Streaming Compression of Scientific Data via weak-SINDy

In this paper a streaming weak-SINDy algorithm is developed specifically for compressing streaming scientific data. The production of scientific data, either via simulation or experiments, is undergoing an stage of exponential growth, which makes data compression important and often necessary for storing and utilizing large scientific data sets. As opposed to classical ``offline" compression algorithms that perform compression on a readily available data set, streaming compression algorithms compress data ``online" while the data generated from simulation or experiments is still flowing through the system. This feature makes streaming compression algorithms well-suited for scientific data compression, where storing the full data set offline is often infeasible. This work proposes a new streaming compression algorithm, streaming weak-SINDy, which takes advantage of the underlying data characteristics during compression. The streaming weak-SINDy algorithm constructs feature matrices and target vectors in the online stage via a streaming integration method in a memory efficient manner. The feature matrices and target vectors are then used in the offline stage to build a model through a regression process that aims to recover equations that govern the evolution of the data. For compressing high-dimensional streaming data, we adopt a streaming proper orthogonal decomposition (POD) process to reduce the data dimension and then use the streaming weak-SINDy algorithm to compress the temporal data of the POD expansion. We propose modifications to the streaming weak-SINDy algorithm to accommodate the dynamically updated POD basis. By combining the built model from the streaming weak-SINDy algorithm and a small amount of data samples, the full data flow could be reconstructed accurately at a low memory cost, as shown in the numerical tests

Reproducible synthesis of C\u3csub\u3e60\u3c/sub\u3e@SWNT in 90% yields

In previous works, we have shown our discovery of C60@SWNT and first described the general mechanism of filling, which involves the vapor phase transport of C60 molecules to openings in the SWNTs\u27 walls. Here, we discuss the high-yield synthesis of C60@SWNT by refinements to our method. Yields are measured by a calibrated weight uptake technique, a methodology that is not subject to many of the potential pitfalls inherent to other techniques that have been applied. At certain processing conditions, yields exceeding 90% were obtained and corroborated by transmission electron microscopy. From our data, we determine the parameters most important for creating endohedral SWNT supramolecular assemblies by the vapor phase method. Our results pave the way for successful single-tube measurements and for high-yield filling with non-fullerenes

Processing of single wall carbon nanotubes and implications for filling experiments

Single wall carbon nanotubes (SWNTs) have been processed in different schemes to get clean material for use in various filling experiments. The SWNTs synthesized by different methods require different processing schemes, and this is presumably due to heterogeneous nature of the various contaminants present along with the carbon nanotubes. For the pulsed laser synthesized SWNTs, a combination of nitric acid, hydrogen peroxide and hydrochloric acid treatment gives best results and the purified SWNTs give best ever filling fraction for fullerene, C60 of ~90%. The processing improves the surface cleanliness of SWNTs, in turn giving greater access for the target molecules, and hence the higher filling fraction. For the carbon arc produced SWNTs, air oxidation followed by treatment with nitric acid has been found to work best and the processed SWNTs have been used for filling experiments with metal chlorides. Both these processing schemes still leave a small fraction of catalyst impurities in the final material, thus the material quality of filled material and hence its properties depend on the processed material used for the filling experiments

Structure and properties of C\u3csub\u3e60\u3c/sub\u3e@SWNT

Our recent achievement of high-yield C60@SWNT synthesis facilitates characterization by various techniques, including selected area electron diffraction (SAD) and Raman spectroscopy. The obtained SAD patterns show that interior C60 molecules sit on a simple 1-D lattice having a parameter of 1.00 nm. Simulated SAD patterns and real-space measurements both support this determination and do not indicate a lattice with a more complex basis, e.g. a dimer basis. Empty and bulk-filled SWNTs (22%, 56%, and 90% yields), each subjected to identical processing steps, were examined by room temperature Raman spectroscopy. Systematic differences are seen between the spectra of filled and unfilled SWNTs, particularly with respect to the G- and RBM-bands of the nanotubes. We present a possible explanation for this behavior

