Time in Static, Dynamic, and Faulty Networks
Authors: Barenboim Leonid
Published: November 2016

We study the distributed (Δ + 1)-vertex-coloring and (2Δ − 1)-edge-coloring problems. These problems are among the most important and intensively studied problems in distributed computing. Despite very intensive research in the last 30 years, no deterministic algorithms for these problems with sublinear (in Δ) time have been known so far. Moreover, for more restricted scenarios and some related problems there are lower bounds of Ω(Δ) [Göös et al. 2014; Hirvonen and Suomela 2012; Kuhn and Wattenhofer 2006; Szegedy and Vishwanathan 1993]. The question of the possibility to devise algorithms that overcome this challenging barrier is one of the most fundamental questions in distributed symmetry breaking [Barenboim and Elkin 2009, 2011; Göös et al. 2014; Hirvonen and Suomela 2012; Kuhn 2009; Panconesi and Rizzi 2001]. In this article, we settle this question for (Δ + 1)-vertex-coloring and (2Δ − 1)-edge-coloring by devising deterministic algorithms that require
O
(Δ
3/4
log Δ + log
*
n
) time in the static, dynamic, and faulty settings. (The term log
*
n
is unavoidable in view of the lower bound of Linial [1987].) Moreover, for (1 +
o
(1))Δ-vertex-coloring and (2 +
o
(1))Δ-edge-coloring we devise algorithms with Õ(√Δ + log
*
n
) deterministic time. This is roughly a quadratic improvement comparing to the state-of-the-art that requires
O
(Δ + log
*
n
) time [Barenboim and Elkin 2009; Kuhn 2009; Panconesi and Rizzi 2001]. Our results are actually more general than that since they apply also to a variant of the list-coloring problem that generalizes ordinary coloring.

Our results are obtained using a novel technique for coloring partially colored graphs (also known as
fixing
). We partition the uncolored parts into a small number of subgraphs with certain helpful properties. Then we color these subgraphs gradually using a technique that employs
constructions of polynomials
in a novel way. Our construction is inspired by the algorithm of Linial [1987] for ordinary
O
(Δ
2
)-coloring. However, it is a more sophisticated construction that differs from that of Linial [1987] in several important respects. These new insights in using systems of polynomials allow us to significantly speed up the
O
(Δ)-coloring algorithms. Moreover, they allow us to devise algorithms with the same running time also in the more complicated settings of dynamic and faulty networks.
Playing Mastermind With Many Colors
Authors: Doerr Benjamin , Doerr Carola , Spöhel Reto , Thomas Henning
Published: November 2016

We analyze the general version of the classic guessing game Mastermind with
n
positions and
k
colors. Since the case
k
≤
n
1 − ε
, ε > 0 a constant, is well understood, we concentrate on larger numbers of colors. For the most prominent case
k
=
n
, our results imply that Codebreaker can find the secret code with
O
(
n
log log
n
) guesses. This bound is valid also when only black answer pegs are used. It improves the
O
(
n
log
n
) bound first proven by Chvátal. We also show that if both black and white answer pegs are used, then the
O
(
n
log log
n
) bound holds for up to
n
2
log log
n
colors. These bounds are almost tight, as the known lower bound of Ω(
n
) shows. Unlike for
k
≤
n
1 − ε
, simply guessing at random until the secret code is determined is not sufficient. In fact, we show that an optimal nonadaptive strategy (deterministic or randomized) needs Θ(
n
log
n
) guesses.
Multithreaded Stochastic PDES for Reactions and Diffusions in Neurons
Authors: Lin Zhongwei , Tropper Carl , McDougal Robert A. , Ishlam Patoary Mohammand Nazrul , Lytton William W. , Yao Yiping , Hines Michael L.
Published: November 2016

