Generic Subsequence Matching Framework: Modularity, Flexibility, Efficiency

Subsequence matching has appeared to be an ideal approach for solving many problems related to the fields of data mining and similarity retrieval. It has been shown that almost any data class (audio, image, biometrics, signals) is or can be represented by some kind of time series or string of symbols, which can be seen as an input for various subsequence matching approaches. The variety of data types, specific tasks and their partial or full solutions is so wide that the choice, implementation and parametrization of a suitable solution for a given task might be complicated and time-consuming; a possibly fruitful combination of fragments from different research areas may not be obvious nor easy to realize. The leading authors of this field also mention the implementation bias that makes difficult a proper comparison of competing approaches. Therefore we present a new generic Subsequence Matching Framework (SMF) that tries to overcome the aforementioned problems by a uniform frame that simplifies and speeds up the design, development and evaluation of subsequence matching related systems. We identify several relatively separate subtasks solved differently over the literature and SMF enables to combine them in straightforward manner achieving new quality and efficiency. This framework can be used in many application domains and its components can be reused effectively. Its strictly modular architecture and openness enables also involvement of efficient solutions from different fields, for instance efficient metric-based indexes. This is an extended version of a paper published on DEXA 2012.Comment: This is an extended version of a paper published on DEXA 201

A sub-cm micromachined electron microscope

A new approach for fabricating macroscopic (approximately 10x10x10 mm(exp 3)) structures with micron accuracy has been developed. This approach combines the precision of semiconductor processing and fiber optic technologies. A (100) silicon wafer is anisotropically etched to create four orthogonal v-grooves and an aperture on each 10x12 mm die. Precision 308 micron optical fibers are sandwiched between the die to align the v-grooves. The fiber is then anodically bonded to the die above and below it. This procedure is repeated to create thick structures and a stack of 5 or 6 die will be used to create a miniature scanning electron microscope (MSEM). Two die in the structure will have a segmented electrode to deflect the beam and correct for astigmatism. The entire structure is UHV compatible. The performance of an SEM improves as its length is reduced and a sub-cm 2 keV MSEM with a field emission source should have approximately 1 nm resolution. A low voltage high resolution MSEM would be useful for the examination of biological specimens and semiconductors with a minimum of damage. The first MSEM will be tested with existing 6 micron thermionic sources. In the future a micromachined field emission source will be used. The stacking technology presented in this paper can produce an array of MSEMs 1 to 30 mm in length with a 1 mm or larger period. A key question being addressed by this research is the optimum size for a low voltage MSEM which will be determined by the required spatial resolution, field of view, and working distance

Anatomy of the Soft-Photon Approximation in Hadron-Hadron Bremsstrahlung

A modified Low procedure for constructing soft-photon amplitudes has been used to derive two general soft-photon amplitudes, a two-s-two-t special amplitude $M^{TsTts}_{\mu}$ and a two-u-two-t special amplitude $M^{TuTts}_{\mu}$, where s, t and u are the Mandelstam variables. $M^{TsTts}_{\mu}$ depends only on the elastic T-matrix evaluated at four sets of (s,t) fixed by the requirement that the amplitude be free of derivatives ($\partial$T/$\partial$s and /or $\partial$T/$\partial t$). Likewise $M^{TuTts}_{\mu}$ depends only on the elastic T-matrix evaluated at four sets of (u,t). In deriving these amplitudes, we impose the condition that $M^{TsTts}_{\mu}$ and $M^{TuTts}_{\mu}$ reduce to $\bar{M}^{TsTts}_{\mu}$ and $\bar{M}^{TuTts}_{\mu}$, respectively, their tree level approximations. The amplitude $\bar{M}^{TsTts}_{\mu}$ represents photon emission from a sum of one-particle t-channel exchange diagrams and one-particle s-channel exchange diagrams, while the amplitude $\bar{M}^{TuTts} _{\mu}$ represents photon emission from a sum of one-particle t-channel exchange diagrams and one-particle u-channel exchange diagrams. The precise expressions for $\bar{M}^{TsTts}_{\mu}$ and $\bar{M}^{TuTts}_{\mu}$ are determined by using the radiation decomposition identities of Brodsky and Brown. We point out that it is theoretically impossible to describe all bremsstrahlung processes by using only a single class of soft-photon amplitudes. At least two different classes are required: the amplitudes which depend on s and t or the amplitudes which depend on u and t. When resonance effects are important, the amplitude $M^{TsTts}_{\mu}$, not $M^{Low(st)}_{\mu}$, should be used. For processes with strong u-channel exchange effects, the amplitude $M^{TuTts}_{\mu}$ should be the first choice.Comment: 49 pages report # LA-UR-92-270

6-Thioguanine blocks SARS-CoV-2 replication by inhibition of PLpro

The emergence of SARS-CoV-2 has led to a global health crisis that, in addition to vaccines and immunomodulatory therapies, calls for the identification of antiviral therapeutics. The papain-like protease (PLpro) activity of nsp3 is an attractive drug target as it is essential for viral polyprotein cleavage and for deconjugation of ISG15, an antiviral ubiquitin-like protein. We show here that 6-Thioguanine (6-TG), an orally available and widely available generic drug, inhibits SARS-CoV-2 replication in Vero-E6 cells with an EC50 of approximately 2 μM. 6-TG also inhibited PLpro-catalyzed polyprotein cleavage and de-ISGylation in cells and inhibited proteolytic activity of the purified PLpro domai

Plasma metabolite profiles in children with current asthma

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146270/1/cea13183.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146270/2/cea13183_am.pd

