CLAM-Accelerated K-Nearest Neighbors Entropy-Scaling Search of Large High-Dimensional Datasets via an Actualization of the Manifold Hypothesis

Many fields are experiencing a Big Data explosion, with data collection rates outpacing the rate of computing performance improvements predicted by Moore's Law. Researchers are often interested in similarity search on such data. We present CAKES (CLAM-Accelerated $K$-NN Entropy Scaling Search), a novel algorithm for $k$-nearest-neighbor ($k$-NN) search which leverages geometric and topological properties inherent in large datasets. CAKES assumes the manifold hypothesis and performs best when data occupy a low dimensional manifold, even if the data occupy a very high dimensional embedding space. We demonstrate performance improvements ranging from hundreds to tens of thousands of times faster when compared to state-of-the-art approaches such as FAISS and HNSW, when benchmarked on 5 standard datasets. Unlike locality-sensitive hashing approaches, CAKES can work with any user-defined distance function. When data occupy a metric space, CAKES exhibits perfect recall.Comment: As submitted to IEEE Big Data 202

Inorganic Chemistry of the Tripodal Picolinate Ligand Tpaa with Gallium(III) and Radiolabeling with Gallium-68

We report here the improved synthesis of the tripodal picolinate chelator Tpaa, with an overall yield of 41% over five steps, in comparison to the previously reported 6% yield. Tpaa was investigated for its coordination chemistry with Ga(III) and radiolabeling properties with gallium-68 (68Ga). The obtained crystal structure for [Ga(Tpaa)] shows that the three picolinate arms coordinate to the Ga(III) ion, fully occupying the octahedral coordination geometry. This is supported by 1H NMR which shows that the three arms are symmetrical when coordinated to Ga(III). Assessment of the thermodynamic stability through potentiometry gives log KGa-Tpaa = 21.32, with a single species being produced across the range of pH 3.5-7.5. Tpaa achieved >99% radiochemical conversion with 68Ga under mild conditions ([Tpaa] = 6.6 μM, pH 7.4, 37 °C) with a molar activity of 3.1 GBq μmol-1. The resulting complex, [68Ga][Ga(Tpaa)], showed improved stability over the previously reported [68Ga][Ga(Dpaa)(H2O)] in a serum challenge, with 32% of [68Ga][Ga(Tpaa)] remaining intact after 30 min of incubation with fetal bovine serum

Greenland Ice Sheet - Higher non-linearity of ice flow significantly reduces estimated basal motion

In times of warming in polar regions, the prediction of ice sheet discharge is of utmost importance to society, because of its impact on sea level rise. In simulations the flow rate of ice is usually implemented as proportional to the differential stress to the power of the exponent n=3. This exponent influences the softness of the modeled ice, as higher values would produce faster flow under equal stress. We show that the stress exponent, which best fits the observed state of the Greenland Ice Sheet, equals n=4. Our results, which are not dependent on a possible basal sliding component of flow, indicate that most of the interior northern ice sheet is currently frozen to bedrock, except for the large ice streams and marginal ice. Ice in the polar ice sheets flows towards the oceans under its own weight. Knowing how fast the ice flows is of crucial importance to predict future sea level rise. The flow has two components: (1) internal shearing flow of ice and (2) basal motion, which is sliding along the base of ice sheets, especially when the ice melts at this base. To determine the first component we need to know how "soft" the ice is. By considering the flow velocities at the surface of the northern Greenland Ice Sheet and calculating the stresses that cause the flow, we determined that the ice is effectively softer than is usually assumed. Previous studies indicated that the base of the ice is thawed in large parts (up to about 50%) of the Greenland Ice Sheet. Our study shows that that is probably overestimated, because these studies assumed ice to be harder than it actually is. Our new assessment reduces the area with basal motion and thus melting to about 6-13% in the Greenland study area

Synthesis and Characterization of Two Metallic Spin-Glass Phases of FeMo₄Ge₃

Polycrystalline samples of FeMo4Ge3 have been synthesized by the reduction of an oxide mixture at 1248 K and characterized by a combination of diffraction, muon spin relaxation (µ+SR), Mössbauer spectroscopy, magnetometry, transport, and heat-capacity measurements. The compound adopts a tetragonal W5Si3 structure (space group I4/mcm); the iron and molybdenum atoms are disordered over two crystallographic sites, 16k and either 4a or 4b. The synthesis conditions determine which fourfold site is selected; occupation of either leads to the presence of one-dimensional chains of transition metals in the structure. In both cases, the electrical resistivity below 200 K is ~175 µΩ cm. The dc magnetization rapidly rises below 35 K (Fe/Mo on 16k and 4b sites) or 16 K (16k and 4a sites), and a magnetization of 1µB or 0.8µB per Fe atom is observed in 4 T at 2 K. The ac susceptibility and the heat capacity both suggest that these are glasslike magnetic transitions, although the transition shows a more complex temperature dependence (with two maxima in χ ) when the 4b sites are partially occupied by iron. No long-range magnetic order is thought to be present at 5 K in either structural form; this has been proven by neutron diffraction and µ+SR for the case when Fe and Mo occupy the 16k and 4b sites

