Data standardization

With data rapidly becoming the lifeblood of the global economy, the ability to improve its use significantly affects both social and private welfare. Data standardization is key to facilitating and improving the use of data when data portability and interoperability are needed. Absent data standardization, a “Tower of Babel” of different databases may be created, limiting synergetic knowledge production. Based on interviews with data scientists, this Article identifies three main technological obstacles to data portability and interoperability: metadata uncertainties, data transfer obstacles, and missing data. It then explains how data standardization can remove at least some of these obstacles and lead to smoother data flows and better machine learning. The Article then identifies and analyzes additional effects of data standardization. As shown, data standardization has the potential to support a competitive and distributed data collection ecosystem and lead to easier policing in cases where rights are infringed or unjustified harms are created by data-fed algorithms. At the same time, increasing the scale and scope of data analysis can create negative externalities in the form of better profiling, increased harms to privacy, and cybersecurity harms. Standardization also has implications for investment and innovation, especially if lock-in to an inefficient standard occurs. The Article then explores whether market-led standardization initiatives can be relied upon to increase welfare, and the role governmental-facilitated data standardization should play, if at all

Tacrolimus-Induced Intestinal Angioedema: Diagnosis by Capsule Endoscopy

Small intestinal angioedema has been reported with angiotensin converting enzyme inhibitors therapy, but not in implanted patients treated with tacrolimus. We present a kidney transplanted patient, hospitalized with severe diarrhea, diagnosed with tacrolimus-induced intestinal angioedema with abdominal computerized tomography and capsule endoscopy. To the best of our knowledge this is the first described case of tacrolimus-induced small bowel angioedema diagnosed with capsule endoscopy

Early Ultraviolet Observations of Type IIn Supernovae Constrain the Asphericity of Their Circumstellar Material

© 2020. The American Astronomical Society. All rights reserved.. We present a survey of the early evolution of 12 Type IIn supernovae (SNe IIn) at ultraviolet and visible light wavelengths. We use this survey to constrain the geometry of the circumstellar material (CSM) surrounding SN IIn explosions, which may shed light on their progenitor diversity. In order to distinguish between aspherical and spherical CSM, we estimate the blackbody radius temporal evolution of the SNe IIn of our sample, following the method introduced by Soumagnac et al. We find that higher-luminosity objects tend to show evidence for aspherical CSM. Depending on whether this correlation is due to physical reasons or to some selection bias, we derive a lower limit between 35% and 66% for the fraction of SNe IIn showing evidence for aspherical CSM. This result suggests that asphericity of the CSM surrounding SNe IIn is common - consistent with data from resolved images of stars undergoing considerable mass loss. It should be taken into account for more realistic modeling of these events

Assessing the efficiency and significance of Methylated DNA Immunoprecipitation (MeDIP) assays in using in vitro methylated genomic DNA

<p>Abstract</p> <p>Background</p> <p>DNA methylation contributes to the regulation of gene expression during development and cellular differentiation. The recently developed Methylated DNA ImmunoPrecipitation (MeDIP) assay allows a comprehensive analysis of this epigenetic mark at the genomic level in normal and disease-derived cells. However, estimating the efficiency of the MeDIP technique is difficult without previous knowledge of the methylation status of a given cell population. Attempts to circumvent this problem have involved the use of <it>in vitro </it>methylated DNA in parallel to the investigated samples. Taking advantage of this stratagem, we sought to improve the sensitivity of the approach and to assess potential biases resulting from DNA amplification and hybridization procedures using MeDIP samples.</p> <p>Findings</p> <p>We performed MeDIP assays using <it>in vitro </it>methylated DNA, with or without previous DNA amplification, and hybridization to a human promoter array. We observed that CpG content at gene promoters indeed correlates strongly with the MeDIP signal obtained using <it>in vitro </it>methylated DNA, even when lowering significantly the amount of starting material. In analyzing MeDIP products that were subjected to whole genome amplification (WGA), we also revealed a strong bias against CpG-rich promoters during this amplification procedure, which may potentially affect the significance of the resulting data.</p> <p>Conclusion</p> <p>We illustrate the use of <it>in vitro </it>methylated DNA to assess the efficiency and accuracy of MeDIP procedures. We report that efficient and reproducible genome-wide data can be obtained via MeDIP experiments using relatively low amount of starting genomic DNA; and emphasize for the precaution that must be taken in data analysis when an additional DNA amplification step is required.</p

