En jämförelse av molnbaserade realtidsanalystjänster : Skillnader i användbarhet mellan multi-tenant och single-tenant arkitekturer

Internet of Things är ett samlingsbegrepp för den utveckling som innebär att olika typer av enheter kan förses med sensorer och datachip som är uppkopplade mot internet. En ökad mängd data innebär en ökad förfrågan på lösningar som kan lagra, spåra, analysera och bearbeta data. Ett sätt att möta denna förfrågan är att använda sig av molnbaserade realtidsanalystjänster. Multi-tenant och single-tenant är två typer av arkitekturer för molnbaserade realtidsanalystjänster som kan användas för att lösa problemen med hanteringen av de ökade datamängderna. Dessa arkitekturer skiljer sig åt när det gäller komplexitet i utvecklingen. I detta arbete representerar Azure Stream Analytics en multi-tenant arkitektur och HDInsight/Storm representerar en single-tenant arkitektur. För att kunna göra en jämförelse av molnbaserade realtidsanalystjänster med olika arkitekturer, har vi valt att använda oss av användbarhetskriterierna: effektivitet, ändamålsenlighet och användarnöjdhet. Vi kom fram till att vi ville ha svar på följande frågor relaterade till ovannämnda tre användbarhetskriterier: • Vilka likheter och skillnader kan vi se i utvecklingstider? • Kan vi identifiera skillnader i funktionalitet? • Hur upplever utvecklare de olika analystjänsterna? Vi har använt en design and creation strategi för att utveckla två Proof of Concept prototyper och samlat in data genom att använda flera datainsamlingsmetoder. Proof of Concept prototyperna inkluderade två artefakter, en för Azure Stream Analytics och en för HDInsight/Storm. Vi utvärderade dessa genom att utföra fem olika scenarier som var för sig hade 2-5 delmål. Vi simulerade strömmande data genom att låta en applikation kontinuerligt slumpa fram data som vi analyserade med hjälp av de två realtidsanalystjänsterna. Vi har använt oss av observationer för att dokumentera hur vi arbetade med utvecklingen av analystjänsterna samt för att mäta utvecklingstider och identifiera skillnader i funktionalitet. Vi har även använt oss av frågeformulär för att ta reda på vad användare tyckte om analystjänsterna. Vi kom fram till att Azure Stream Analytics initialt var mer användbart än HDInsight/Storm men att skillnaderna minskade efter hand. Azure Stream Analytics var lättare att arbeta med vid simplare analyser medan HDInsight/Storm hade ett bredare val av funktionalitet.

Human bocavirus infection diagnosed serologically among children admitted to hospital with community-acquired pneumonia in a tropical region

Human bocavirus (HBoV) is a human virus associated with respiratory disease in children. Limited information is available on acute infection with HBoV among children admitted to hospital with community-acquired pneumonia in tropical regions and the current diagnosis is inadequate. The aims were to diagnose and describe acute HBoV infections among children hospitalized for community-acquired pneumonia. In Salvador, Brazil, 277 children with community-acquired pneumonia were prospectively enrolled. Paired serum samples were tested by IgG, IgM, and IgG-avidity enzyme immunoassays (EIAs) using recombinant HBoV VP2. HBoV DNA was detected in nasopharyngeal aspirates and serum by a quantitative polymerase-chain reaction (PCR). HBoV DNA was detected in nasopharyngeal aspirates of 62/268 (23%) children and 156/273 (57%) were seropositive. Acute primary HBoV infection was reliably diagnosed (bearing at least two acute markers: Positive IgM, a fourfold increase/conversion of IgG, low IgG avidity or viremia) in 21 (8%) of 273 patients, 90% of 20 had HBoV DNA in nasopharyngeal aspirates, 83% with a high DNA load. The median age of infection with HBoV was 16 months, range 5-36.Community-acquired pneumonia was confirmed radiographically in 85% of 20 patients with acute HBoV infection diagnosed serologically. HBoV DNA was found in nasopharyngeal aspirates of 42/246(17%) children without an acute primary HBoV infection and available nasopharyngeal aspirate. Four children with HBoV secondary immune responses were detected, lacking both IgM and viremia. HBoV infection was diagnosed accurately in children aged 5-36 months with community-acquired pneumonia confirmed radiographically. PCR of nasopharyngeal aspirates is not a reliable marker of acute HBoV infection. J. Med. Virol. 84:253-258, 2012. (C) 2011 Wiley Periodicals, Inc.

