Interactive Model Expansion in an Observable Environment

Many practical problems can be understood as the search for a state of affairs that extends a fixed partial state of affairs, the \emph{environment}, while satisfying certain conditions that are formally specified. Such problems are found in, e.g., engineering, law or economics. We study this class of problems in a context where some of the relevant information about the environment is not known by the user at the start of the search. During the search, the user may consider tentative solutions that make implicit hypotheses about these unknowns. To ensure that the solution is appropriate, these hypotheses must be verified by observing the environment. Furthermore, we assume that, in addition to knowledge of what constitutes a solution, knowledge of general laws of the environment is also present. We formally define partial solutions with enough verified facts to guarantee the existence of complete and appropriate solutions. Additionally, we propose an interactive system to assist the user in their search by determining 1) which hypotheses implicit in a tentative solution must be verified in the environment, and 2) which observations can bring useful information for the search. We present an efficient method to over-approximate the set of relevant information, and evaluate our implementation.Comment: This paper is an extended and revised version of a conference paper appearing in the proceedings of ICLP 2023 and to be published in Theory and Practice of Logic Programmin

The first report of the coproduction of CMY-16 and ArmA 16S rRNA methylases in carbapenemase-ESBL producing Escherichia coli isolates

The main aim of this work was to assess the occurrence and to characterize AmpC genes and to investigate the co-existence of 16S rRNA methylases and carbapenemases genes among the ESBL producing Escherichia coli strains. 180 Escherichia coli clinical strains were collected from the university hospital of Constantine located in the eastern part of Algeria. 42 ESBL-producers were phenotypically identified and also confirmed genotypically able to produce CTX-M-15 [n=33], CTX-M-1 [n=5], CTX-M-14 [n=1], SHV-2 [n=1], and two strains have been revealed producing the blaOXA-48 genes associated with blaTEM-1. Among the ESBL-producing strains three expressed additionally an AmpC phenotype which corresponded to the carriage of a blaCMY gene shown by sequencing to correspond to CMY-2 (1 isolate) CMY-16 (2 isolates). The two E. coli isolates produce CMY-16 that belonged to phylogroup D while the single CMY-2 producing isolate belonged to phylogroup C. Antibiotic resistance of the aminoglycoside family by production of 16S rRNA methylases was detected by an end-point multiplex PCR assay which concerns genes coding for different 16S rRNA methylases (rmtD, rmtA, rmtB, armA, npmA, and rmtC). An armA gene was identified in 2 strains. This study shows for the first time the co-existance of CMY-16 and armA genes with blaTEM-1 and blaOXA-48 producing E. coli strains. DOI: http://dx.doi.org/10.5281/zenodo.377665

MEMS-enabled silicon photonic integrated devices and circuits

Photonic integrated circuits have seen a dramatic increase in complexity over the past decades. This development has been spurred by recent applications in datacenter communications and enabled by the availability of standardized mature technology platforms. Mechanical movement of wave-guiding structures at the micro- and nanoscale provides unique opportunities to further enhance functionality and to reduce power consumption in photonic integrated circuits. We here demonstrate integration of MEMS-enabled components in a simplified silicon photonics process based on IMEC's Standard iSiPP50G Silicon Photonics Platform and a custom release process

Increasing proportion of carbapenemase-producing Enterobacteriaceae and emergence of a MCR-1 producer through a multicentric study among hospital-based and private laboratories in Belgium from September to November 2015

Carbapenemase-producing Enterobacteriaceae (CPE) strains have been increasingly reported in Belgium. We aimed to determine the proportion of CPE among Enterobacteriaceae isolated from hospitalised patients and community outpatients in Belgium in 2015. For the hospitalised patients, the results were compared to a previous similar survey performed in the same hospitals in 2012. Twenty-four hospital-based and 10 private laboratories collected prospectively 200 non-duplicated Enterobacteriaceae isolates from clinical specimens. All isolates were screened locally by carbapenem disk diffusion using European Committee on Antimicrobial Susceptibility Testing methodology. Putative CPE strains with inhibition zone diameters below the screening breakpoints were referred centrally for confirmation of carbapenemase production. From September to November 2015, we found a proportion of clinical CPE of 0.55% (26/4,705) and of 0.60% (12/1,991) among hospitalised patients and among ambulatory outpatients respectively. Klebsiella pneumoniae (26/38) and OXA-48-like carbapenemase (28/38) were the predominant species and enzyme among CPE. One OXA-48-producing Escherichia coli isolated from a hospital was found carrying plasmid-mediated MCR-1 colistin resistance. Compared with the 2012 survey, we found a significant increased proportion of clinical CPE (0.55% in 2015 vs 0.25% in 2012; p = 0.02) and an increased proportion of hospitals (13/24 in 2015 vs 8/24 in 2012) with at least one CPE detected. The study results confirmed the concerning spread of CPE including a colistin-resistant MCR-1 producer in hospitals and the establishment of CPE in the community in Belgium

Temocillin and piperacillin/tazobactam resistance by disc diffusion as antimicrobial surrogate markers for the detection of carbapenemase-producing Enterobacteriaceae in geographical areas with a high prevalence of OXA-48 producers