Cells exhibit stochastic behavior when the number of molecules is small. Hence a stochastic reaction-diffusion simulator capable of working at scale can provide a more accurate view of molecular dynamics within the cell. This article describes a parallel discrete event simulator, Neuron Time Warp-Multi Thread (NTW-MT), developed for the simulation of reaction diffusion models of neurons. To the best of our knowledge, this is the first parallel discrete event simulator oriented toward stochastic simulation of chemical reactions in a neuron. The simulator was developed as part of the NEURON project. NTW-MT is optimistic and thread based, which attempts to capitalize on multicore architectures used in high performance machines. It makes use of a multilevel queue for the pending event set and a single rollback message in place of individual antimessages to disperse contention and decrease the overhead of processing rollbacks. Global Virtual Time is computed asynchronously both within and among processes to get rid of the overhead for synchronizing threads. Memory usage is managed in order to avoid locking and unlocking when allocating and deallocating memory and to maximize cache locality. We verified our simulator on a calcium buffer model. We examined its performance on a calcium wave model, comparing it to the performance of a process based optimistic simulator and a threaded simulator which uses a single priority queue for each thread. Our multithreaded simulator is shown to achieve superior performance to these simulators. Finally, we demonstrated the scalability of our simulator on a larger Calcium-Induced Calcium Release (CICR) model and a more detailed CICR model.
Strengthening of Steel Columns under Load: Torsional-Flexural Buckling
Authors: Vild Martin , Bajer Miroslav
Published: November 2016

The paper presents experimental and numerical research into the strengthening of steel columns under load using welded plates. So far, the experimental research in this field has been limited mostly to flexural buckling of columns and the preload had low effect on the column load resistance. This paper focuses on the local buckling and torsional-flexural buckling of columns. Three sets of three columns each were tested. Two sets corresponding to the base section (D) and strengthened section (E) were tested without preloading and were used for comparison. Columns from set (F) were first preloaded to the load corresponding to the half of the load resistance of the base section (D). Then the columns were strengthened and after they cooled, they were loaded to failure. The columns strengthened under load (F) had similar average resistance as the columns welded without preloading (E), meaning the preload affects even members susceptible to local buckling and torsional-flexural buckling only slightly. This is the same behaviour as of the tested columns from previous research into flexural buckling. The study includes results gained from finite element models of the problem created in ANSYS software. The results obtained from the experiments and numerical simulations were compared.
Vagus Nerve Stimulation Enhances Extinction of Conditioned Fear in Rats and Modulates Arc Protein, CaMKII, and GluN2B-Containing NMDA Receptors in the Basolateral Amygdala
Authors: Alvarez-Dieppa Amanda C. , Griffin Kimberly , Cavalier Sheridan , McIntyre Christa K.
Published: November 2016

Vagus nerve stimulation (VNS) enhances the consolidation of extinction of conditioned fear. High frequency stimulation of the infralimbic cortex (IL) produces long-term potentiation in the basolateral amygdala (BLA) in rats given VNS-paired extinction training, whereas the same stimulation produces long-term depression in sham-treated rats. The present study investigated the state of synaptic plasticity-associated proteins in the BLA that could be responsible for this shift. Male Sprague-Dawley rats were separated into 4 groups: auditory fear conditioning only (fear-conditioned); fear conditioning + 20 extinction trials (extended-extinction); fear conditioning + 4 extinction trials paired with sham stimulation (sham-extinction); fear conditioning + 4 extinction trials paired with VNS (VNS-extinction). Freezing was significantly reduced in extended-extinction and VNS-extinction rats. Western blots were used to quantify expression and phosphorylation state of synaptic plasticity-associated proteins such as Arc, CaMKII, ERK, PKA, and AMPA and NMDA receptors. Results show significant increases in GluN2B expression and phosphorylated CaMKII in BLA samples from VNS- and extended-extinction rats. Arc expression was significantly reduced in VNS-extinction rats compared to all groups. Administration of the GluN2B antagonist ifenprodil immediately after fear extinction training blocked consolidation of extinction learning. Results indicate a role for BLA CaMKII-induced GluN2B expression and reduced Arc protein in VNS-enhanced extinction.
Refractory Obstructive Sleep Apnea in a Patient with Diffuse Idiopathic Skeletal Hyperostosis
Authors: Darakjian Ara , Darakjian Ani B. , Chang Edward T. , Camacho Macario
Published: November 2016