Symptomatic plate removal after treatment of facial fractures

AIMS: To identify the rates and reasons for plate removal (PR) among patients treated for facial fractures. MATERIALS AND METHODS: A retrospective review of files of 238 patients. RESULTS: Forty-eight patients (20.2%) had plates removed. The reason for removal was objective in 33.3% and subjective in 29.2%. The most common subjective reason was cold sensitivity, and the most common objective reason was wound dehiscence/infection. Women had PR for subjective reasons more often than men (p=0.018). Removal was performed more often for subjective reasons after zygomatico-orbital fractures than after mandibular fractures (p=0.002). Plates inserted in the mandible from an intraoral approach were removed more frequently than extraorally inserted mandibular plates, intraorally inserted maxillary plates, and extraorally inserted plates in other locations (p<0.001). Orbital rim plates had a higher risk of being removed than maxillary or frontal bone plates (p=0.02). CONCLUSIONS: Subjective discomfort is a notable reason for PR among Finnish patients, suggesting that the cold climate has an influence on the need for removal. Patients receiving mandibular osteosynthesis with miniplates from an intraoral approach are at risk of hardware removal because of wound dehiscence/infection and loose/broken hardware, reminding us that more rigid fixation devices should not be forgotten despite the widespread use of miniplates.

Risk factors contributing to symptomatic miniplate removal: a retrospective study of 153 bilateral sagittal split osteotomy patients

Removal of miniplates is a controversial topic in oral and maxillofacial surgery. Originally, miniplates were designed to be removed on completion of bone healing. The introduction of low profile titanium miniplates has led to the routine removal of miniplates becoming comparatively rare in many parts of the world. Few studies have investigated the reasons for non-routine removal of miniplates and the factors that affect osteosynthesis after osteotomy in large numbers of patients. The aim of the present study was to investigate complications related to osteosynthesis after bilateral sagittal split osteotomy (BSSO) in a large number (n=153) of patients. In addition to the rates of removal, emphasis was placed on investigating the reasons and risk factors associated with symptomatic miniplate removal. The rate of plate removal per patient was 18.6%, the corresponding rate per plate being 18.2%. Reasons for plate removal included plate-related complications in 16 patients and subjective discomfort in 13 patients. Half of the plates were removed during the first postoperative year. Smoking was the only significant predictor for plate removal. Patients undergoing orthognathic surgery should be screened with regard to smoking and encouraged and assisted to cease smoking, at least perioperatively.

Occurrence and types of associated injuries in patients with fractures of the facial bones

PURPOSE: To identify the occurrence, types, and severity of associated injuries outside the facial region among patients diagnosed with facial fractures, and to analyze whether there are any factors related to associated injuries. MATERIALS AND METHODS: This was a cross-sectional study of 401 patients diagnosed with facial fractures during the 2-year period from 2003 to 2004. RESULTS: Associated injuries were observed in 101 patients (25.2%). The most common type of injury was a limb injury (13.5%), followed by brain (11.0%), chest (5.5%), spine (2.7%), and abdominal (0.8%) injuries. Multiple associated injuries were observed in 10% and polytrauma in 7.5%. The mortality rate was 0.2%. The occurrence of associated injury correlated significantly with trauma mechanism and fracture type; high-speed accidents and severe facial fractures were significant predictors of associated injury. CONCLUSIONS: Associated injuries are frequent among patients who have sustained facial fractures. The results underscore the importance of multiprofessional collaboration in diagnosis and sequencing of treatment, but also the importance of arranging appropriate clinical rotations for maxillofacial residents in training.

