Rational development and application of biomarkers in the field of autoimmunity: A conceptual framework guiding clinicians and researchers.

Clear guidance is needed in the development and implementation of laboratory biomarkers in medicine. So far, no standardized phased approach is established that would pilot researchers and clinicians in this process. This leads to often incompletely validated biomarkers, which can bear the consequence of wrong applications, misinterpretation and inadequate management in the clinical context. In this conceptual article, we describe a stepwise approach to develop and comprehensively validate laboratory biomarkers. We will delineate basic steps including technical performance, pre-analytical issues, and biological variation, as well as advanced aspects of biomarker utility comprising interpretability, diagnostic and prognostic accuracy, and health-care outcomes. These aspects will be illustrated by using well-known examples from the field of immunology. The application of this conceptual framework will guide researchers in conducting meaningful projects to develop and evaluate biomarkers for the use in clinical practice. Furthermore, clinicians will be able to adequately interpret pre-clinical and clinical diagnostic literature and rationally apply biomarkers in clinical practice. Improvement in the implementation and application of biomarkers might relevantly change the management and outcomes of our patients for the better

Krotov: A Python implementation of Krotov's method for quantum optimal control

We present a new open-source Python package, krotov, implementing the quantum optimal control method of that name. It allows to determine time-dependent external fields for a wide range of quantum control problems, including state-to-state transfer, quantum gate implementation and optimization towards an arbitrary perfect entangler. Krotov's method compares to other gradient-based optimization methods such as gradient-ascent and guarantees monotonic convergence for approximately time-continuous control fields. The user-friendly interface allows for combination with other Python packages, and thus high-level customization

Mutation screening of the medium-chain acyl-CoA dehydrogenase (MCAD) and the ornithine transcarbamylase (OTC) genes by multiplex PCR amplification and sequencing

Background: Sequencing based mutation screening assays of genes encompassing large numbers of exons could be substantially optimized by multiplex PCR, which enables simultaneous amplification of many targets in one reaction. In the present study, a multiplex PCR protocol originally developed for fragment analysis was evaluated for sequencing based mutation screening of the ornithine transcarbamylase (OTC) and the medium-chain acyl-CoA dehydrogenase (MCAD) genes. Methods: Single exon and multiplex PCR protocols were applied to generate PCR templates for subsequent DNA sequencing of all exons of the OTC and the MCAD genes. For each PCR protocol and using the same DNA samples, 66 OTC and 98 MCAD sequence reads were generated. The sequences derived from the two different PCR methods were compared at the level of individual signal-to-noise ratios of the four bases and the proportion of high-quality base-signals. Results: The single exon and the multiplex PCR protocol gave qualitatively comparable results for the two genes. Conclusions: Many existing sequencing based mutation analysis protocols may be easily optimized with the proposed method, since the multiplex PCR protocol was successfully applied without any re-design of the PCR primers and other optimization steps for generating sequencing templates for the OTC and MCAD genes, respectively. Clin Chem Lab Med 2009;47:56-

Pairing in fermionic systems: A quantum information perspective

The notion of "paired" fermions is central to important condensed matter phenomena such as superconductivity and superfluidity. While the concept is widely used and its physical meaning is clear there exists no systematic and mathematical theory of pairing which would allow to unambiguously characterize and systematically detect paired states. We propose a definition of pairing and develop methods for its detection and quantification applicable to current experimental setups. Pairing is shown to be a quantum correlation different from entanglement, giving further understanding in the structure of highly correlated quantum systems. In addition, we will show the resource character of paired states for precision metrology, proving that the BCS states allow phase measurements at the Heisenberg limit.Comment: 23 pages, 4 figure

