Prospective Multicenter Validation of the Stockholm3 Test in a Central European Cohort.

BACKGROUND: It has been shown that the Stockholm3 test decreases overdetection of prostate cancer (PCa) while retaining the ability to detect clinically significant PCa (csPCa) in a Swedish population. However, the test includes potentially population-specific testing of single-nucleotide polymorphisms and has yet not been validated outside Scandinavia. OBJECTIVE: To assess the performance of the Stockholm3 test in discriminating csPCa in a Central European cohort undergoing prostate biopsy (PBx). DESIGN, SETTING, AND PARTICIPANTS: This prospective multicenter validation study was conducted from August 2020 to September 2022 at two centers in Switzerland and one center in Germany. The study involved 342 men undiagnosed with PCa who were scheduled for PBx after prostate-specific antigen (PSA) testing and subsequent magnetic resonance imaging (MRI) of the prostate. Before PBx, participants had a blood sample taken for Stockholm3 testing. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: The primary outcome was the accuracy of the Stockholm3 test in detecting csPCa (International Society of Urological Pathology grade group [GG] ≥2) according to the area under the receiver operating characteristic curve (AUC), sensitivity, and specificity, and the clinical consequences of using the model. RESULTS AND LIMITATIONS: The Stockholm3 test with a cutoff of 11% for csPCa detection had sensitivity of 92.3% (95% confidence interval [CI] 86.9-95.9%), specificity of 32.6% (95% CI 26.0-39.8%), a positive predictive value of 53.2% (95% CI 47.0-59.2%), and a negative predictive value of 83.6% (95% CI 73-91.2%). It showed superior discrimination for csPCa (AUC 0.77, 95% CI 0.72-0.82) in comparison to PSA (AUC 0.66, 95% CI 0.61-0.72; p < 0.001). Using a Stockholm3 cutoff of 11%, PBx could have been omitted for 73 men (21.0%), and 12/154 (8%) csPCa and 2/72 (2.8%) GG >2 cases would have been missed. Limitations include population selection bias. CONCLUSIONS: Our results show favorable clinical outcomes for the blood-based Stockholm3 biomarker test in a Central European patient cohort. PATIENT SUMMARY: The Stockholm3 blood test shows better accuracy in predicting prostate cancer than the more common PSA (prostate-specific antigen) test.

Levitated Optomechanics with Meta-Atoms.

We propose to introduce additional control in levitated optomechanics by trapping a meta-atom, i.e., a subwavelength and high-permittivity dielectric particle supporting Mie resonances. In particular, we theoretically demonstrate that optical levitation and center-of-mass ground-state cooling of silicon nanoparticles in vacuum is not only experimentally feasible but it offers enhanced performance over widely used silica particles in terms of trap frequency, trap depth, and optomechanical coupling rates. Moreover, we show that, by adjusting the detuning of the trapping laser with respect to the particle's resonance, the sign of the polarizability becomes negative, enabling levitation in the minimum of laser intensity, e.g., at the nodes of a standing wave. The latter opens the door to trapping nanoparticles in the optical near-field combining red and blue-detuned frequencies, in analogy to two-level atoms, which is of interest for generating strong coupling to photonic nanostructures and short-distance force sensing.

Interaction between an Optically Levitated Nanoparticle and Its Thermal Image: Internal Thermometry via Displacement Sensing.

We propose and theoretically analyze an experiment where displacement sensing of an optically levitated nanoparticle in front of a surface can be used to measure the induced dipole-dipole interaction between the nanoparticle and its thermal image. This is achieved by using a surface that is transparent to the trapping light but reflective to infrared radiation, with a reflectivity that can be time modulated. This dipole-dipole interaction relies on the thermal radiation emitted by a silica nanoparticle having sufficient temporal coherence to correlate the reflected radiation with the thermal fluctuations of the dipole. The resulting force is orders of magnitude stronger than the thermal gradient force, and it strongly depends on the internal temperature of the nanoparticle for a particle-to-surface distance greater than two micrometers. We argue that it is experimentally feasible to use displacement sensing of a levitated nanoparticle in front of a surface as an internal thermometer in ultrahigh vacuum. Experimental access to the internal physics of a levitated nanoparticle in vacuum is crucial to understanding the limitations that decoherence poses to current efforts devoted to preparing a nanoparticle in a macroscopic quantum superposition state.