Mitochondrial dysfunction and Purkinje cell loss in autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS)

Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is a childhood-onset neurological disease resulting from mutations in the SACS gene encoding sacsin, a 4,579-aa protein of unknown function. Originally identified as a founder disease in Québec, ARSACS is now recognized worldwide. Prominent features include pyramidal spasticity and cerebellar ataxia, but the underlying pathology and pathophysiological mechanisms are unknown. We have generated an animal model for ARSACS, sacsin knockout mice, that display age-dependent neurodegeneration of cerebellar Purkinje cells. To explore the pathophysiological basis for this observation, we examined the cell biological properties of sacsin. We show that sacsin localizes to mitochondria in non-neuronal cells and primary neurons and that it interacts with dynamin-related protein 1, which participates in mitochondrial fission. Fibroblasts from ARSACS patients show a hyperfused mitochondrial network, consistent with defects in mitochondrial fission. Sacsin knockdown leads to an overly interconnected and functionally impaired mitochondrial network, and mitochondria accumulate in the soma and proximal dendrites of sacsin knockdown neurons. Disruption of mitochondrial transport into dendrites has been shown to lead to abnormal dendritic morphology, and we observe striking alterations in the organization of dendritic fields in the cerebellum of knockout mice that precedes Purkinje cell death. Our data identifies mitochondrial dysfunction/mislocalization as the likely cellular basis for ARSACS and indicates a role for sacsin in regulation of mitochondrial dynamics.

Identification of a highly conserved valine-glycine-phenylalanine amino acid triplet required for HIV-1 Nef function

Background The Nef protein of HIV facilitates virus replication and disease progression in infected patients. This role as pathogenesis factor depends on several genetically separable Nef functions that are mediated by interactions of highly conserved protein-protein interaction motifs with different host cell proteins. By studying the functionality of a series of nef alleles from clinical isolates, we identified a dysfunctional HIV group O Nef in which a highly conserved valine-glycine-phenylalanine (VGF) region, which links a preceding acidic cluster with the following proline-rich motif into an amphipathic surface was deleted. In this study, we aimed to study the functional importance of this VGF region. Results The dysfunctional HIV group O8 nef allele was restored to the consensus sequence, and mutants of canonical (NL4.3, NA-7, SF2) and non-canonical (B2 and C1422) HIV-1 group M nef alleles were generated in which the amino acids of the VGF region were changed into alanines (VGF→AAA) and tested for their capacity to interfere with surface receptor trafficking, signal transduction and enhancement of viral replication and infectivity. We found the VGF motif, and each individual amino acid of this motif, to be critical for downregulation of MHC-I and CXCR4. Moreover, Nef’s association with the cellular p21-activated kinase 2 (PAK2), the resulting deregulation of cofilin and inhibition of host cell actin remodeling, and targeting of Lck kinase to the trans-golgi-network (TGN) were affected as well. Of particular interest, VGF integrity was essential for Nef-mediated enhancement of HIV virion infectivity and HIV replication in peripheral blood lymphocytes. For targeting of Lck kinase to the TGN and viral infectivity, especially the phenylalanine of the triplet was essential. At the molecular level, the VGF motif was required for the physical interaction of the adjacent proline-rich motif with Hck. Conclusion Based on these findings, we propose that this highly conserved three amino acid VGF motif together with the acidic cluster and the proline-rich motif form a previously unrecognized amphipathic surface on Nef. This surface appears to be essential for the majority of Nef functions and thus represents a prime target for the pharmacological inhibition of Nef.

Poly(A)-binding protein-interacting protein 1 binds to eukaryotic translation initiation factor 3 to stimulate translation.

Poly(A)-binding protein (PABP) stimulates translation initiation by binding simultaneously to the mRNA poly(A) tail and eukaryotic translation initiation factor 4G (eIF4G). PABP activity is regulated by PABP-interacting (Paip) proteins. Paip1 binds PABP and stimulates translation by an unknown mechanism. Here, we describe the interaction between Paip1 and eIF3, which is direct, RNA independent, and mediated via the eIF3g (p44) subunit. Stimulation of translation by Paip1 in vivo was decreased upon deletion of the N-terminal sequence containing the eIF3-binding domain and upon silencing of PABP or several eIF3 subunits. We also show the formation of ternary complexes composed of Paip1-PABP-eIF4G and Paip1-eIF3-eIF4G. Taken together, these data demonstrate that the eIF3-Paip1 interaction promotes translation. We propose that eIF3-Paip1 stabilizes the interaction between PABP and eIF4G, which brings about the circularization of the mRNA.

