Fast Shortest Path Distance Estimation in Large Networks

We study the problem of preprocessing a large graph so that point-to-point shortest-path queries can be answered very fast. Computing shortest paths is a well studied problem, but exact algorithms do not scale to huge graphs encountered on the web, social networks, and other applications. In this paper we focus on approximate methods for distance estimation, in particular using landmark-based distance indexing. This approach involves selecting a subset of nodes as landmarks and computing (offline) the distances from each node in the graph to those landmarks. At runtime, when the distance between a pair of nodes is needed, we can estimate it quickly by combining the precomputed distances of the two nodes to the landmarks. We prove that selecting the optimal set of landmarks is an NP-hard problem, and thus heuristic solutions need to be employed. Given a budget of memory for the index, which translates directly into a budget of landmarks, different landmark selection strategies can yield dramatically different results in terms of accuracy. A number of simple methods that scale well to large graphs are therefore developed and experimentally compared. The simplest methods choose central nodes of the graph, while the more elaborate ones select central nodes that are also far away from one another. The efficiency of the suggested techniques is tested experimentally using five different real world graphs with millions of edges; for a given accuracy, they require as much as 250 times less space than the current approach in the literature which considers selecting landmarks at random. Finally, we study applications of our method in two problems arising naturally in large-scale networks, namely, social search and community detection.

Towards Formalizing Java's Weak References

Weak references provide the programmer with limited control over the process of memory management. By using them, a programmer can make decisions based on previous actions that are taken by the garbage collector. Although this is often helpful, the outcome of a program using weak references is less predictable due to the nondeterminism they introduce in program evaluation. It is therefore desirable to have a framework of formal tools to reason about weak references and programs that use them. We present several calculi that formalize various aspects of weak references, inspired by their implementation in Java. We provide a calculus to model multiple levels of non-strong references, where a different garbage collection policy is applied to each level. We consider different collection policies such as eager collection and lazy collection. Similar to the way they are implemented in Java, we give the semantics of eager collection to weak references and the semantics of lazy collection to soft references. Moreover, we condition garbage collection on the availability of time and space resources. While time constraints are used in order to restrict garbage collection, space constraints are used in order to trigger it. Finalizers are a problematic feature in Java, especially when they interact with weak references. We provide a calculus to model finalizer evaluation. Since finalizers have little meaning in a language without side-effect, we introduce a limited form of side effect into the calculus. We discuss determinism and the separate notion of uniqueness of (evaluation) outcome. We show that in our calculus, finalizer evaluation does not affect uniqueness of outcome.

Entorhinal cortex volume in older adults: reliability and validity considerations for three published measurement protocols.

Measuring the entorhinal cortex (ERC) is challenging due to lateral border discrimination from the perirhinal cortex. From a sample of 39 nondemented older adults who completed volumetric image scans and verbal memory indices, we examined reliability and validity concerns for three ERC protocols with different lateral boundary guidelines (i.e., Goncharova, Dickerson, Stoub, & deToledo-Morrell, 2001; Honeycutt et al., 1998; Insausti et al., 1998). We used three novice raters to assess inter-rater reliability on a subset of scans (216 total ERCs), with the entire dataset measured by one rater with strong intra-rater reliability on each technique (234 total ERCs). We found moderate to strong inter-rater reliability for two techniques with consistent ERC lateral boundary endpoints (Goncharova, Honeycutt), with negligible to moderate reliability for the technique requiring consideration of collateral sulcal depth (Insausti). Left ERC and story memory associations were moderate and positive for two techniques designed to exclude the perirhinal cortex (Insausti, Goncharova), with the Insausti technique continuing to explain 10% of memory score variance after additionally controlling for depression symptom severity. Right ERC-story memory associations were nonexistent after excluding an outlier. Researchers are encouraged to consider challenges of rater training for ERC techniques and how lateral boundary endpoints may impact structure-function associations.

Human CD19 and CD40L deficiencies impair antibody selection and differentially affect somatic hypermutation.

Individuals with genetic defects in CD40 ligand (CD40L) or B-cell antigen receptor coreceptor molecules CD19 and CD81 suffer from an antibody deficiency. Still, these patients carry low levels of memory B cells and serum antibodies.

Confidence, not consistency, characterizes flashbulb memories.

On September 12, 2001, 54 Duke students recorded their memory of first hearing about the terrorist attacks of September 11 and of a recent everyday event. They were tested again either 1, 6, or 32 weeks later. Consistency for the flashbulb and everyday memories did not differ, in both cases declining over time. However, ratings of vividness, recollection, and belief in the accuracy of memory declined only for everyday memories. Initial visceral emotion ratings correlated with later belief in accuracy, but not consistency, for flashbulb memories. Initial visceral emotion ratings predicted later posttraumatic stress disorder symptoms. Flashbulb memories are not special in their accuracy, as previously claimed, but only in their perceived accuracy.