Objectives To assess the performance of the agar disc diffusion method for the detection of carbapenemase-producing Enterobacteriaceae (CPE) referred to the national reference laboratories (NRLs) in Belgium and France. Methods All Enterobacteriaceae isolates referred to the NRLs for the confirmation of CPE in 2012 were included. The inhibition zone diameters of meropenem, piperacillin/tazobactam and temocillin using CLSI disc diffusion methodology were recorded. Phenotypic and molecular detection of carbapenemases was performed on all isolates. Results A total of 1354 Enterobacteriaceae isolates, including 435 (32.1%) confirmed CPE isolates [OXA-48 (n = 323), KPC (n = 60), VIM (n = 32) and NDM (n = 20)] and 919 carbapenemase-negative isolates, were tested. Using recommended interpretative criteria, non-susceptibility to meropenem had poor sensitivity (52.0% by CLSI susceptibility breakpoint and 80.0% by EUCAST screening breakpoints), while non-susceptibility to piperacillin/tazobactam (according to CLSI breakpoint) or to temocillin (according to Fuchs, Barry, Thornsberry et al. Eur J Clin Microbiol 1985; 4: 30-3) was highly sensitive (99.8% and 98.2%, respectively) but poorly specific (29.4% and 42.9%, respectively) for the detection of CPE. Temocillin diameters <12 mm alone had high specificity (90.0%) and the combination of temocillin diameters ≥12 mm with piperacillin/tazobactam diameters ≥16 mm observed in 40% of all referred isolates displayed excellent negative predictive value (99.2%). Conclusions In geographical areas with a high prevalence of OXA-48 producers, recommended meropenem susceptibility or screening breakpoints failed to detect CPE in a large proportion of isolates. The combination of modified zone diameter cut-offs for piperacillin/tazobactam (≥16 mm) and temocillin (≥12 mm) can be used to rule out the presence of carbapenemase and avoid unnecessary additional testing for confirmation of CP

Silicon photonic MEMS add-drop filter

We demonstrate a compact add-drop filter based on a MEMS ring resonator implemented in IMEC's iSiPP50G silicon photonics platform. The device exhibits a port extinction of 20 dB and a port isolation of > 50 dB, upon actuation range of 0 V to 27 V

Low-voltage silicon photonic MEMS switch with vertical actuation

We present a vertically movable silicon photonic MEMS switch realized in IMEC's standard silicon photonics platform followed by a dedicated postprocessing for MEMS release. The device has six optical ports, which enable four switching configurations with a safe electrical isolation of the switch's actuator. A low actuation voltage of 3.75 V is required to efficiently switch the optical signal from the drop port to the through port of the device. The device exhibits port extinctions of 16 dB and 26 dB at its OFF and ON states, respectively. With an insertion loss of 35 nm, this component paves the way for low-power scalable circuits in MEMS-enabled silicon photonics

Development of an NGS-based workflow for improved monitoring of circulating plasmids in support of risk assessment of antimicrobial resistance gene dissemination

Antimicrobial resistance (AMR) is one of the most prominent public health threats. AMR genes localized on plasmids can be easily transferred between bacterial isolates by horizontal gene transfer, thereby contributing to the spread of AMR. Next-generation sequencing (NGS) technologies are ideal for the detection of AMR genes; however, reliable reconstruction of plasmids is still a challenge due to large repetitive regions. This study proposes a workflow to reconstruct plasmids with NGS data in view of AMR gene localization, i.e., chromosomal or on a plasmid. Whole-genome and plasmid DNA extraction methods were compared, as were assemblies consisting of short reads (Illumina MiSeq), long reads (Oxford Nanopore Technologies) and a combination of both (hybrid). Furthermore, the added value of conjugation of a plasmid to a known host was evaluated. As a case study, an isolate harboring a large, low-copymcr-1-carrying plasmid (>200 kb) was used. Hybrid assemblies of NGS data obtained from whole-genome DNA extractions of the original isolates resulted in the most complete reconstruction of plasmids. The optimal workflow was successfully applied to multidrug-resistantSalmonellaKentucky isolates, where the transfer of an ESBL-gene-containing fragment from a plasmid to the chromosome was detected. This study highlights a strategy including wet and dry lab parameters that allows accurate plasmid reconstruction, which will contribute to an improved monitoring of circulating plasmids and the assessment of their risk of transfer

Wafer-level vacuum sealing for packaging of silicon photonic MEMS

Silicon (Si) photonic micro-electro-mechanical systems (MEMS), with its low-power phase shifters and tunable couplers, is emerging as a promising technology for large-scale reconfigurable photonics with potential applications for example in photonic accelerators for artificial intelligence (AI) workloads. For silicon photonic MEMS devices, hermetic/vacuum packaging is crucial to the performance and longevity, and to protect the photonic devices from contamination. Here, we demonstrate a wafer-level vacuum packaging approach to hermetically seal Si photonic MEMS wafers produced in the iSiPP50G Si photonics foundry platform of IMEC. The packaging approach consists of transfer bonding and sealing the silicon photonic MEMS devices with 30 μm-thick Si caps, which were prefabricated on a 100 mm-diameter silicon-on-insulator (SOI) wafer. The packaging process achieved successful wafer-scale vacuum sealing of various photonic devices. The functionality of photonic MEMS after the hermetic/vacuum packaging was confirmed. Thus, the demonstrated thin Si cap packaging shows the possibility of a novel vacuum sealing method for MEMS integrated in standard Si photonics platforms

Low power inelastic light scattering at small detunings in silicon wire waveguides at telecom wavelengths

When a pump beam is propagating through a silicon nanophotonic waveguide, a very small fraction of the light is scattered to other frequencies. At very low intensity, the amount of scattered light is proportional to the power of the pump beam. We show that the scattering intensity increases linearly within the temperature range 300-575 K and that the photon flux decreases as the inverse of the frequency detuning {\nu} over the investigated bandwidth 0.4 THz < |{\nu}| < 2.5 THz. The simplest interpretation of these observations is that the pump beam is scattered on a 1 dimensional thermal bath of excitations. Finally, the implications of this scattering process for quantum optics applications of silicon nanophotonic structures are discussed.Comment: 11 pages, 5 figures, to submit to Journal of the Optical Society