A method to incorporate the effect of taxonomic uncertainty on multivariate analyses of ecological data

Researchers in ecology commonly use multivariate analyses (e.g. redundancy analysis, canonical correspondence analysis, Mantel correlation, multivariate analysis of variance) to interpret patterns in biological data and relate these patterns to environmental predictors. There has been, however, little recognition of the errors associated with biological data and the influence that these may have on predictions derived from ecological hypotheses. We present a permutational method that assesses the effects of taxonomic uncertainty on the multivariate analyses typically used in the analysis of ecological data. The procedure is based on iterative randomizations that randomly re-assign non identified species in each site to any of the other species found in the remaining sites. After each re-assignment of species identities, the multivariate method at stake is run and a parameter of interest is calculated. Consequently, one can estimate a range of plausible values for the parameter of interest under different scenarios of re-assigned species identities. We demonstrate the use of our approach in the calculation of two parameters with an example involving tropical tree species from western Amazonia: 1) the Mantel correlation between compositional similarity and environmental distances between pairs of sites, and; 2) the variance explained by environmental predictors in redundancy analysis (RDA). We also investigated the effects of increasing taxonomic uncertainty (i.e. number of unidentified species), and the taxonomic resolution at which morphospecies are determined (genus-resolution, family-resolution, or fully undetermined species) on the uncertainty range of these parameters. To achieve this, we performed simulations on a tree dataset from southern Mexico by randomly selecting a portion of the species contained in the dataset and classifying them as unidentified at each level of decreasing taxonomic resolution. An analysis of covariance showed that both taxonomic uncertainty and resolution significantly influence the uncertainty range of the resulting parameters. Increasing taxonomic uncertainty expands our uncertainty of the parameters estimated both in the Mantel test and RDA. The effects of increasing taxonomic resolution, however, are not as evident. The method presented in this study improves the traditional approaches to study compositional change in ecological communities by accounting for some of the uncertainty inherent to biological data. We hope that this approach can be routinely used to estimate any parameter of interest obtained from compositional data tables when faced with taxonomic uncertainty.

Structure and function of the C-terminal PABC domain of human poly(A)-binding protein

We have determined the solution structure of the C-terminal quarter of human poly(A)-binding protein (hPABP). The protein fragment contains a protein domain, PABC [for poly(A)-binding protein C-terminal domain], which is also found associated with the HECT family of ubiquitin ligases. By using peptides derived from PABP interacting protein (Paip) 1, Paip2, and eRF3, we show that PABC functions as a peptide binding domain. We use chemical shift perturbation analysis to identify the peptide binding site in PABC and the major elements involved in peptide recognition. From comparative sequence analysis of PABC-binding peptides, we formulate a preliminary PABC consensus sequence and identify human ataxin-2, the protein responsible for type 2 spinocerebellar ataxia (SCA2), as a potential PABC ligand.

Formic acid mixing ratio (CIMS) and 3D wind data, plus SOSAA model runs -- Hyytiälä, Finland, Apr-Jun 2014

These are data of eddy covariance flux measurements of formic acid (HCOOH), performed by a chemical ionization mass spectrometer (CIMS) over a boreal forest canopy in Hyytiälä, Finland, in spring/summer 2014. Results from the 1-D chemical transport model runs using SOSAA (Simulate Organic vapours, Sulphuric Acid and Aerosols) are included as well. The data accompany a submission of a manuscript to Geophysical Research Letters for consideration for publication (Schobesberger et al.).

The role of the 8-18 helix of CGRP 8-37 in mediating high affinity binding to CGRP receptors; coulombic and steric interactions

