Taking an Object-Centric View on Dynamic Information with Object Flow Analysis

A large body of research analyzes the runtime execution of a system to extract abstract behavioral views. Those approaches primarily analyze control flow by tracing method execution events or they analyze object graphs of heap snapshots. However, they do not capture how objects are passed through the system at runtime. We refer to the exchange of objects as the object flow, and we claim that object flow is necessary to analyze if we are to understand the runtime of an object-oriented application. We propose and detail Object Flow Analysis, a novel dynamic analysis technique that takes this new information into account. To evaluate its usefulness, we present a visual approach that allows a developer to study classes and components in terms of how they exchange objects at runtime. We illustrate our approach on three case studies.

Einsatz von RFID in der Pharmazeutischen Industrie

Die Radio Frequenz Identifikation (RFID) gilt als wichtigste technologische Neuerung in der Informationslogistik. Wird RFID in der produzierenden Industrie hauptsächlich zur Betriebsdaten-erfassung und im Handel zur Wareneingangs-/ Warenausgangskontrolle verwendet, so können ins-besondere in der Pharmazeutischen Industrie die Vorteile der Technologie voll ausgereizt werden. Die wohl wichtigste Anwendung ist die lückenlose Rückverfolgung entlang der Lieferkette, wie sie in den USA bereits in einigen Staaten für alle pharmazeutischen Produkte vorgeschrieben und auch in Deutschland für bestimmte Produkte erforderlich ist. Zudem können die RFID Transponder auf der Produktver-packung als fälschungssicheres Merkmal eingesetzt werden. Bei temperatursensiblen Produkten können Transponder mit zusätzlicher Sensorik zur Überwachung der Kühlkette dienen. Gleichzeitig kann der Transponder auch als Diebstahlsicherung im innerbetrieblichen Bereich sowie auch im Handel dienen und ermöglicht dabei eine höhere Sicherheit als die bisher eingesetzten 1-Bit Transponder. Die Trans-pondertechnologie kann außerdem den Barcode ganz oder teilweise ersetzen und so einen großen Beitrag zur Prozessautomatisierung leisten.

Topologically Accurate Dual Isosurfacing Using Ray Intersection

“Dual contouring” approaches provide an alternative to standard Marching Cubes (MC) method to extract and approximate an isosurface from trivariate data given on a volumetric mesh. These dual approaches solve some of the problems encountered by the MC methods. We present a simple method based on the MC method and the ray intersection technique to compute isosurface points in the cell interior. One of the advantages of our method is that it does not require us to use Hermite interpolation scheme, unlike other dual contouring methods. We perform a complete analysis of all possible configurations to generate a look-up table for all configurations. We use the look-up table to optimize the ray-intersection method to obtain minimum number of points necessarily sufficient for defining topologically correct isosurfaces in all possible configurations. Isosurface points are connected using a simple strategy.

BrainMaps.org - Interactive High-Resolution Digital Brain Atlases and Virtual Microscopy

BrainMaps.org is an interactive high-resolution digital brain atlas and virtual microscope that is based on over 20 million megapixels of scanned images of serial sections of both primate and non-primate brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet. Complete brain datasets for various species, including Homo sapiens, Macaca mulatta, Chlorocebus aethiops, Felis catus, Mus musculus, Rattus norvegicus, and Tyto alba, are accessible online. The methods and tools we describe are useful for both research and teaching, and can be replicated by labs seeking to increase accessibility and sharing of neuroanatomical data. These tools offer the possibility of visualizing and exploring completely digitized sections of brains at a sub-neuronal level, and can facilitate large-scale connectional tracing, histochemical and stereological analyses.

Optical Indoor Positioning of Vehicles

Indoor positioning is the backbone of many advanced intra-logistic applications. As opposed to unified outdoor satellite positioning systems, there are many different technical approaches to indoor positioning. Depending on the application, there are different trade-offs between accuracy, range, and costs. In this paper we present a new concept for a 4-degree-of-freedom (4-DOF) positioning system to be used for vehicle tracing in a logistic facility. The system employs optical data transmission between active infrastructure and receiver devices. Compared to existing systems, these optical technologies promise to achieve better accuracy at lower costs. We will introduce the positioning algorithm and an experimental setup of the system.