Amino acid based gallium-68 chelators capable of radiolabeling at neutral pH

Gallium-68 ( 68 Ga) has been the subject of increasing interest for its potential in the production of radiotracers for diagnosis of diseases. In this work we report the complexation of 68 Ga by the amino acid based tripodal chelate H 3 Dpaa, and two bifunctional derivatives, H 3 Dpaa.dab and H 4 Dpaa.ga, under a range of conditions with particular emphasis on the rapid complexation of 68 Ga at pH 7.4. 100 μM H 3 Dpaa achieved a radiochemical yield of 95% at pH 7.4 in 5 minutes at 37 °C. The bifunctional derivatives H 4 Dpaa.ga and H 3 Dpaa.dab achieved 94% and 84% radiochemical yields, respectively, under the same conditions. The resulting Ga(iii) complexes show thermodynamic stabilities of logK GaDpaa = 18.53, logK GaDpaa.dab = 22.08, logK GaDpaa.ga = 18.36. Unfortunately, the resulting radiolabelled species do not present sufficient serum stability for in vivo application. Herein we show a flexible synthesis for bifunctional chelators based on amino acids that rapidly complex 68 Ga under physiological conditions

SMN Protein Can Be Reliably Measured in Whole Blood with an Electrochemiluminescence (ECL) Immunoassay: Implications for Clinical Trials

Spinal muscular atrophy (SMA) is caused by defects in the survival motor neuron 1 (SMN1) gene that encodes survival motor neuron (SMN) protein. The majority of therapeutic approaches currently in clinical development for SMA aim to increase SMN protein expression and there is a need for sensitive methods able to quantify increases in SMN protein levels in accessible tissues. We have developed a sensitive electrochemiluminescence (ECL)-based immunoassay for measuring SMN protein in whole blood with a minimum volume requirement of 5μL. The SMN-ECL immunoassay enables accurate measurement of SMN in whole blood and other tissues. Using the assay, we measured SMN protein in whole blood from SMA patients and healthy controls and found that SMN protein levels were associated with SMN2 copy number and were greater in SMA patients with 4 copies, relative to those with 2 and 3 copies. SMN protein levels did not vary significantly in healthy individuals over a four-week period and were not affected by circadian rhythms. Almost half of the SMN protein was found in platelets. We show that SMN protein levels in C/C-allele mice, which model a mild form of SMA, were high in neonatal stage, decreased in the first few weeks after birth, and then remained stable throughout the adult stage. Importantly, SMN protein levels in the CNS correlated with SMN levels measured in whole blood of the C/C-allele mice. These findings have implications for the measurement of SMN protein induction in whole blood in response to SMN-upregulating therapy

Phase II Open Label Study of Valproic Acid in Spinal Muscular Atrophy

UNLABELLED:Preliminary in vitro and in vivo studies with valproic acid (VPA) in cell lines and patients with spinal muscular atrophy (SMA) demonstrate increased expression of SMN, supporting the possibility of therapeutic benefit. We performed an open label trial of VPA in 42 subjects with SMA to assess safety and explore potential outcome measures to help guide design of future controlled clinical trials. Subjects included 2 SMA type I ages 2-3 years, 29 SMA type II ages 2-14 years and 11 type III ages 2-31 years, recruited from a natural history study. VPA was well-tolerated and without evident hepatotoxicity. Carnitine depletion was frequent and temporally associated with increased weakness in two subjects. Exploratory outcome measures included assessment of gross motor function via the modified Hammersmith Functional Motor Scale (MHFMS), electrophysiologic measures of innervation including maximum ulnar compound muscle action potential (CMAP) amplitudes and motor unit number estimation (MUNE), body composition and bone density via dual-energy X-ray absorptiometry (DEXA), and quantitative blood SMN mRNA levels. Clear decline in motor function occurred in several subjects in association with weight gain; mean fat mass increased without a corresponding increase in lean mass. We observed an increased mean score on the MHFMS scale in 27 subjects with SMA type II (p<or=0.001); however, significant improvement was almost entirely restricted to participants <5 years of age. Full length SMN levels were unchanged and Delta7SMN levels were significantly reduced for 2 of 3 treatment visits. In contrast, bone mineral density (p<or=0.0036) and maximum ulnar CMAP scores (p<or=0.0001) increased significantly. CONCLUSIONS:While VPA appears safe and well-tolerated in this initial pilot trial, these data suggest that weight gain and carnitine depletion are likely to be significant confounding factors in clinical trials. This study highlights potential strengths and limitations of various candidate outcome measures and underscores the need for additional controlled clinical trials with VPA targeting more restricted cohorts of subjects. TRIAL REGISTRATION:ClinicalTrials.gov

