Efficient Estimation of Heat Kernel PageRank for Local Clustering

Given an undirected graph G and a seed node s, the local clustering problem aims to identify a high-quality cluster containing s in time roughly proportional to the size of the cluster, regardless of the size of G. This problem finds numerous applications on large-scale graphs. Recently, heat kernel PageRank (HKPR), which is a measure of the proximity of nodes in graphs, is applied to this problem and found to be more efficient compared with prior methods. However, existing solutions for computing HKPR either are prohibitively expensive or provide unsatisfactory error approximation on HKPR values, rendering them impractical especially on billion-edge graphs. In this paper, we present TEA and TEA+, two novel local graph clustering algorithms based on HKPR, to address the aforementioned limitations. Specifically, these algorithms provide non-trivial theoretical guarantees in relative error of HKPR values and the time complexity. The basic idea is to utilize deterministic graph traversal to produce a rough estimation of exact HKPR vector, and then exploit Monte-Carlo random walks to refine the results in an optimized and non-trivial way. In particular, TEA+ offers practical efficiency and effectiveness due to non-trivial optimizations. Extensive experiments on real-world datasets demonstrate that TEA+ outperforms the state-of-the-art algorithm by more than four times on most benchmark datasets in terms of computational time when achieving the same clustering quality, and in particular, is an order of magnitude faster on large graphs including the widely studied Twitter and Friendster datasets.Comment: The technical report for the full research paper accepted in the SIGMOD 201

A common founding clone with TP53 and PTEN mutations gives rise to a concurrent germ cell tumor and acute megakaryoblastic leukemia

We report the findings from a patient who presented with a concurrent mediastinal germ cell tumor (GCT) and acute myeloid leukemia (AML). Bone marrow pathology was consistent with a diagnosis of acute megakaryoblastic leukemia (AML M7), and biopsy of an anterior mediastinal mass was consistent with a nonseminomatous GCT. Prior studies have described associations between hematological malignancies, including AML M7 and nonseminomatous GCTs, and it was recently suggested that a common founding clone initiated both cancers. We performed enhanced exome sequencing on the GCT and the AML M7 from our patient to define the clonal relationship between the two cancers. We found that both samples contained somatic mutations in PTEN (C136R missense) and TP53 (R213 frameshift). The mutations in PTEN and TP53 were present at ∼100% variant allele frequency (VAF) in both tumors. In addition, we detected and validated five other shared somatic mutations. The copy-number analysis of the AML exome data revealed an amplification of Chromosome 12p. We also identified a heterozygous germline variant in FANCA (S858R), which is known to be associated with Fanconi anemia but is of uncertain significance here. In summary, our data not only support a common founding clone for these cancers but also suggest that a specific set of distinct genomic alterations (in PTEN and TP53) underlies the rare association between GCT and AML. This association is likely linked to the treatment resistance and extremely poor outcome of these patients. We cannot resolve the clonal evolution of these tumors given limitations of our data

Hydrodynamical Simulations of the Lyman Alpha Forest: Model Comparisons

We investigate the properties of the Lyman alpha forest as predicted by numerical simulations for a range of currently viable cosmological models. This is done in order to understand the dependencies of the forest on cosmological parameters. Focusing on the redshift range from two to four, we show that: (1) most of the evolution in the distributions of optical depth, flux and column density can be understood by simple scaling relations, (2) the shape of optical depth distribution is a sensitive probe of the amplitude of density fluctuations on scales of a few hundred kpc, (3) the mean of the b distribution (a measure of the width of the absorption lines) is also very sensitive to fluctuations on these scales, and decreases as they increase. We perform a preliminary comparison to observations, where available. A number of other properties are also examined, including the evolution in the number of lines, the two-point flux distribution and the HeII opacity.Comment: 37 pages, 21 figures, submitted to Ap

Natural Experiment Examining Impact of Aggressive Screening and Treatment on Prostate Cancer Mortality in Two Fixed Cohorts from Seattle Area and Connecticut

To determine whether the more intensive screening and treatment for prostate cancer in the Seattle≠Puget Sound area in 1987≠90 led to lower mortality from prostate cancer than in Connecticut

Graphite Nanoeraser

We present here a method for cleaning intermediate-size (5~50nm) contamination from highly oriented pyrolytic graphite. Electron beam deposition causes a continuous increase of carbonaceous material on graphene and graphite surfaces, which is difficult to remove by conventional techniques. Direct mechanical wiping using a graphite nanoeraser is observed to drastically reduce the amount of contamination. After the mechanical removal of contamination, the graphite surfaces were able to self-retract after shearing, indicating that van der Waals contact bonding is restored. Since contact bonding provides an indication of a level of cleanliness normally only attainable in a high-quality clean-room, we discuss potential applications in preparation of ultraclean surfaces.Comment: 10 pages, two figure

SnTox3 Acts in Effector Triggered Susceptibility to Induce Disease on Wheat Carrying the Snn3 Gene