Pollen percentage thresholds of Abies alba based on 13-year annual records of pollen deposition in modified Tauber traps: perspectives of application to fossil situations

Abies alba (fir), a submontane tree from Central European mountains and uplands, is of special interest for palaeoecological and palaeoclimate interpretations due to its sensitivity to air and soil humidity. Its present distribution limit in the uplands of SE Poland is still a matter of debate. In the Holocene fir expanded to Poland very late, but early fir populations are supposed to occur in the Šumava Mts (Czech Republic). The study aims: to estimate pollen thresholds for fir presence/absence in Bohemia (Czech Republic) and Poland on the basis of modified Tauber pollen traps; to use these thresholds for tracing fir presence in two pollen diagrams from Poland (Słone and Bezedna lakes) in the border zone between the Roztocze region (with fir forest stands today) and Polesie (where fir has never played an important role); and to investigate how the percentage presence/absence threshold can be used to trace the occurrence and abundance of fir trees in the Šumava Mts based on the pollen diagrams of Rokytecká slat' and Mrtvý luh. The fir pollen thresholds estimated in terms of PAR (pollen accumulation rates or pollen influx) range from 843 (grains cm− 2 year− 1) (Roztocze) to 61 (Krkonoše) and 49 (Šumava). Percentage thresholds range from 0.3% in Krkonoše where fir trees are not present within 4 km to 22% in fir-dominated woodland of the Roztocze, providing evidence of strong underrepresentation of fir in the pollen deposition. Application of these percentage thresholds to the Słone and Bezedna pollen diagrams indicates that occurrence of fir in the region is possible from 3.5 cal ky BP onwards, though the evidence is not decisive. In the Šumava, a low representation of fir pollen (1–2%) reflecting presence of scattered fir trees was detected as early as ca. 7.0 cal ky BP.

Development of two real-time PCR assays for the detection of Mycoplasma hyopneumoniae in clinical samples

In order to improve the diagnosis of enzootic pneumonia (EP) in pigs two real-time polymerase chain reaction (rtPCR) assays for the detection of Mycoplasma hyopneumoniae in bronchial swabs from lung necropsies were established and validated in parallel. As a gold standard, the current "mosaic diagnosis" was taken, including epidemiological tracing, clinical signs, macro- and histopathological lesions of the lungs and immunofluorescence. One rtPCR is targeting a repeated DNA element of the M. hyopneumoniae genome (REP assay), the other a putative ABC transporter gene (ABC assay). Both assays were shown to be specific for M. hyopneumoniae and did not cross react with other bacteria and mollicutes from pig. With material from pigs of defined EP-negative farms the two assays showed to be 100% specific. When testing lungs from pig farms with EP, the REP assay detected 50% and the ABC assay 90% of the farms as positive. Both tests together detected all positive farms. Within a positive herd the two assays tested similarly with on average over 90% of the lung samples analysed from a single farm showing positive scores. A series of samples with suspicion of EP and samples from pigs with diseases other than respiratory taken from current routine diagnostic was assayed. None of the assays showed false positive results. The sensitivities in this sample group were 50% for the REP and 70% for the ABC assays and for both assays together 85%. The two assays run in parallel are therefore a valuable tool for the improvement of the current diagnosis of EP.

Are They Really Lost? "True" Status and Reasons for Treatment Discontinuation among HIV Infected Patients on Antiretroviral Therapy Considered Lost to Follow Up in Urban Malawi

INTRODUCTION Patients who are lost to follow-up (LTFU) while on antiretroviral therapy (ART) pose challenges to the long-term success of ART programs. We describe the extent to which patients considered LTFU are misclassified as true disengagement from care when they are still alive on ART and explain reasons for ART discontinuation using our active tracing program to further improve ART retention programs and policies. METHODS We identified adult ART patients who missed clinic appointment by more than 3 weeks between January 2006 and December 2010, assuming that such patients would miss their doses of antiretroviral drugs. Patients considered LTFU who consented during ART registration were traced by phone or home visits; true ART status after tracing was documented. Reasons for ART discontinuation were also recorded for those who stopped ART. RESULTS Of the 4,560 suspected LTFU cases, 1,384 (30%) could not be traced. Of the 3,176 successfully traced patients, 952 (30%) were dead and 2,224 (70%) were alive, of which 2,183 (99.5%) started ART according to phone-based self-reports or physical verification during in-person interviews. Of those who started ART, 957 (44%) stopped ART and 1,226 (56%) reported still taking ART at the time of interview by sourcing drugs from another clinic, using alternative ART sources or making brief ART interruptions. Among 940 cases with reasons for ART discontinuations, failure to remember (17%), too weak/sick (12%), travel (46%), and lack of transport to the clinic (16%) were frequently cited; reasons differed by gender. CONCLUSION The LTFU category comprises sizeable proportions of patients still taking ART that may potentially bias retention estimates and misdirect resources at the clinic and national levels if not properly accounted for. Clinics should consider further decentralization efforts, increasing drug allocations for frequent travels, and improving communication on patient transfers between clinics to increase retention and adherence.