Subordinates' competency : a potential trigger for workplace ostracism

While the competence of subordinates is considered desirable in the workplace, it may create challenges in managing people in organizations. This study examines why subordinates’ competence triggers ostracism within the workplace based on social comparison theory and previous insecurity studies. Data from both managers (N=130) and their subordinates (N=231) provided findings which affirm that, first, some managers regard competent subordinates as potential challengers and thus develop a feeling of insecurity, which creates motivation for the ostracism of those competent subordinates. Second, those subordinates who feel ostracized by managers, may show less commitment towards their managers, feel less confident and engage in negative gossip about their managers. The implications of competence triggered ostracism for management include that competent subordinates require active management and development to avoid potentially damaging relationships between managers and subordinates emerging which would be detrimental to the organization

Particles at oil–air surfaces : powdered oil, liquid oil marbles, and oil foam

The type of material stabilized by four kinds of fluorinated particles (sericite and bentonite platelet clays and spherical zinc oxide) in air–oil mixtures has been investigated. It depends on the particle wettability and the degree of shear. Upon vigorous agitation, oil dispersions are formed in all the oils containing relatively large bentonite particles and in oils of relatively low surface tension (γla < 26 mN m⁻¹) like dodecane, 20 cS silicone, and cyclomethicone containing the other fluorinated particles. Particle-stabilized oil foams were obtained in oils having γla > 26 mN m⁻¹ where the advancing air–oil–solid contact angle θ lies between ca. 90° and 120°. Gentle shaking, however, gives oil-in-air liquid marbles with all the oil–particle systems except for cases where θ is <60°. For oils of tension >24 mN m⁻¹ with omniphobic zinc oxide and sericite particles for which advancing θ ≥ 90°, dry oil powders consisting of oil drops in air which do not leak oil could be made upon gentle agitation up to a critical oil:particle ratio (COPR). Above the COPR, catastrophic phase inversion of the dry oil powders to air-in-oil foams was observed. When sheared on a substrate, the dry oil powders containing at least 60 wt % of oil release the encapsulated oil, making these materials attractive formulations in the cosmetic and food industries

Maternal Diet Quality During Pregnancy and Offspring Hepatic Fat in Early Childhood: The Healthy Start Study

Background: Overnutrition in utero may increase offspring risk of nonalcoholic fatty liver disease (NAFLD), but the specific contribution of maternal diet quality during pregnancy to this association remains understudied in humans. Objectives: This study aimed to examine the associations of maternal diet quality during pregnancy with offspring hepatic fat in early childhood (median: 5 y old, range: 4–8 y old). Methods: Data were from 278 mother–child pairs in the longitudinal, Colorado-based Healthy Start Study. Multiple 24-h recalls were collected from mothers during pregnancy on a monthly basis (median: 3 recalls, range: 1–8 recalls starting after enrollment), and used to estimate maternal usual nutrient intakes and dietary pattern scores [Healthy Eating Index-2010 (HEI-2010), Dietary Inflammatory Index (DII), and Relative Mediterranean Diet Score (rMED)]. Offspring hepatic fat was measured in early childhood by MRI. Associations of maternal dietary predictors during pregnancy with offspring log-transformed hepatic fat were assessed using linear regression models adjusted for offspring demographics, maternal/perinatal confounders, and maternal total energy intake. Results: Higher maternal fiber intake and rMED scores during pregnancy were associated with lower offspring hepatic fat in early childhood in fully adjusted models [Back-transformed β (95% CI): 0.82 (0.72, 0.94) per 5 g/1000 kcal fiber; 0.93 (0.88, 0.99) per 1 SD for rMED]. In contrast, higher maternal total sugar and added sugar intakes, and DII scores were associated with higher offspring hepatic fat [Back-transformed β (95% CI): 1.18 (1.05, 1.32) per 5% kcal/d added sugar; 1.08 (0.99, 1.18) per 1 SD for DII]. Analyses of dietary pattern subcomponents also revealed that lower maternal intakes of green vegetables and legumes and higher intake of “empty calories” were associated with higher offspring hepatic fat in early childhood. Conclusions: Poorer maternal diet quality during pregnancy was associated with greater offspring susceptibility to hepatic fat in early childhood. Our findings provide insights into potential perinatal targets for the primordial prevention of pediatric NAFLD

Computational Characterization of 3′ Splice Variants in the GFAP Isoform Family

Glial fibrillary acidic protein (GFAP) is an intermediate filament (IF) protein specific to central nervous system (CNS) astrocytes. It has been the subject of intense interest due to its association with neurodegenerative diseases, and because of growing evidence that IF proteins not only modulate cellular structure, but also cellular function. Moreover, GFAP has a family of splicing isoforms apparently more complex than that of other CNS IF proteins, consistent with it possessing a range of functional and structural roles. The gene consists of 9 exons, and to date all isoforms associated with 3′ end splicing have been identified from modifications within intron 7, resulting in the generation of exon 7a (GFAPδ/ε) and 7b (GFAPκ). To better understand the nature and functional significance of variation in this region, we used a Bayesian multiple change-point approach to identify conserved regions. This is the first successful application of this method to a single gene – it has previously only been used in whole-genome analyses. We identified several highly or moderately conserved regions throughout the intron 7/7a/7b regions, including untranslated regions and regulatory features, consistent with the biology of GFAP. Several putative unconfirmed features were also identified, including a possible new isoform. We then integrated multiple computational analyses on both the DNA and protein sequences from the mouse, rat and human, showing that the major isoform, GFAPα, has highly conserved structure and features across the three species, whereas the minor isoforms GFAPδ/ε and GFAPκ have low conservation of structure and features at the distal 3′ end, both relative to each other and relative to GFAPα. The overall picture suggests distinct and tightly regulated functions for the 3′ end isoforms, consistent with complex astrocyte biology. The results illustrate a computational approach for characterising splicing isoform families, using both DNA and protein sequences