Diffuse Idiopathic Skeletal Hyperostosis (DISH) can cause ossification of ligaments and may affect the spine. We report a case of obstructive sleep apnea in a patient with significant upper airway narrowing secondary to cervical DISH. This patient had an initial apnea-hypopnea index (AHI) of 145 events/hour and was treated with uvulopalatopharyngoplasty, genial tubercle advancement, hyoid suspension, septoplasty, inferior turbinoplasties, and radiofrequency ablations to the tongue base which reduced his AHI to 40 events/hour. He redeveloped symptoms, was started on positive airway pressure (PAP) therapy, and later underwent a maxillomandibular advancement which improved his AHI to 16.3 events/hour. A few years later his AHI was 100.4 events/hour. His disease has gradually progressed over time and he was restarted on PAP therapy. Despite PAP titration, years of using PAP therapy, and being 100 percent compliant for the past three months (average daily use of 7.6 hours/night), he has an AHI of 5.1 events/hour and has persistent hypersomnia with an Epworth Sleep Scale questionnaire score of 18/24. At this time he is pending further hypersomnia work-up. DISH patients require prolonged follow-up to monitor the progression of disease, and they may require unconventional measures for adequate treatment of obstructive sleep apnea.
On the Possibility of the Jerk Derivative in Electrical Circuits
Authors: Gómez-Aguilar J. F. , Rosales-García J. , Escobar-Jiménez R. F. , López-López M. G. , Alvarado-Martínez V. M. , Olivares-Peregrino V. H.
Published: November 2016

A subclass of dynamical systems with a time rate of change of acceleration are called Newtonian jerky dynamics. Some mechanical and acoustic systems can be interpreted as jerky dynamics. In this paper we show that the jerk dynamics are naturally obtained for electrical circuits using the fractional calculus approach with order γ. We consider fractional LC and RL electrical circuits with 1⩽γ<2 for different source terms. The LC circuit has a frequency ω dependent on the order of the fractional differential equation γ, since it is defined as ω(γ)=ω0γγ1-γ, where ω0 is the fundamental frequency. For γ=3/2, the system is described by a third-order differential equation with frequency ω~ω03/2, and assuming γ=2 the dynamics are described by a fourth differential equation for jerk dynamics with frequency ω~ω02.
Sleep-Disordered Breathing Exacerbates Muscle Vasoconstriction and Sympathetic Neural Activation in Patients with Systolic Heart Failure
Authors: Lobo Denise M. L. , Trevizan Patricia F. , Toschi-Dias Edgar , Oliveira Patricia A. , Piveta Rafael B. , Almeida Dirceu R. , Mady Charles , Bocchi Edimar A. , Lorenzi-Filho Geraldo , Middlekauff Holly R. , Negrão Carlos E.
Published: November 2016

Background—

Sleep-disordered breathing (SDB) is common in patients with heart failure (HF), and hypoxia and hypercapnia episodes activate chemoreceptors stimulating autonomic reflex responses. We tested the hypothesis that muscle vasoconstriction and muscle sympathetic nerve activity (MSNA) in response to hypoxia and hypercapnia would be more pronounced in patients with HF and SDB than in patients with HF without SDB (NoSBD).

Methods and Results—

Ninety consecutive patients with HF, New York Heart Association functional class II–III, and left ventricular ejection fraction ≤40% were screened for the study. Forty-one patients were enrolled: NoSDB (n=13, 46 [39–53] years) and SDB (n=28, 57 [54–61] years). SDB was characterized by apnea–hypopnea index ≥15 events per hour (polysomnography). Peripheral (10% O
2
and 90% N
2
, with CO
2
titrated) and central (7% CO
2
and 93% O
2
) chemoreceptors were stimulated for 3 minutes. Forearm and calf blood flow were evaluated by venous occlusion plethysmography, MSNA by microneurography, and blood pressure by beat-to-beat noninvasive technique. Baseline forearm blood flow, forearm vascular conductance, calf blood flow, and calf vascular conductance were similar between groups. MSNA was higher in the SDB group. During hypoxia, the vascular responses (forearm blood flow, forearm vascular conductance, calf blood flow, and calf vascular conductance) were significantly lower in the SDB group compared with the NoSDB group (
P
<0.01 to all comparisons). Similarly, during hypercapnia, the vascular responses (forearm blood flow, forearm vascular conductance, calf blood flow, and calf vascular conductance) were significantly lower in the SDB group compared with the NoSDB group (
P
<0.001 to all comparisons). MSNA were higher in response to hypoxia (
P
=0.024) and tended to be higher to hypercapnia (
P
=0.066) in the SDB group.