1. The role of individual residues in the 8-18 helix of CGRP 8-37 in promoting high-affinity binding to CGRP 1 receptors expressed on rat L6 and human SK-N-MC cells has been examined. The relative potencies of various derivatives were estimated from their ability to inhibit the human αCGRP-mediated increase in cyclic AMP production and the binding of [ 125I]-human αCGRP. 3. Arg 11 and Arg 18 were replaced by serines to give [Ser 11.18]CGRP 8-37. These bound with pKi values <6 to SK-N-MC cells and had apparent pA 2 values of 5.81 ± 0.04 and 5.31 ± 0.11 on SK-N-MC and L6 cells. CGRP 8-37 had a pKi of 8.22 on SK-N-MC cells and pK b values on the above cell lines of 8.95±0.04 and 8.76±0.04. 3. The arginines were replaced with glutamic acid residues. [Glu 11]CGRP 8-37 had a pK b of 7.14±0.14 on SK-N-MC cells (pKi=7.05±0.05) and 6.99±0.08 on L6 cells. [Glu 18]CGRP 8-37 had a pK b of 7.10±0.0.08 on SK-N-MC cells (pKi=6.91±0.23) and 7.12±0.09 on L6 cells. 4. Leu 12, Leu 15 and Leu 16 were replaced by benzoyl-phenylalanine (bpa) residues. On SK-N-MC cells, the apparent pA 2 values of [bpa 12]-, [bpa 15]- and [bpa 16]CGRP 8-37 were respectively 7.43±0.23, 8.34±0.11 and 5.66±0.16 (pKi values of 7.14±0.17, 7.66±0.21 and <6): on L6 cells they were 7.96±0.36, 8.28±0.21 and 6.09±0.04 (all n=3). 5. It is concluded that the Arg 11 and Arg 18 are involved in specific electrostatic interactions with other residues, either on the CGRP 1 receptors or elsewhere on CGRP 8-37. Leu 16 is in a conformationally restricted site when CGRP 8-37 binds to CGRP 1 receptors, unlike Leu 12 and Leu 15.

Recurrent CDKN1B (p27) mutations in hairy cell leukemia

Hairy cell leukemia (HCL) is marked by near 100% mutational frequency of BRAFV600E mutations. Recurrent cooperating genetic events that may contribute to HCL pathogenesis or affect the clinical course of HCL are currently not described. Therefore, we performed whole exome sequencing to explore the mutational landscape of purine analog refractory HCL. In addition to the disease-defining BRAFV600E mutations, we identified mutations in EZH2, ARID1A, and recurrent inactivating mutations of the cell cycle inhibitor CDKN1B (p27). Targeted deep sequencing of CDKN1B in a larger cohort of HCL patients identify deleterious CDKN1B mutations in 16% of patients with HCL (n = 13 of 81). In 11 of 13 patients the CDKN1B mutation was clonal, implying an early role of CDKN1B mutations in the pathogenesis of HCL. CDKN1B mutations were not found to impact clinical characteristics or outcome in this cohort. These data identify HCL as having the highest frequency of CDKN1B mutations among cancers and identify CDNK1B as the second most common mutated gene in HCL. Moreover, given the known function of CDNK1B, these data suggest a novel role for alterations in regulation of cell cycle and senescence in HCL with CDKN1B mutations.

Optisen radiolinkin toteuttaminen ohjelmistoradiolla

Tämän tutkielman tavoitteena oli toteuttaa optinen radiolinkki hyödyntäen ohjelmistoradiota. Työn alkuosassa käydään läpi ohjelmistoradiota yleisellä tasolla sekä yleisesti nykyisin käytössä olevia optisia tiedonsiirtotapoja. Työn keskiosassa käsitellään työhön käytettävä laitteisto ja ohjelmistot sekä optisen radioetuasteen suunnittelu ja toteutus. Työn loppuosassa analysoidaan toteutetun etuasteen toimintaa. Ohjelmistoradio, yleisemmin ohjelmallisesti määritetty radiolaite, jonka toiminnallisuutta, kuten modulaatioita, suodattimia ja kommunikointiin käytettävää taajuuskaistaa, pystytään muuttamaan ohjelmallisesti ilman laitteistomuutoksia. Useimmiten ohjelmistoradioiden toiminnallisuus määrätään ohjelmoimalla ohjelmistoradio-oheislaitteen ohjelmoitavia porttipiirejä, eli FPGA-piirejä. Optisen radioetuasteen suunnittelun pohjana käytettiin audiokäyttöön tarkoitettua infrapunalähetintä ja – vastaanotinta, jotka muokattiin toimimaan näkyvän valon aallonpituuksilla. Ohjelmistoradio-oheislaitteena toimi Ettus USRP1 varustettuna matalataajuisilla lähetin- ja vastaanotintytärkorteilla. Ohjelmistoradion ohjelmointiympäristönä toimi Linux Ubuntu, ja ohjelmistona GNURadio sekä sen graafinen ohjelmointikäyttöliittymä Gnu Radio Companion. Tutkielman lopputuloksena saatiin aikaan piirilevylle rakennettu optisen radioetuasteen prototyyppi, jolla pystyttiin siirtämään digitaalista audiota 300 kbps tiedonsiirtonopeudella muutamien senttimetrien matkalla pimeässä tilassa.