SMA CARNI-VAL Trial Part I: Double-Blind, Randomized, Placebo-Controlled Trial of L-Carnitine and Valproic Acid in Spinal Muscular Atrophy

Valproic acid (VPA) has demonstrated potential as a therapeutic candidate for spinal muscular atrophy (SMA) in vitro and in vivo.Two cohorts of subjects were enrolled in the SMA CARNIVAL TRIAL, a non-ambulatory group of "sitters" (cohort 1) and an ambulatory group of "walkers" (cohort 2). Here, we present results for cohort 1: a multicenter phase II randomized double-blind intention-to-treat protocol in non-ambulatory SMA subjects 2-8 years of age. Sixty-one subjects were randomized 1:1 to placebo or treatment for the first six months; all received active treatment the subsequent six months. The primary outcome was change in the modified Hammersmith Functional Motor Scale (MHFMS) score following six months of treatment. Secondary outcomes included safety and adverse event data, and change in MHFMS score for twelve versus six months of active treatment, body composition, quantitative SMN mRNA levels, maximum ulnar CMAP amplitudes, myometry and PFT measures.At 6 months, there was no difference in change from the baseline MHFMS score between treatment and placebo groups (difference = 0.643, 95% CI = -1.22-2.51). Adverse events occurred in >80% of subjects and were more common in the treatment group. Excessive weight gain was the most frequent drug-related adverse event, and increased fat mass was negatively related to change in MHFMS values (p = 0.0409). Post-hoc analysis found that children ages two to three years that received 12 months treatment, when adjusted for baseline weight, had significantly improved MHFMS scores (p = 0.03) compared to those who received placebo the first six months. A linear regression analysis limited to the influence of age demonstrates young age as a significant factor in improved MHFMS scores (p = 0.007).This study demonstrated no benefit from six months treatment with VPA and L-carnitine in a young non-ambulatory cohort of subjects with SMA. Weight gain, age and treatment duration were significant confounding variables that should be considered in the design of future trials.Clinicaltrials.gov NCT00227266

Proteomic Analysis of GLUT4 Storage Vesicles Reveals Tumor Suppressor Candidate 5 (TUSC5) as a Novel Regulator of Insulin Action in Adipocytes.

Insulin signaling augments glucose transport by regulating glucose transporter 4 (GLUT4) trafficking from specialized intracellular compartments, termed GLUT4 storage vesicles (GSVs), to the plasma membrane. Proteomic analysis of GSVs by mass spectrometry revealed enrichment of 59 proteins in these vesicles. We measured reduced abundance of 23 of these proteins following insulin stimulation and assigned these as high confidence GSV proteins. These included established GSV proteins such as GLUT4 and insulin-responsive aminopeptidase, as well as six proteins not previously reported to be localized to GSVs. Tumor suppressor candidate 5 (TUSC5) was shown to be a novel GSV protein that underwent a 3.7-fold increase in abundance at the plasma membrane in response to insulin. siRNA-mediated knockdown of TUSC5 decreased insulin-stimulated glucose uptake, although overexpression of TUSC5 had the opposite effect, implicating TUSC5 as a positive regulator of insulin-stimulated glucose transport in adipocytes. Incubation of adipocytes with TNFα caused insulin resistance and a concomitant reduction in TUSC5. Consistent with previous studies, peroxisome proliferator-activated receptor (PPAR) γ agonism reversed TNFα-induced insulin resistance. TUSC5 expression was necessary but insufficient for PPARγ-mediated reversal of insulin resistance. These findings functionally link TUSC5 to GLUT4 trafficking, insulin action, insulin resistance, and PPARγ action in the adipocyte. Further studies are required to establish the exact role of TUSC5 in adipocytes