Conclusions—

Patients with HF and SDB have more severe muscle vasoconstriction during hypoxia and hypercapnia than HF patients without SDB, which seems to be associated with endothelial dysfunction and, in part, increased MSNA response.
Cutting the Prehospital On-Scene Time of Stroke Thrombolysis in Helsinki
Authors: Puolakka Tuukka , Kuisma Markku , Länkimäki Sami , Puolakka Jyrki , Hallikainen Juhana , Rantanen Kirsi , Lindsberg Perttu J.
Published: November 2016

Background and Purpose—

Significant portion of the prehospital delay consists of minutes spent on the scene with the patient. We implemented a training program for the emergency medical services personnel with the aim to optimize the on-scene time (OST) and to study the impact of different elements of prehospital practice to the OST duration.

Methods—

In this prospective interventional study, key operational emergency medical service performance variables were analyzed from all thrombolysis candidates transported to the Helsinki University Hospital emergency department. The catchment period was 4 months before and 4 months after the implementation.

Results—

One hundred and forty-one patients were managed as thrombolysis candidates before and 148 patients after the training program implementation. The OST duration for the groups was 25 (20.5–31) and 22.5 (18–28.5) minutes, respectively (
P
<0.001). Physician consultations via telephone were associated with a longer (odds ratio 0.546 [0.333–0.893]) and advanced life support training with a shorter OST (odds ration 1.760 [1.070–2.895]).

Conclusions—

Implementation of the emergency medical services training program successfully decreased the OST of thrombolysis candidates by 10%. Higher expertise level of the ambulance crew was associated with shorter OST, and decisions to consult a physician via telephone were reflected by longer OST.
Racing Away from Race: The Literary Aesthetics of Islam and Gender in Mohammed Naseehu Ali’s The Prophet of Zongo Street and Abubakar Adam Ibrahim’s The Whispering Trees
Authors: Edwin Shirin
Published: November 2016

Some literary discussions on Islam in West Africa argue that African Muslims owe allegiance more to Arab race and culture since the religion has an Arab origin while owing less to indigenous and therefore “authentic” African cultures. Most notably, in his famous quarrel with Ali Mazrui, the Nobel laureate Wole Soyinka wrenches race to serve a tendentious historicism about African Muslims as racially Arab and therefore foreign to African culture. In their fiction, two new West African writers, Mohammed Naseehu Ali and Abubakar Adam Ibrahim, allegorize African Islamic identity as tied to Arab race and culture as madness, lunacy and even death. In particular, Ali’s short story “The Prophet of Zongo Street” engages with this obsessive dialectic between African Islamic identity and Arab race. Although not explicitly thematizing Islamic identity as tied to Arab race or culture, three other stories by the same authors, Ali’s story “Mallam Sile” and Ibrahim’s stories “The Whispering Trees” and “Closure,” gender the dialectic between race and Islamic identity. Ali and Ibrahim show African Muslim women’s abilities to effect change in difficult situations and relationships—marriage, romance, legal provisions on inheritance, prayer and honor. In so doing, I argue, these authors reflect a potential solution to the difficult debate in African literary criticism on Islamic identity and Arab race and culture.
Probing the Theological Resources of a Seventeenth-Century tārīkh: the Tārīkh al-Sūdān and Ashʿarī kalām
Authors: Mathee Mohamed Shahid
Published: November 2016

Modern Western scholars, journalists, travellers, and colonial officials have shown an interest in Timbuktu’s famous seventeenth-century chronicles ever since they heard of them in the mid nineteenth-century. The three tārīkhs (chronicles) are the Tārīkh al-Sūdān, the so-called Tarīkh al-fattāsh, and the Notice historique. The first Western written works began to be produced at the end of the nineteenth century and burgeoned over the twentieth century with several large projects continuing into the present century, as recent as 2015. These works were primarily, though not exclusively, concerned with the authorship, sources, and political properties of the tārīkhs. This article is interested in Muslim theology as a resource of the Tārīkh al-Sūdān, one the three tārīkhs. It focuses in particular on the precepts of Ashʿarī kalām (theology) of Sunni Islam as the key resource the author of the Tarīkh al-Sūdān.