Exhausted CD8 T cells downregulate the IL-18 receptor and become unresponsive to inflammatory cytokines and bacterial co-infections.

During many chronic infections virus-specific CD8 T cells succumb to exhaustion as they lose their ability to respond to antigenic activation. Combinations of IL-12, IL-18, and IL-21 have been shown to induce the antigen-independent production of interferon (IFN)-γ by effector and memory CD8 T cells. In this study we investigated whether exhausted CD8 T cells are sensitive to activation by these cytokines. We show that effector and memory, but not exhausted, CD8 T cells produce IFN-γ and upregulate CD25 following exposure to certain combinations of IL-12, IL-18, and IL-21. The unresponsiveness of exhausted CD8 T cells is associated with downregulation of the IL-18-receptor-α (IL-18Rα). Although IL-18Rα expression is connected with the ability of memory CD8 T cells to self-renew and efflux rhodamine 123, the IL-18Rα(lo) exhausted cells remained capable of secreting this dye. To further evaluate the consequences of IL-18Rα downregulation, we tracked the fate of IL-18Rα-deficient CD8 T cells in chronically infected mixed bone marrow chimeras and discovered that IL-18Rα affects the initial but not later phases of the response. The antigen-independent responsiveness of exhausted CD8 T cells was also investigated following co-infection with Listeria monocytogenes, which induces the expression of IL-12 and IL-18. Although IL-18Rα(hi) memory cells upregulated CD25 and produced IFN-γ, the IL-18Rα(lo) exhausted cells failed to respond. Collectively, these findings indicate that as exhausted T cells adjust to the chronically infected environment, they lose their susceptibility to antigen-independent activation by cytokines, which compromises their ability to detect bacterial co-infections.

Dominant Splice Site Mutations in PIK3R1 Cause Hyper IgM Syndrome, Lymphadenopathy and Short Stature.

The purpose of this research was to use next generation sequencing to identify mutations in patients with primary immunodeficiency diseases whose pathogenic gene mutations had not been identified. Remarkably, four unrelated patients were found by next generation sequencing to have the same heterozygous mutation in an essential donor splice site of PIK3R1 (NM_181523.2:c.1425 + 1G > A) found in three prior reports. All four had the Hyper IgM syndrome, lymphadenopathy and short stature, and one also had SHORT syndrome. They were investigated with in vitro immune studies, RT-PCR, and immunoblotting studies of the mutation's effect on mTOR pathway signaling. All patients had very low percentages of memory B cells and class-switched memory B cells and reduced numbers of naïve CD4+ and CD8+ T cells. RT-PCR confirmed the presence of both an abnormal 273 base-pair (bp) size and a normal 399 bp size band in the patient and only the normal band was present in the parents. Following anti-CD40 stimulation, patient's EBV-B cells displayed higher levels of S6 phosphorylation (mTOR complex 1 dependent event), Akt phosphorylation at serine 473 (mTOR complex 2 dependent event), and Akt phosphorylation at threonine 308 (PI3K/PDK1 dependent event) than controls, suggesting elevated mTOR signaling downstream of CD40. These observations suggest that amino acids 435-474 in PIK3R1 are important for its stability and also its ability to restrain PI3K activity. Deletion of Exon 11 leads to constitutive activation of PI3K signaling. This is the first report of this mutation and immunologic abnormalities in SHORT syndrome.

Parallel bandwidth characteristics calculations for thin avalanche photodiodes on a SGI Origin 2000 supercomputer

An important factor for high-speed optical communication is the availability of ultrafast and low-noise photodetectors. Among the semiconductor photodetectors that are commonly used in today’s long-haul and metro-area fiber-optic systems, avalanche photodiodes (APDs) are often preferred over p-i-n photodiodes due to their internal gain, which significantly improves the receiver sensitivity and alleviates the need for optical pre-amplification. Unfortunately, the random nature of the very process of carrier impact ionization, which generates the gain, is inherently noisy and results in fluctuations not only in the gain but also in the time response. Recently, a theory characterizing the autocorrelation function of APDs has been developed by us which incorporates the dead-space effect, an effect that is very significant in thin, high-performance APDs. The research extends the time-domain analysis of the dead-space multiplication model to compute the autocorrelation function of the APD impulse response. However, the computation requires a large amount of memory space and is very time consuming. In this research, we describe our experiences in parallelizing the code in MPI and OpenMP using CAPTools. Several array partitioning schemes and scheduling policies are implemented and tested. Our results show that the code is scalable up to 64 processors on a SGI Origin 2000 machine and has small average errors.