Estimating Ribeye Area Using a Longitudinal Ultrasound Image of the 12th and 13th Rib Section

A study was performed to determine the feasability of using a measurement of ribeye depth (RED) from a longitudinal ultrasound image to estimate ribeye area (REA). The correlation between RED obtained with ultrasound and REA from a tracing was high for both implanted (r = .49) and non-implanted (r = .45) steers. The mean bias between predicted REA and actual REA was not different from zero. This analysis shows that RED could be an accurate indicator of REA.

Flow disturbances in stent-related coronary evaginations: a computational fluid-dynamic simulation study

Aims: Angiographic ectasias and aneurysms in stented segments have been associated with late stent thrombosis. Using optical coherence tomography (OCT), some stented segments show coronary evaginations reminiscent of ectasias. The purpose of this study was to explore, using computational fluid-dynamic (CFD) simulations, whether OCT-detected coronary evaginations can induce local changes in blood flow. Methods and results: OCT-detected evaginations are defined as outward bulges in the luminal vessel contour between struts, with the depth of the bulge exceeding the actual strut thickness. Evaginations can be characterised cross ectionally by depth and along the stented segment by total length. Assuming an ellipsoid shape, we modelled 3-D evaginations with different sizes by varying the depth from 0.2-1.0 mm, and the length from 1-9 mm. For the flow simulation we used average flow velocity data from non-diseased coronary arteries. The change in flow with varying evagination sizes was assessed using a particle tracing test where the particle transit time within the segment with evagination was compared with that of a control vessel. The presence of the evagination caused a delayed particle transit time which increased with the evagination size. The change in flow consisted locally of recirculation within the evagination, as well as flow deceleration due to a larger lumen - seen as a deflection of flow towards the evagination. Conclusions: CFD simulation of 3-D evaginations and blood flow suggests that evaginations affect flow locally, with a flow disturbance that increases with increasing evagination size.

Proton entry into the near-lunar plasma wake for magnetic field aligned flow

We report the first observation of protons in the near-lunar (100-200 km from the surface) and deeper (near anti-subsolar point) plasma wake when the interplanetary magnetic field (IMF) and solar wind velocity (vsw) are parallel (aligned flow; angle between IMF and vsw≤10°). More than 98% of the observations during aligned flow condition showed the presence of protons in the wake. These observations are obtained by the Solar Wind Monitor sensor of the Sub-keV Atom Reflecting Analyser experiment on Chandrayaan-1. The observation cannot be explained by the conventional fluid models for aligned flow. Back tracing of the observed protons suggests that their source is the solar wind. The larger gyroradii of the wake protons compared to that of solar wind suggest that they were part of the tail of the solar wind velocity distribution function. Such protons could enter the wake due to their large gyroradii even when the flow is aligned to IMF. However, the wake boundary electric field may also play a role in the entry of the protons into the wake.

Evaluation of control and surveillance strategies for classical swine fever using a simulation model

Classical swine fever (CSF) outbreaks can cause enormous losses in naïve pig populations. How to best minimize the economic damage and number of culled animals caused by CSF is therefore an important research area. The baseline CSF control strategy in the European Union and Switzerland consists of culling all animals in infected herds, movement restrictions for animals, material and people within a given distance to the infected herd and epidemiological tracing of transmission contacts. Additional disease control measures such as pre-emptive culling or vaccination have been recommended based on the results from several simulation models; however, these models were parameterized for areas with high animal densities. The objective of this study was to explore whether pre-emptive culling and emergency vaccination should also be recommended in low- to moderate-density areas such as Switzerland. Additionally, we studied the influence of initial outbreak conditions on outbreak severity to improve the efficiency of disease prevention and surveillance. A spatial, stochastic, individual-animal-based simulation model using all registered Swiss pig premises in 2009 (n=9770) was implemented to quantify these relationships. The model simulates within-herd and between-herd transmission (direct and indirect contacts and local area spread). By varying the four parameters (a) control measures, (b) index herd type (breeding, fattening, weaning or mixed herd), (c) detection delay for secondary cases during an outbreak and (d) contact tracing probability, 112 distinct scenarios were simulated. To assess the impact of scenarios on outbreak severity, daily transmission rates were compared between scenarios. Compared with the baseline strategy (stamping out and movement restrictions) vaccination and pre-emptive culling neither reduced outbreak size nor duration. Outbreaks starting in a herd with weaning piglets or fattening pigs caused higher losses regarding to the number of culled premises and were longer lasting than those starting in the two other index herd types. Similarly, larger transmission rates were estimated for these index herd type outbreaks. A longer detection delay resulted in more culled premises and longer duration and better transmission tracing increased the number of short outbreaks. Based on the simulation results, baseline control strategies seem sufficient to control CSF in low-medium animal-dense areas. Early detection of outbreaks is crucial and risk-based surveillance should be focused on weaning piglet and fattening pig premises.