Inhibition of the \u3cem\u3edapE\u3c/em\u3e-Encoded \u3cem\u3eN\u3c/em\u3e-Succinyl- ʟ, ʟ-diaminopimelic Acid Desuccinylase from \u3cem\u3eNeisseria meningitidis\u3c/em\u3e by ʟ-Captopril

Binding of the competitive inhibitor ʟ-captopril to the dapE-encoded N-succinyl-ʟ, ʟ-diaminopimelic acid desuccinylase from Neisseria meningitidis (NmDapE) was examined by kinetic, spectroscopic, and crystallographic methods. ʟ-Captopril, an angiotensin-converting enzyme (ACE) inhibitor, was previously shown to be a potent inhibitor of the DapE from Haemophilus influenzae (HiDapE) with an IC50 of 3.3 μM and a measured Ki of 1.8 μM and displayed a dose-responsive antibiotic activity toward Escherichia coli. ʟ-Captopril is also a competitive inhibitor of NmDapE with a Ki of 2.8 μM. To examine the nature of the interaction of ʟ-captopril with the dinuclear active site of DapE, we have obtained electron paramagnetic resonance (EPR) and magnetic circular dichroism (MCD) data for the enzymatically hyperactive Co(II)-substituted forms of both HiDapE and NmDapE. EPR and MCD data indicate that the two Co(II) ions in DapE are antiferromagnetically coupled, yielding an S = 0 ground state, and suggest a thiolate bridge between the two metal ions. Verification of a thiolate-bridged dinuclear complex was obtained by determining the three-dimensional X-ray crystal structure of NmDapE in complex with ʟ-captopril at 1.8 Å resolution. Combination of these data provides new insights into binding of ʟ-captopril to the active site of DapE enzymes as well as important inhibitor–active site residue interaction’s. Such information is critical for the design of new, potent inhibitors of DapE enzymes

One-dimensional Diffusion-limited Relaxation of Photoexcitations in Suspensions of Single-walled Carbon Nanotubes

We report pump-probe transient absorption spectroscopy on carbon nanotubes with a high initial excitation density. We find that the recovery of the ground state optical absorption is well described by a 1/√t relaxation, indicating that the long time population relaxation is controlled by one-dimensional diffusion limited two body recombination

Identification of PKD1L1 Gene Variants in Children with the Biliary Atresia Splenic Malformation Syndrome

Biliary atresia (BA) is the most common cause of end‐stage liver disease in children and the primary indication for pediatric liver transplantation, yet underlying etiologies remain unknown. Approximately 10% of infants affected by BA exhibit various laterality defects (heterotaxy) including splenic abnormalities and complex cardiac malformations — a distinctive subgroup commonly referred to as the biliary atresia splenic malformation (BASM) syndrome. We hypothesized that genetic factors linking laterality features with the etiopathogenesis of BA in BASM patients could be identified through whole exome sequencing (WES) of an affected cohort. DNA specimens from 67 BASM subjects, including 58 patient‐parent trios, from the NIDDK‐supported Childhood Liver Disease Research Network (ChiLDReN) underwent WES. Candidate gene variants derived from a pre‐specified set of 2,016 genes associated with ciliary dysgenesis and/or dysfunction or cholestasis were prioritized according to pathogenicity, population frequency, and mode of inheritance. Five BASM subjects harbored rare and potentially deleterious bi‐allelic variants in polycystin 1‐like 1, PKD1L1, a gene associated with ciliary calcium signaling and embryonic laterality determination in fish, mice and humans. Heterozygous PKD1L1 variants were found in 3 additional subjects. Immunohistochemical analysis of liver from the one BASM subject available revealed decreased PKD1L1 expression in bile duct epithelium when compared to normal livers and livers affected by other non‐cholestatic diseases. Conclusion WES identified bi‐allelic and heterozygous PKD1L1 variants of interest in 8 BASM subjects from the ChiLDReN dataset. The dual roles for PKD1L1 in laterality determination and ciliary function suggest that PKD1L1 is a new, biologically plausible, cholangiocyte‐expressed candidate gene for the BASM syndrome