Iron–molybdenum-oxo complexes as initiators for olefin autoxidation with O2

The reaction between [(TPA)Fe(MeCN)2](OTf)2 and [nBu4N](Cp*MoO3) yields the novel tetranuclear complex [(TPA)Fe(μ-Cp*MoO3)]2(OTf)2, 1, with a rectangular [Mo–O–Fe–O–]2 core containing high-spin iron(II) centres. 1 proved to be an efficient initiator/(pre)catalyst for the autoxidation of cis-cyclooctene with O2 to give cyclooctene epoxide. To test, which features of 1 are essential in this regard, analogues with zinc(II) and cobalt(II) central atoms, namely [(TPA)Zn(Cp*MoO3)](OTf), 3, and [(TPA)Co(Cp*MoO3)](OTf), 4, were prepared, which proved to be inactive. The precursor compounds of 1, [(TPA)Fe(MeCN)2](OTf)2 and [nBu4N](Cp*MoO3) as well as Cp2*Mo2O5, were found to be inactive, too. Reactivity studies in the absence of cyclooctene revealed that 1 reacts both with O2 and PhIO via loss of the Cp* ligands to give the triflate salt 2 of the known cation [((TPA)Fe)2(μ-O)(μ-MoO4)]2+. The cobalt analogue 4 reacts with O2 in a different way yielding [((TPA)Co)2(μ-Mo2O8)](OTf)2, 5, featuring a Mo2O84− structural unit which is novel in coordination chemistry. The compound [(TPA)Fe(μ-MoO4)]2, 6, being related to 1, but lacking Cp* ligands failed to trigger autoxidation of cyclooctene. However, initiation of autoxidation by Cp* radicals was excluded via experiments including thermal dissociation of Cp2*

Endovascular repair of an actively hemorrhaging gunshot injury to the abdominal aorta

Endovascular stents have had a limited role in the management of trauma and vascular emergencies involving active hemorrhage. We describe a patient with delayed rupture of the infrarenal aorta after intra-abdominal sepsis caused the breakdown of a primary aortic repair. A stent-graft repair was performed, as concomitant injuries did not allow anterior access to the aorta. This report describes the successful endovascular repair of an actively hemorrhaging penetrating abdominal aortic injury. Endovascular approaches to aortic injuries may be valuable in settings where a hostile abdomen precludes traditional open repair

The Optimal Control Landscape for the Generation of Unitary Transformations with Constrained Dynamics

The reliable and precise generation of quantum unitary transformations is essential to the realization of a number of fundamental objectives, such as quantum control and quantum information processing. Prior work has explored the optimal control problem of generating such unitary transformations as a surface optimization problem over the quantum control landscape, defined as a metric for realizing a desired unitary transformation as a function of the control variables. It was found that under the assumption of non-dissipative and controllable dynamics, the landscape topology is trap-free, implying that any reasonable optimization heuristic should be able to identify globally optimal solutions. The present work is a control landscape analysis incorporating specific constraints in the Hamiltonian corresponding to certain dynamical symmetries in the underlying physical system. It is found that the presence of such symmetries does not destroy the trap-free topology. These findings expand the class of quantum dynamical systems on which control problems are intrinsically amenable to solution by optimal control.Comment: Submitted to Journal of Mathematical Physic

Trypanosoma brucei aquaglyceroporin 2 is a high-affinity transporter for pentamidine and melaminophenyl arsenic drugs and the main genetic determinant of resistance to these drugs.