Stratigraphic analysis of lake level fluctuations in Lake Ohrid: an integration of high resolution hydro-acoustic data and sediment cores

Abstract. Ancient Lake Ohrid is a steep-sided, oligotrophic, karst lake that was tectonically formed most likely within the Pliocene and often referred to as a hotspot of endemic biodiversity. This study aims on tracing significant lake level fluctuations at Lake Ohrid using high-resolution acoustic data in combination with lithological, geochemical, and chronological information from two sediment cores recovered from sub-aquatic terrace levels at ca. 32 and 60m water depth. According to our data, significant lake level fluctuations with prominent lowstands of ca. 60 and 35m below the present water level occurred during Marine Isotope Stage (MIS) 6 and MIS 5, respectively. The effect of these lowstands on biodiversity in most coastal parts of the lake is negligible, due to only small changes in lake surface area, coastline, and habitat. In contrast, biodiversity in shallower areas was more severely affected due to disconnection of today sublacustrine springs from the main water body. Multichannel seismic data from deeper parts of the lake clearly image several clinoform structures stacked on top of each other. These stacked clinoforms indicate significantly lower lake levels prior to MIS 6 and a stepwise rise of water level with intermittent stillstands since its existence as water-filled body, which might have caused enhanced expansion of endemic species within Lake Ohrid.

Clinical and microbiological aspects of linezolid resistance mediated by the cfr gene encoding a 23S rRNA methyltransferase.

The cfr (chloramphenicol-florfenicol resistance) gene encodes a 23S rRNA methyltransferase that confers resistance to linezolid. Detection of linezolid resistance was evaluated in the first cfr-carrying human hospital isolate of linezolid and methicillin-resistant Staphylococcus aureus (designated MRSA CM-05) by dilution and diffusion methods (including Etest). The presence of cfr was investigated in isolates of staphylococci colonizing the patient's household contacts and clinical isolates recovered from patients in the same unit where MRSA CM-05 was isolated. Additionally, 68 chloramphenicol-resistant Colombian MRSA isolates recovered from hospitals between 2001 and 2004 were screened for the presence of the cfr gene. In addition to erm(B), the erm(A) gene was also detected in CM-05. The isolate belonged to sequence type 5 and carried staphylococcal chromosomal cassette mec type I. We were unable to detect the cfr gene in any of the human staphylococci screened (either clinical or colonizing isolates). Agar and broth dilution methods detected linezolid resistance in CM-05. However, the Etest and disk diffusion methods failed to detect resistance after 24 h of incubation. Oxazolidinone resistance mediated by the cfr gene is rare, and acquisition by a human isolate appears to be a recent event in Colombia. The detection of cfr-mediated linezolid resistance might be compromised by the use of the disk diffusion or Etest method.

Regulation of {\it myogenin\/} transcription during mouse embryogenesis

The formation of skeletal muscle during vertebrate development involves the induction of mesoderm and subsequent generation of myoblasts that ultimately differentiate into mature muscles. The recent identification of a group of myogenic regulators that can convert fibroblasts to myoblasts has contributed to our understanding of the molecular events that underlie the establishment of the skeletal muscle phenotype. Members of this group of myogenic regulators share a helix-loop-helix (HLH) motif that mediates DNA binding. The myogenic HLH proteins bind to the consensus sequence CANNTG, referred to as an E-box, and activate muscle-specific transcription. In addition to E-boxes, other motifs, such as the MEF-2 binding site, have been shown to mediate muscle-specific transcription. The myogenic HLH proteins are expressed in the myogenic precursors in somites and limb buds, and in differentiated muscle fibers during embryogenesis, consistent with their roles as regulators for muscle development. The myogenic HLH proteins appear to auto-activate their own and cross-activate one another's expression in cultured cells. Myogenin is one of the myogenic HLH proteins and likely the regulator for terminal muscle differentiation. Myogenin is a common target of diverse regulatory pathways. To search for upstream regulators of myogenin, we studied regulation of myogenin transcription during mouse embryogenesis. We showed that the myogenin promoter contains a binding site for MEF-2, which can mediate indirectly the autoregulation of myogenin transcription. We found that a transgene under the control of a 1.5 kb 5$\sp\prime$ flanking sequence can recapitulate the temporal and spatial expression pattern of the endogenous myogenin gene during mouse embryogenesis. By tracing embryonic cells that activate myogenin-lacZ during embryogenesis, we found no evidence that lacZ was expressed in myogenic precursors migrating from somites to limb buds, suggesting the existence of regulators other than myogenic HLH proteins that can maintain cells in the myogenic lineage. Mutations of an E-box and a MEF-2 site in the myogenin promoter suppressed transcription in subsets of myogenic precursors in mouse embryos. These results suggest that myogenic HLH proteins and MEF-2 participate in separable regulatory pathways controlling myogenin transcription and provide evidence for positional regulation of myogenic regulators in the embryo. ^