Venus infers

These poems mark the fault lines of myth, dream and memory, of a doubled identity emerging from the clash of war, desire and the cacophony of the city. 1974/Dead Sister , a narrative poem with a cast that includes Lewis Carroll’s Alice, Freud’s Dora, the Lady of Shalott, Ophelia, Esther, female cowboys and other deposed goddesses is ‘an autobiography’ of an imaginary dead twin. Alev Adil delineates the traces of a sense of displacement, but while the poems mark those frenetic uncertainties and erasures they celebrate the plenitude of new stories, epistemologies and possibilities born out of falling into fracture (the fracture of memory, gender, identity, culture) more than they mourn any loss. Venus Infers is haunted by the deities of ancient Greek myths and their contemporary manifestations. Eurydice is hiding out in Hackney, sometimes glimpsed on the Jubilee Line; Ariadne remembers her ancient palace as she prowls the endless corridors of a London hotel; Penelope still waits for peace in the ruins of Marash/Varosha. Cyprus often features in these poems, both as a landscape for myth and as a site for contemporary, and contested, memories. [From the Author]

The Postmodern Non-city in Miquel de Palol’s "El Jardí del Set Crepuscles"

El Jardí del Set Crepuscles –primera novela del escritor y arquitecto catalán Miquel de Palol– nos brinda la oportunidad de reflexionar acerca de la metamorfosis experimentada por la ciudad occidental a principios de los años setenta del siglo pasado. De acuerdo con autores como Henri Lefebvre, David Harvey, Giandomenico Amendola o Edward Soja, el surgimiento de la ciudad posmoderna en el marco de la transición hacia el modo de acumulación postfordista se presenta acompañado por un debilitamiento del tejido social y de la esfera pública y cívica. El objetivo del presente artículo es ilustrar las estrategias narrativas y retóricas con las que el texto de Miquel de Palol representa, y analiza, dicho fenómeno.

Inductive reasoning and semantic cognition: More than just different names for the same thing?

We describe evidence that certain inductive phenomena are associated with IQ, that different inductive phenomena emerge at different ages, and that the effects of causal knowledge on induction are decreased under conditions of memory load. On the basis of this evidence we argue that there is more to inductive reasoning than semantic cognition.

Truth Recovery and Transitional Justice: Deferring human rights issues

This book investigates why some societies defer the solution of transitional justice issues, such as the disappeared/missing, even after successful democratic consolidation. It also explains why the same societies finally decide to deal with these human rights issues. In short, it considers the interesting and understudied phenomenon of post-transitional justice. The prolonged silences in Spain, Cyprus and Greece contradict the experience of other countries -- such as South Africa, Bosnia, and Guatemala -- where truth recovery for disappeared/missing persons was a central element of the transition to peace and democracy. Despite democratization, the exhumation of mass graves containing the victims from the violence in Cyprus (1963-1974) and the Spanish civil war (1936-1939) was delayed until the early 2000s, when both countries suddenly decided to revisit the past. Cyprus and Spain are not alone: this is an increasing trend among countries trying to come to terms with past violence. Interestingly, despite similar background conditions, Greece is resisting the trend, challenging both theory and regional experience. Truth Recovery and Transitional Justice considers three interrelated issues. First, what factors can explain prolonged silence on the issue of missing persons in some transitional settings? Second, which processes can address the occasional yet puzzling transformation of victims’ groups from opponents of truth recovery to vocal pro-reconciliation pressure groups? Third, under which conditions is it better to tie victims’ rights to an overall political settlement? The book looks at Spain and Cyprus to show how they have attempted to bring closure to deep trauma by exhuming and identifying their missing, albeit under considerably different conditions. It then probes the generalizability of the conclusions on Spain and Cyprus by looking at the Greek experience; oddly, despite similar background conditions, Greece remains resistant to post-transitional justice norms. Interestingly, each case study takes a different approach to transitional justice.

Approximate Computing with Unreliable Dynamic Memories

Embedded memories account for a large fraction of the overall silicon area and power consumption in modern SoC(s). While embedded memories are typically realized with SRAM, alternative solutions, such as embedded dynamic memories (eDRAM), can provide higher density and/or reduced power consumption. One major challenge that impedes the widespread adoption of eDRAM is that they require frequent refreshes potentially reducing the availability of the memory in periods of high activity and also consuming significant amount of power due to such frequent refreshes. Reducing the refresh rate while on one hand can reduce the power overhead, if not performed in a timely manner, can cause some cells to lose their content potentially resulting in memory errors. In this paper, we consider extending the refresh period of gain-cell based dynamic memories beyond the worst-case point of failure, assuming that the resulting errors can be tolerated when the use-cases are in the domain of inherently error-resilient applications. For example, we observe that for various data mining applications, a large number of memory failures can be accepted with tolerable imprecision in output quality. In particular, our results indicate that by allowing as many as 177 errors in a 16 kB memory, the maximum loss in output quality is 11%. We use this failure limit to study the impact of relaxing reliability constraints on memory availability and retention power for different technologies.