Alu Exonization Events Reveal Features Required for Precise Recognition of Exons by the Splicing Machinery

Despite decades of research, the question of how the mRNA splicing machinery precisely identifies short exonic islands within the vast intronic oceans remains to a large extent obscure. In this study, we analyzed Alu exonization events, aiming to understand the requirements for correct selection of exons. Comparison of exonizing Alus to their non-exonizing counterparts is informative because Alus in these two groups have retained high sequence similarity but are perceived differently by the splicing machinery. We identified and characterized numerous features used by the splicing machinery to discriminate between Alu exons and their non-exonizing counterparts. Of these, the most novel is secondary structure: Alu exons in general and their 5′ splice sites (5′ss) in particular are characterized by decreased stability of local secondary structures with respect to their non-exonizing counterparts. We detected numerous further differences between Alu exons and their non-exonizing counterparts, among others in terms of exon–intron architecture and strength of splicing signals, enhancers, and silencers. Support vector machine analysis revealed that these features allow a high level of discrimination (AUC = 0.91) between exonizing and non-exonizing Alus. Moreover, the computationally derived probabilities of exonization significantly correlated with the biological inclusion level of the Alu exons, and the model could also be extended to general datasets of constitutive and alternative exons. This indicates that the features detected and explored in this study provide the basis not only for precise exon selection but also for the fine-tuned regulation thereof, manifested in cases of alternative splicing

The Spectacular Ultraviolet Flash from the Peculiar Type Ia Supernova 2019yvq

Early observations of Type Ia supernovae (SNe Ia) provide essential clues for understanding the progenitor system that gave rise to the terminal thermonuclear explosion. We present exquisite observations of SN 2019yvq, the second observed SN Ia, after iPTF 14atg, to display an early flash of emission in the ultraviolet (UV) and optical. Our analysis finds that SN 2019yvq was unusual, even when ignoring the initial flash, in that it was moderately underluminous for an SN Ia (${M}_{g}\approx -18.5$ mag at peak) yet featured very high absorption velocities ($v\approx 15{\rm{,0}}00$ km s−1 for Si ii λ6355 at peak). We find that many of the observational features of SN 2019yvq, aside from the flash, can be explained if the explosive yield of radioactive 56Ni is relatively low (we measure ${M}_{{56}_{\mathrm{Ni}}}=0.31\pm 0.05\,{M}_{\odot }$) and it and other iron-group elements are concentrated in the innermost layers of the ejecta. To explain both the UV/optical flash and peak properties of SN 2019yvq we consider four different models: interaction between the SN ejecta and a nondegenerate companion, extended clumps of 56Ni in the outer ejecta, a double-detonation explosion, and the violent merger of two white dwarfs. Each of these models has shortcomings when compared to the observations; it is clear additional tuning is required to better match SN 2019yvq. In closing, we predict that the nebular spectra of SN 2019yvq will feature either H or He emission, if the ejecta collided with a companion, strong [Ca ii] emission, if it was a double detonation, or narrow [O i] emission, if it was due to a violent merger

Interrelationship between Dendritic Cell Trafficking and Francisella tularensis Dissemination following Airway Infection