Cavity-Based 3D Cooling of a Levitated Nanoparticle via Coherent Scattering.

We experimentally realize cavity cooling of all three translational degrees of motion of a levitated nanoparticle in vacuum. The particle is trapped by a cavity-independent optical tweezer and coherently scatters tweezer light into the blue detuned cavity mode. For vacuum pressures around 10^{-5} mbar, minimal temperatures along the cavity axis in the millikelvin regime are observed. Simultaneously, the center-of-mass (c.m.) motion along the other two spatial directions is cooled to minimal temperatures of a few hundred millikelvin. Measuring temperatures and damping rates as the pressure is varied, we find that the cooling efficiencies depend on the particle position within the intracavity standing wave. This data and the behavior of the c.m. temperatures as functions of cavity detuning and tweezer power are consistent with a theoretical analysis of the experiment. Experimental limits and opportunities of our approach are outlined.

PBP2a in ß-Lactam-Resistant Laboratory Mutants and Clinical Isolates: Disruption Versus Reduced Penicillin Affinity.

Alterations in PBP2a have been recognized in cefotaxime-resistant laboratory mutants and ß-lactam-resistant clinical isolates of Streptococcus pneumoniae. DNA sequencing revealed fundamental differences between these two settings. Internal stop codons in pbp2a occurred in all three laboratory mutants analyzed, caused by a mutation in pbp2a of mutant C604, and tandem duplications within pbp2a resulting in premature stop codons in another two mutants C403 and C406. In contrast, mosaic PBP2a genes were observed in several penicillin-resistant clinical isolates from South Africa, the Czech Republic, Hungary, and in the clone Poland23F-16, with sequence blocks diverging from sensitive strains by over 4%. Most of these pbp2a variants except pbp2a from the South African strain contained sequences related to pbp2a of Streptococcus mitis B6, confirming that this species serves as reservoir for penicillin-resistance determinants.

New Aspects of the Interplay between Penicillin Binding Proteins, murM, and the Two-Component System CiaRH of Penicillin-Resistant Streptococcus pneumoniae Serotype 19A Isolates from Hungary.

The Streptococcus pneumoniae clone Hungary19A-6 expresses unusually high levels of ß-lactam resistance, which is in part due to mutations in the MurM gene, encoding a transferase involved in the synthesis of branched peptidoglycan. Moreover, it contains the allele ciaH232, encoding the histidine kinase CiaH (M. Müller, P. Marx, R. Hakenbeck, and R. Brückner, Microbiology 157:3104-3112, 2011, https://doi.org/10.1099/mic.0.053157-0). High-level penicillin resistance primarily requires the presence of low-affinity (mosaic) penicillin binding protein (PBP) genes, as, for example, in strain Hu17, a closely related member of the Hungary19A-6 lineage. Interestingly, strain Hu15 is ß-lactam sensitive due to the absence of mosaic PBPs. This unique situation prompted us to investigate the development of cefotaxime resistance in transformation experiments with genes known to play a role in this phenotype, pbp2x, pbp1a, murM, and ciaH, and penicillin-sensitive recipient strains R6 and Hu15. Characterization of phenotypes, peptidoglycan composition, and CiaR-mediated gene expression revealed several novel aspects of penicillin resistance. The murM gene of strain Hu17 (murMHu17), which is highly similar to murM of Streptococcus mitis, induced morphological changes which were partly reversed by ciaH232. murMHu17 conferred cefotaxime resistance only in the presence of the pbp2x of strain Hu17 (pbp2xHu17). The ciaH232 allele contributed to a remarkable increase in cefotaxime resistance in combination with pbp2xHu17 and pbp1a of strain Hu17 (pbp1aHu17), accompanied by higher levels of expression of CiaR-regulated genes, documenting that ciaH232 responds to PBP1aHu17-mediated changes in cell wall synthesis. Most importantly, the proportion of branched peptides relative to the proportion of linear muropeptides increased in cells containing mosaic PBPs, suggesting an altered enzymatic activity of these proteins.