The necrotrophic fungus Stagonospora nodorum produces multiple proteinaceous host-selective toxins (HSTs) which act in effector triggered susceptibility. Here, we report the molecular cloning and functional characterization of the SnTox3-encoding gene, designated SnTox3, as well as the initial characterization of the SnTox3 protein. SnTox3 is a 693 bp intron-free gene with little obvious homology to other known genes. The predicted immature SnTox3 protein is 25.8 kDa in size. A 20 amino acid signal sequence as well as a possible pro sequence are predicted. Six cysteine residues are predicted to form disulfide bonds and are shown to be important for SnTox3 activity. Using heterologous expression in Pichia pastoris and transformation into an avirulent S. nodorum isolate, we show that SnTox3 encodes the SnTox3 protein and that SnTox3 interacts with the wheat susceptibility gene Snn3. In addition, the avirulent S. nodorum isolate transformed with SnTox3 was virulent on host lines expressing the Snn3 gene. SnTox3-disrupted mutants were deficient in the production of SnTox3 and avirulent on the Snn3 differential wheat line BG220. An analysis of genetic diversity revealed that SnTox3 is present in 60.1% of a worldwide collection of 923 isolates and occurs as eleven nucleotide haplotypes resulting in four amino acid haplotypes. The cloning of SnTox3 provides a fundamental tool for the investigation of the S. nodorum-wheat interaction, as well as vital information for the general characterization of necrotroph-plant interactions.This work was supported by USDA-ARS CRIS projects 5442-22000-043-00D and 5442-22000-030-00D

An oligofluorene truxene based distributed feedback laser for biosensing applications

The first example of an all-organic oligofluorene truxene based distributed feedback laser for the detection of a specific protein–small molecule interaction is reported. The protein avidin was detected down to View the MathML source1μgmL−1 using our biotin-labelled biosensor platform. This interaction was both selective and reversible when biotin was replaced with desthiobiotin. Avidin detection was not perturbed by Bovine Serum Albumin up to View the MathML source50,000μgmL−1. Our biosensor offers a new detection platform that is both highly sensitive, modular and potentially re-usable

Effects of carpal tunnel syndrome on force coordination and muscle coherence during precision pinch

Carpal tunnel syndrome (CTS), caused by entrapment of the median nerve in the carpal tunnel, impairs hand function including dexterous manipulation. The purpose of this study was to investigate the effects of CTS on force coordination and muscle coherence during low-intensity sustained precision pinch while the wrist assumed different postures. Twenty subjects (10 CTS patients and 10 asymptomatic controls) participated in this study. An instrumented pinch device was used to measure the thumb and index finger forces while simultaneously collecting surface electromyographic activities of the abductor pollicis brevis (APB) and first dorsal interosseous (FDI) muscles. Subjects performed a sustained precision pinch at 10% maximum pinch force for 15 sec with the wrist stabilized at 30° extension, neutral, or 30° flexion using customized splints. The force discrepancy and the force coordination angle between the thumb and index finger forces were calculated, as well as the β-band (15-30 Hz) coherence between APB and FDI. The index finger applied greater force than the thumb (p 0.05). The directional force coordination was not significantly affected by wrist posture or CTS (p > 0.05). In general, digit force coordination during precision pinch seems to be sensitive to wrist flexion, but is not affected by CTS. The β-band muscular coherence was increased by wrist flexion for CTS patients (p < 0.05), which could be a compensatory mechanism for the flexion-induced exacerbation of CTS symptoms. This study demonstrates that wrist flexion negatively influences muscle and force coordination in CTS patients supporting the avoidance of flexion posture for symptom exacerbation and functional performance

Change in Depression, Confidence, and Physical Function Among Older Adults With Mild Cognitive Impairment

Background and Purpose Nearly a quarter of those in the US over age 71 experience mild cognitive impairment (MCI). Persons with MCI (PwMCI) battle depression and progressive disengagement from daily activities, which contribute to participation restriction and activity limitation. Daily engagement in meaningful activity (DEMA) is a tailored intervention designed to benefit PwMCI and their caregivers through preserved engagement and supported adjustment to cognitive changes. This secondary analysis was guided by the International Classification of Functioning, Disability and Health (ICF) model. Aims were to (i) explore the extent to which change in self-rated activity performance and physical function can predict change in depressive symptoms, (ii) evaluate for difference in confidence and depressive symptoms at ICF levels of activity and participation, and (iii) quantify the impact of daily engagement at the ICF level of participation on physical function. Methods A secondary analysis was conducted using data from the parent study, which was a two-group randomized trial involving PwMCI and their informal caregivers participating in the Indiana Alzheimer Disease Center DEMA program. Quantitative analysis (dyads: DEMA N = 20, Information Support N = 20) examined outcomes at posttest and follow-up. Analysis employed linear regression to model the relationship between explanatory and dependent variables and independent t-test to examine for difference in confidence, depression, and physical function. Results and Discussion At posttest, change in self-rated performance predicted change in depressive symptoms. Those in the DEMA group who engaged in activity at the ICF level of participation demonstrated a significant increase in confidence and physical function. Although not significant, the control group posttest results showed a mean decrease in confidence. Conclusions Results demonstrate a positive impact of DEMA on depressive symptoms, confidence, and physical function. Change in occupational performance predicted change in depressive symptoms. Confidence significantly improved among those who engaged at the ICF participation level. A larger, randomized controlled longitudinal trial is needed to better assess the impact of DEMA on physical function, activity, participation restriction and quality of life