OBJECTIVES: Trypanosoma brucei drug transporters include the TbAT1/P2 aminopurine transporter and the high-affinity pentamidine transporter (HAPT1), but the genetic identity of HAPT1 is unknown. We recently reported that loss of T. brucei aquaglyceroporin 2 (TbAQP2) caused melarsoprol/pentamidine cross-resistance (MPXR) in these parasites and the current study aims to delineate the mechanism by which this occurs. METHODS: The TbAQP2 loci of isogenic pairs of drug-susceptible and MPXR strains of T. brucei subspecies were sequenced. Drug susceptibility profiles of trypanosome strains were correlated with expression of mutated TbAQP2 alleles. Pentamidine transport was studied in T. brucei subspecies expressing TbAQP2 variants. RESULTS: All MPXR strains examined contained TbAQP2 deletions or rearrangements, regardless of whether the strains were originally adapted in vitro or in vivo to arsenicals or to pentamidine. The MPXR strains and AQP2 knockout strains had lost HAPT1 activity. Reintroduction of TbAQP2 in MPXR trypanosomes restored susceptibility to the drugs and reinstated HAPT1 activity, but did not change the activity of TbAT1/P2. Expression of TbAQP2 sensitized Leishmania mexicana promastigotes 40-fold to pentamidine and >1000-fold to melaminophenyl arsenicals and induced a high-affinity pentamidine transport activity indistinguishable from HAPT1 by Km and inhibitor profile. Grafting the TbAQP2 selectivity filter amino acid residues onto a chimeric allele of AQP2 and AQP3 partly restored susceptibility to pentamidine and an arsenical. CONCLUSIONS: TbAQP2 mediates high-affinity uptake of pentamidine and melaminophenyl arsenicals in trypanosomes and TbAQP2 encodes the previously reported HAPT1 activity. This finding establishes TbAQP2 as an important drug transporter

Regulation of the CRL4(Cdt2) ubiquitin ligase and cell-cycle exit by the SCF(Fbxo11) ubiquitin ligase

F-box proteins and DCAF proteins are the substrate binding subunits of the Skp1-Cul1-F-box protein (SCF) and Cul4-RING protein ligase (CRL4) ubiquitin ligase complexes, respectively. Using affinity purification and mass spectrometry, we determined that the F-box protein FBXO11 interacts with CDT2, a DCAF protein that controls cell-cycle progression, and recruits CDT2 to the SCF(FBXO11)complex to promote its proteasomal degradation. In contrast to most SCF substrates, which exhibit phosphodegron-dependent binding to F-box proteins, CDK-mediated phosphorylation of Thr464 present in the CDT2 degron inhibits recognition by FBXO11. Finally, our results show that the functional interaction between FBXO11 and CDT2 is evolutionary conserved from worms to humans and plays an important role in regulating the timing of cell-cycle exit.Fil: Rossi, Mario. University Of New York; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigación en Biomedicina de Buenos Aires; ArgentinaFil: Duan, Shanshan. University Of New York; Estados Unidos. Howard Hughes Medical Institute; Estados UnidosFil: Jeong, Yeon Tae. University Of New York; Estados UnidosFil: Horn, Moritz. Max Planck Institute for Biology of Ageing; Alemania. University of Cologne; AlemaniaFil: Saraf, Anita. The Stowers Institute for Medical Research; Estados UnidosFil: Florens, Laurence. The Stowers Institute for Medical Research; Estados UnidosFil: Washburn, Michael P.. The Stowers Institute for Medical Research; Estados Unidos. University of Kansas; Estados UnidosFil: Antebi, Adam. Max Planck Institute for Biology of Ageing; Alemania. University of Cologne; AlemaniaFil: Pagano, Michele. University Of New York; Estados Unidos. Howard Hughes Medical Institute; Estados Unido

Barrier-free subsurface incorporation of 3d metal atoms into Bi(111) films

By combining scanning tunneling microscopy with density functional theory it is shown that the Bi(111) surface provides a well-defined incorporation site in the first bilayer that traps highly coordinating atoms such as transition metals (TMs) or noble metals. All deposited atoms assume exactly the same specific sevenfold coordinated subsurface interstitial site while the surface topography remains nearly unchanged. Notably, 3d TMs show a barrier-free incorporation. The observed surface modification by barrier-free subsorption helps to suppress aggregation in clusters. It allows a tuning of the electronic properties not only for the pure Bi(111) surface, but may also be observed for topological insulators formed by substrate-stabilized Bi bilayers. © 2015 American Physical Society.DFG/SFB/616DFG/SPP/1601DFG/Pf238/3