Draft Genome Sequences of Two Streptococcus pneumoniae Serotype 19A Sequence Type 226 Clinical Isolates from Hungary, Hu17 with High-Level Beta-Lactam Resistance and Hu15 of a Penicillin-Sensitive Phenotype.

The draft genome sequences of two multiple-antibiotic-resistant Streptococcus pneumoniae isolates from Hungary, Hu15 and Hu17, are reported here. Strain Hu15 is penicillin susceptible, whereas Hu17 is a high-level-penicillin-resistant strain. Both isolates belong to the serotype 19A sequence type 226, a single-locus variant (in the ddl locus) of the Hungary19A-6 clone.

Ultrashort Pulses for Far-Field Nanoscopy.

We show that ultrashort pulses can be focused, in a particular instant, to a spot size given by the wavelength associated with its spectral width. For attosecond pulses this spot size is within the nanometer scale. Then we show that a two-level system can be left excited after interacting with an ultrashort pulse whose spectral width is larger than the transition frequency, and that the excitation probability depends not on the field amplitude but on the field intensity. The latter makes the excitation profile have the same spot size as the ultrashort pulse. This unusual phenomenon is caused by quantum electrodynamics in the ultrafast light-matter interaction regime since the usually neglected counterrotating terms describing the interaction with the free electromagnetic modes are crucial for making the excitation probability nonzero and depend on the field intensity. These results suggest that a train of coherent attosecond pulses could be used to excite fluorescent markers with nanoscale resolution. The detection of the light emitted after fluorescence-or any other method used to detect the excitation-could then lead to a new scheme for far-field light nanoscopy.

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Transfer of penicillin resistance from Streptococcus oralis to Streptococcus pneumoniae identifies murE as resistance determinant.

Beta-lactam resistant clinical isolates of Streptococcus pneumoniae contain altered penicillin-binding protein (PBP) genes and occasionally an altered murM, presumably products of interspecies gene transfer. MurM and MurN are responsible for the synthesis of branched lipid II, substrate for the PBP catalyzed transpeptidation reaction. Here we used the high-level beta-lactam resistant S. oralis Uo5 as donor in transformation experiments with the sensitive laboratory strain S. pneumoniae R6 as recipient. Surprisingly, piperacillin-resistant transformants contained no alterations in PBP genes but carried murEUo5 encoding the UDP-N-acetylmuramyl tripeptide synthetase. Codons 83-183 of murEUo5 were sufficient to confer the resistance phenotype. Moreover, the promoter of murEUo5 , which drives a twofold higher expression compared to that of S. pneumoniae R6, could also confer increased resistance. Multiple independent transformations produced S. pneumoniae R6 derivatives containing murEUo5 , pbp2xUo5 , pbp1aUo5 and pbp2bUo5 , but not murMUo5 sequences; however, the resistance level of the donor strain could not be reached. S. oralis Uo5 harbors an unusual murM, and murN is absent. Accordingly, the peptidoglycan of S. oralis Uo5 contained interpeptide bridges with one L-Ala residue only. The data suggest that resistance in S. oralis Uo5 is based on a complex interplay of distinct PBPs and other enzymes involved in peptidoglycan biosynthesis.

Altered lipid composition in Streptococcus pneumoniae cpoA mutants.