In utero exposure to butyl benzyl phthalate induces modifications in the morphology and the gene expression profile of the mammary gland: an experimental study in rats

<p>Abstract</p> <p>Background</p> <p>Environmental estrogens are exogenous estrogen-mimicking compounds that can interfere with endogenous endocrine systems. Several of these endocrine disruptors have been shown to alter normal development and influence tumorigenesis in experimental models. N-butyl benzyl phthalate (BBP), a widely used plasticizer, is a well-known endocrine disruptor. The aim of this study was to elucidate the effect of prenatal exposure to BBP on the morphology, proliferative index, and genomic signature of the rat mammary gland at different ages.</p> <p>Methods</p> <p><it>In utero </it>exposure was performed by gavage of pregnant Sprague Dawley CD rats with 120mg or 500mg BBP/kg/day from day 10 post-conception to delivery. Female litters were euthanized at 21, 35, 50 and 100 days. The morphology and proliferative index of the mammary gland were studied from whole mount preparations and BrdU incorporation, respectively. Gene expression profile was assessed by microarrays. Several genes found differentially expressed and related to different functional categories were further validated by real time RT-PCR.</p> <p>Results</p> <p>Prenatal exposure of BBP induced delayed vaginal opening and changes in the post-natal mammary gland long after the end of the treatment, mainly by 35 days of age. Exposure to the high dose resulted in modifications in architecture and proliferative index of the mammary gland, mostly affecting the undifferentiated terminal end buds. Moreover, the expression profiles of this gland in the exposed rats were modified in a dose-dependent fashion. Analysis of functional categories showed that modified genes were related to immune function, cell signaling, proliferation and differentiation, or metabolism.</p> <p>Conclusions</p> <p>Our data suggest that <it>in utero </it>exposure to BBP induced a delayed pubertal onset and modified morphology of the mammary gland. These alterations were accompanied by modifications in gene expression previously associated with an increased susceptibility to carcinogenesis.</p

Isometric Embeddings and Noncommutative Branes in Homogeneous Gravitational Waves

We characterize the worldvolume theories on symmetric D-branes in a six-dimensional Cahen-Wallach pp-wave supported by a constant Neveu-Schwarz three-form flux. We find a class of flat noncommutative euclidean D3-branes analogous to branes in a constant magnetic field, as well as curved noncommutative lorentzian D3-branes analogous to branes in an electric background. In the former case the noncommutative field theory on the branes is constructed from first principles, related to dynamics of fuzzy spheres in the worldvolumes, and used to analyse the flat space limits of the string theory. The worldvolume theories on all other symmetric branes in the background are local field theories. The physical origins of all these theories are described through the interplay between isometric embeddings of branes in the spacetime and the Penrose-Gueven limit of AdS3 x S3 with Neveu-Schwarz three-form flux. The noncommutative field theory of a non-symmetric spacetime-filling D-brane is also constructed, giving a spatially varying but time-independent noncommutativity analogous to that of the Dolan-Nappi model.Comment: 52 pages; v2: References adde

Musicologists and Data Scientists Pull out all the Stops: Defining Renaissance Cadences Systematically

Digital tools offer many ways to find musical patterns with machines. But the task of formulating digital-musical queries systematically, interpreting the results, and refining our methods to yield intelligent insights about musical practice is far more difficult. In this presentation, a team of musicologists and data scientists will share our experiences in developing CRIM Intervals, a Python-Pandas toolkit designed to support Citations: The Renaissance Imitation Mass, modeling human expertise in terms that can be used by computers to analyze encoded musical scores, and presenting the results of automated score-reading in forms that scholars can interrogate and refine. This presentation explains how we developed these tools, from understanding the constraints that define a given musical event, to the development of the tools needed to model those constraints, and in turn to the stages of refinement needed to eliminate false negatives and positives