Francisella tularensis, the etiological agent of the inhalation tularemia, multiplies in a variety of cultured mammalian cells. Nevertheless, evidence for its in vivo intracellular residence is less conclusive. Dendritic cells (DC) that are adapted for engulfing bacteria and migration towards lymphatic organs could serve as potential targets for bacterial residence and trafficking. Here, we focus on the in vivo interactions of F. tularensis with DC following airway infection of mice. Lethal airway infection of mice with the live vaccine strain (LVS) results in trafficking of a CD11bhigh/CD11cmed/autofluorescencelow DC subset from the respiratory tract to the draining mediastinal lymph node (MdLN). Simultaneously, a rapid, massive bacterial colonization of the MdLN occurs, characterized by large bacterial foci formation. Analysis of bacteria in the MdLN revealed a major population of extracellular bacteria, which co-exists with a substantial fraction of intracellular bacteria. The intracellular bacteria are viable and reside in cells sorted for DC marker expression. Moreover, in vivo vital staining experiments indicate that most of these intracellular bacteria (∼75%) reside in cells that have migrated from the airways to the MdLN after infection. The correlation between DC and bacteria accumulation in the MdLN was further demonstrated by manipulating DC migration to the MdLN through two independent pathways. Impairment of DC migration to the MdLN, either by a sphingosine-1-phosphate receptor agonist (FTY720) or by the D prostanoid receptor 1 agonist (BW245C), resulted in reduced bacterial colonization of MdLN. Moreover, BW245C treatment delayed the onset of morbidity and the time to death of the infected mice. Taken together, these results suggest that DC can serve as an inhabitation niche for F. tularensis in the early stages of infection, and that DC trafficking plays a role in pathogen dissemination. This underscores the therapeutic potential of DC migration impairing drugs in tularemia treatment

Evidence for Late-stage Eruptive Mass Loss in the Progenitor to SN2018gep, a Broad-lined Ic Supernova: Pre-explosion Emission and a Rapidly Rising Luminous Transient

We present detailed observations of ZTF18abukavn (SN2018gep), discovered in high-cadence data from the Zwicky Transient Facility as a rapidly rising (1.4 ± 0.1 mag hr-1) and luminous (Mg,peak = -20 mag) transient. It is spectroscopically classified as a broad-lined stripped-envelope supernova (Ic-BL SN). The high peak luminosity (Lbol ≳ 3 × 1044 erg s-1), the short rise time (trise = 3 days in g band), and the blue colors at peak (g-r ∼ -0.4) all resemble the high-redshift Ic-BL iPTF16asu, as well as several other unclassified fast transients. The early discovery of SN2018gep (within an hour of shock breakout) enabled an intensive spectroscopic campaign, including the highest-temperature (Teff ≳ 40,000 K) spectra of a stripped-envelope SN. A retrospective search revealed luminous (Mg ∼ Mr ≈ mag) emission in the days to weeks before explosion, the first definitive detection of precursor emission for a Ic-BL. We find a limit on the isotropic gamma-ray energy release E γ,iso 10 days) light curve requires an additional energy source, which could be the radioactive decay of Ni-56

RsaI repetitive DNA in Buffalo Bubalus bubalis representing retrotransposons, conserved in bovids, are part of the functional genes

<p>Abstract</p> <p>Background</p> <p>Repetitive sequences are the major components of the eukaryotic genomes. Association of these repeats with transcribing sequences and their regulation in buffalo <it>Bubalus bubalis </it>has remained largely unresolved.</p> <p>Results</p> <p>We cloned and sequenced <it>RsaI </it>repeat fragments pDp1, pDp2, pDp3, pDp4 of 1331, 651, 603 and 339 base pairs, respectively from the buffalo, <it>Bubalus bubalis</it>. Upon characterization, these fragments were found to represent retrotransposons and part of some functional genes. The resultant clones showed cross hybridization only with buffalo, cattle, goat and sheep genomic DNA. Real Time PCR, detected ~2 × 10⁴copies of pDp1, ~ 3000 copies of pDp2 and pDp3 and ~ 1000 of pDp4 in buffalo, cattle, goat and sheep genomes, respectively. <it>RsaI </it>repeats are transcriptionally active in somatic tissues and spermatozoa. Accordingly, pDp1 showed maximum expression in lung, pDp2 and pDp3 both in Kidney, and pDp4 in ovary. Fluorescence <it>in situ </it>hybridization showed repeats to be distributed all across the chromosomes.</p> <p>Conclusions</p> <p>The data suggest that <it>RsaI </it>repeats have been incorporated into the exonic regions of various transcribing genes, possibly contributing towards the architecture and evolution of the buffalo and related genomes. Prospects of our present work in the context of comparative and functional genomics are highlighted.</p