BACKGROUND: Penicillin-resistance in Streptococcus pneumoniae is mainly due to alterations in genes encoding the target enzymes for beta-lactams, the penicillin-binding proteins (PBPs). However, non-PBP genes are altered in beta-lactam-resistant laboratory mutants and confer decreased susceptibility to beta-lactam antibiotics. Two piperacillin resistant laboratory mutants of Streptococcus pneumoniae R6 contain mutations in the putative glycosyltransferase gene cpoA. The CpoA gene is part of an operon including another putative glycosyltransferase gene spr0982, both of which being homologous to glycolipid synthases present in other Gram-positive bacteria. RESULTS: We now show that the cpoA mutants as well as a cpoA deletion mutant are defective in the synthesis of galactosyl-glucosyl-diacylglycerol (GalGlcDAG) in vivo consistent with the in vitro function of CpoA as α-GalGlcDAG synthase as shown previously. In addition, the proportion of phosphatidylglycerol increased relative to cardiolipin in cpoA mutants. Moreover, cpoA mutants are more susceptible to acidic stress, have an increased requirement for Mg(2+) at low pH, reveal a higher resistance to lysis inducing conditions and are hypersensitive to bacitracin. CONCLUSIONS: The data show that deficiency of the major glycolipid GalGlcDAG causes a pleitotropic phenotype of cpoA mutant cells consistent with severe membrane alterations. We suggest that the cpoA mutations selected with piperacillin are directed against the lytic response induced by the beta-lactam antibiotic.

Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin.

We extended a previously developed force matching approach to systems with covalent QM/MM boundaries and describe its user-friendly implementation in the publicly available software package CPMD. We applied this approach to the challenging case of the retinal protonated Schiff base in dark state bovine rhodopsin. We were able to develop a highly accurate force field that is able to capture subtle structural changes within the chromophore that have a pronounced influence on the optical properties. The optical absorption spectrum calculated from configurations extracted from a MD trajectory using the new force field is in excellent agreement with QM/MM and experimental references.

Streptococcus pneumoniae R6 interspecies transformation: genetic analysis of penicillin resistance determinants and genome-wide recombination events.

Interspecies gene transfer has been implicated as the major driving force for the evolution of penicillin resistance in Streptococcus pneumoniae. Genomic alterations of S. pneumoniae R6 introduced during four successive transformations with DNA of the high-level penicillin-resistant Streptococcus mitis B6 with beta-lactam selection have now been determined and the contribution of genes to high resistance levels was analysed genetically. Essential for high level resistance to penicillins of the transformant CCCB was the combination of murM(B) (6) and the 3' region of pbp2b(B) (6) . Sequences of both genes were detected in clinical isolates of S. pneumoniae, confirming the participation of S. mitis in the global gene pool of beta-lactam resistance determinants. The S. mitis PBP1b gene which contains an authentic stop codon within the transpeptidase domain is now shown to contribute only marginal to resistance, but it is possible that the presence of its transglycosylase domain is important in the context of cognate PBPs. The genome sequence of CCCB revealed 36 recombination events, including deletion and acquisition of genes and repeat elements. A total of 78 genes were affected representing 67 kb or 3.3% of the genome, documenting extensive alterations scattered throughout the genome.

Mutations in Streptococcus pneumoniae penicillin-binding protein 2x: importance of the C-terminal penicillin-binding protein and serine/threonine kinase-associated domains for beta-lactam binding.

Penicillin-binding protein 2x (PBP2x) mutations that occur during the selection with beta-lactams are located within the central penicillin-binding/transpeptidase (TP) domain, and are believed to mediate resistance by interfering with the formation of a covalent complex of the active site serine with the antibiotic. We now investigated the effect of two point mutations found in two independently obtained laboratory mutants that are located at the surface of the TP domain with their side chains facing outside (G422D respectively R426C). They have no significant effect on resistance to cefotaxime in vivo or on binding to Bocillin™FL to the active site in vitro using purified PBP2x derivatives, thus apparently do not affect the active site directly. In contrast, in silico modeling revealed that they affect van der Waal's interactions with the PASTA1 (PBP and serine/threonine kinase associated) domain of the C-terminal extension and a noncovalent cefuroxime molecule found in the X-ray structure of an acylated PBP2x, suggesting some effect of the mutations on the interaction of the TP domain with PASTA1 and/or with the antibiotic associated with PASTA1. The effect of the PASTA domains on covalent binding of PBP2x to Bocillin FL was then investigated using a series of soluble truncated PBP2x derivatives. Deletion of 127 C-terminal residues, that is, of both PASTA domains, decreased binding dramatically by ∼90%. Surprisingly, deletion of only 40 amino acids resulted in the same phenotype, whereas the absence of 30 amino acids affected binding marginally by 10%, documenting a crucial role of the C-terminal domain for beta-lactam binding.

Molecular mechanisms of ß-lactam resistance in Streptococcus pneumoniae.

Alterations in the target enzymes for ß-lactam antibiotics, the penicillin-binding proteins (PBPs), have been recognized as a major resistance mechanism in Streptococcus pneumoniae. Mutations in PBPs that confer a reduced affinity to ß-lactams have been identified in laboratory mutants and clinical isolates, and document an astounding variability of sites involved in this phenotype. Whereas point mutations are selected in the laboratory, clinical isolates display a mosaic structure of the affected PBP genes, the result of interspecies gene transfer and recombination events. Depending on the selective ß-lactam, different combinations of PBP genes and mutations within are involved in conferring resistance, and astoundingly in non-PBP genes as well.

Concerted and Sequential Proton Transfer Mechanisms in Water-Separated Acid-Base Encounter Pairs.

The proton transfer mechanisms involved inside aqueous, solvent-separated encounter complexes between phenol and carboxyl moieties are studied using ab initio molecular dynamics and computational time-resolved vibrational spectroscopy. This model framework can be viewed as a ground-state analog of the excited-state proton transfer reactions that have been actively investigated using ultrafast spectroscopy. Three qualitatively distinct proton transfer pathways are observed in the simulations. These can be described as direct concerted, direct sequential, and through bulk transfers. The primary difference between the sequential and concerted mechanism is the involvement of a reaction intermediate in which the proton fluctuates for several picoseconds through the hydrogen bonds connecting donor and acceptor but resides primarily on an intervening water molecule in the encounter complex. These results contribute to our molecular level understanding of the diverse processes involved in proton transfer within water-separated encounter complexes.

Genome of Streptococcus oralis strain Uo5.

Streptococcus oralis, a commensal species of the human oral cavity, belongs to the Mitis group of streptococci, which includes one of the major human pathogens as well, S. pneumoniae. We report here the first complete genome sequence of this species. S. oralis Uo5, a high-level penicillin- and multiple-antibiotic-resistant isolate from Hungary, is competent for genetic transformation under laboratory conditions. Comparative and functional genomics of Uo5 will be important in understanding the evolution of pathogenesis among Mitis streptococci and their potential to engage in interspecies gene transfer.

A computational study of ultrafast acid dissociation and acid-base neutralization reactions. II. The relationship between the coordination state of solvent molecules and concerted versus sequential acid dissociation.

We investigate the role played by the coordination state of pre-existing water wires during the dissociation of moderately strong acids by means of first-principles molecular dynamics calculations. By preparing 2,4,6-tricyanophenol (calc. pKa∼0.5) in two different initial states, we are able to observe sequential as well as concerted trajectories of dissociation: On one hand, equilibrium dissociation takes place on a ∼50 ps timescale; proton conduction occurs through three-coordinated water wires in this case, by means of sequential Grotthus hopping. On the other hand, by preparing 2,4,6-tricyanophenol in a hydration state inherited from that of equilibrated phenol (calc. pKa=7.6), the moderately strong acid finds itself in a presolvated state from which dissociation can take place on a ∼1 ps timescale. In this case, concerted dissociation trajectories are observed, which consist of proton translocation through two intervening, four-coordinated, water molecules in 0.1-1.0 ps. The present results suggest that, in general, the mechanism of proton translocation depends on how the excess proton is injected into a hydrogen bond network. In particular, if the initial conditions favour proton release to a fourfold H-bonded water molecule, proton translocation by as much as 6-8 Šcan take place on a sub-picosecond timescale.