gebhart/patrepeval huggingface dataset:
Von Plattformen zu miRNA-Biomarkern : Methoden zur miRNA-Molekulardiagnostik (2018)

An obvious way to improve human healthcare is to develop new and more effective drugs.&#13;\nAnother opportunity is however to develop solutions that allow to utilize the available&#13;\ndrugs better. This includes more accurate and early diagnosis of pathologies, improved&#13;\ntherapy selection as well as digital and patient centric solutions in healthcare systems.&#13;\nEspecially in molecular diagnostics new biomarkers have been developed and partially&#13;\nshown promising results in terms of improving patient care. In this work I describe the&#13;\ndevelopment of respective platform techniques, biomarkers and computational solutions&#13;\nduring my PhD thesis.&#13;\nFirst, I briefly introduce the concept of a flexible microarray platform and assays, such as&#13;\nthe MPEA assay, tailored for the fast and efficient quantification of miRNA signatures.&#13;\nThen, I describe how we made use of respective platforms along with computational&#13;\nsolutions to improve the understanding of physiological and pathophysiological&#13;\nprocesses. Further, I present results on my efforts to develop new molecular diagnostic&#13;\nbiomarkers based on circulating miRNAs. Here, my special focus was in cancer (most&#13;\nimportantly lung cancer) and diseases affecting the Central Nervous System (most&#13;\nimportantly Multiple Sclerosis, Alzheimer’s Disease and Parkinson’s Disease). Together&#13;\nwith the supervisors of my thesis I was among the first researchers worldwide to&#13;\nrecognize that small non-coding RNAs (most importantly microRNAs) measured from&#13;\nbody fluids have a great potential as biomarkers. An obvious advantage to messenger&#13;\nRNAs is the small length of the molecules of only 17-22 nucleotides. This makes&#13;\nmicroRNAs stable in vivo but also in vitro.&#13;\nFinally, I will mention recent developments in patient care. The current trend is clearly&#13;\nthe digitalization of central parts of healthcare. This affects all stakeholders in the&#13;\nhealthcare system, most importantly medical doctors and patients. Especially patient&#13;\nempowerment and self-containment of medical data is becoming more important. Again,&#13;\nMultiple Sclerosis is used as an example. But also for physicians, computational tools have&#13;\nto be implemented to support them in making treatment decisions from highly complex&#13;\ndata. In sum, my thesis describes the road from developing a molecular diagnostic&#13;\nplatform over the research on biomarkers for detecting disease in time towards holistic&#13;\ncomputational solutions to improve patient care.
Micromirror fabrication for co-packaged optics using 3D nanoimprint technology (2022)

Co-packaged optics (CPO) is a key technology for addressing power bottlenecks in datacenters by integrating optical and electrical components and replacing electrical wiring with optical links. In the CPO module where silicon chips are embedded on the substrate and polymer waveguides are integrated as optical connections, a pair of 3D micromirrors can achieve low-loss and wideband optical coupling from silicon photonics to polymer waveguides. The shape of the polymer micromirror patterned by grayscale photo lithography depends on process conditions and requires high fabrication accuracy. In this study, photonanoimprint technology is adopted for stable micromirror fabrication. The imprint process for a polymer micromirror was considered from a hyperelastic analysis using the finite element method. The master mold was prepared using grayscale lithography with photosensitive polyimide as a template of a polydimethylsiloxane (PDMS) replica mold. The micromirror fabrication was demonstrated on a 4-in. silicon wafer. By imprinting into a guide groove structure with a PDMS replica mold, over 30 μm-height micromirrors were stably obtained multiple times by a step-and-repeat imprint. The linear part of the patterned mirror by the imprint process was more than 23.5 μm for four times imprinting, and the fabricated mirror shape was improved compared with grayscale lithography. The total height misalignment is 5 μm for 12 mirrors in four imprints, and 70% coupling efficiency in calculation was achieved.
An Ultra-High Speed Whole Slide Image Viewing System (2012)

The preliminary results of adapting the Sony PlayStation®3 (PS3®) as an ultra-high speed WSI viewing system were promising. The achieved speed is consistent with what would be needed to use WSI in daily practice.
ChemInform Abstract: Highly Regioselective Access to 7‐Substituted 1,4,7,10‐ Tetraazacyclododecane‐1‐carbaldehyde Derivatives: Synthetic Aspects and NMR Elucidation of the Structures. X‐Ray Crystal Structures of 7‐ Triphenylmethyl‐1,4,7,10‐tetraazacyclododecane‐1‐carbaldehyde (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: Stereoselective C‐C Bond Formation in Carbohydrates by Radical Cyclization Reactions. Part 5. Application for the Synthesis of α‐C(2)‐Branched Sugars. (1990)

Abstract Radical‐induced cyclization of the iodo carbohydrates (I) results in predominant formation of the fused furans (II).
Cyclic nucleotide- and inositol phosphate-gated ion channels in lobster olfactory receptor neurons. (1994)

The idea of having two second messenger pathways in olfaction, one mediated by cAMP and the other by inositol 1,4,5-trisphosphate, is supported by evidence that both second messengers directly activate distinct ion channels in the outer dendrite of lobster olfactory receptor neurons. Evidence that both types of second messenger-gated channels can occur in the same patch of membrane suggests that channels of both types can be expressed in one neuron. Evidence of more than one type of inositol phosphate-gated channel in this highly specialized region of the neuron furthers the idea that the output of individual olfactory receptor cells is regulated through multiple effectors and allows that effector diversity may contribute to functional diversity among olfactory receptor cells.
Observations on the Risk of Resistance With the Extended Use of Vancomycin (1998)

Use of vancomycin as the primary therapeutic agent in seriously burned patients was not associated with increased risk of VRE isolation or VRE infection.
Methodology for measuring conformation of solvent-disrupted protein subunits using T-WAVE ion mobility MS: An investigation into eukaryotic initiation factors (2009)

The methodology developed in the research presented herein makes use of chaotropic solvents to gently dissociate subunits from an intact macromolecular complex and subsequently allows for the measurement of collision cross section (CCS) for both the recombinant (R-eIF3k) and solvent dissociated form of the subunit (S-eIF3k). In this particular case, the k subunit from the eukaryotic initiation factor 3 (eIF3) was investigated in detail. Experimental and theoretical CCS values show both the recombinant and solvent disrupted forms of the protein to be essentially the same. The ultimate goal of the project is to structurally characterize all the binding partners of eIF3, determine which subunits interact directly, and investigate how subunits may change conformation when they form complexes with other proteins. Research presented herein is the first report showing retention of solution conformation of a protein as evidenced by CCS measurements of both recombinant and solvent disrupted versions of the same protein.
Capillary Electrophoresis and Electron Capture Dissociation Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Peptide Mixture and Protein Digest Analysis (2002)

Recent advances in peptide fragmentation techniques and mass spectrometry have opened up the possibility of combining peptide separation techniques, such as capillary electrophoresis (CE) and capillary liquid chromatography, with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and electron capture dissociation (ECD) in order to characterize peptide mixtures and protein digests. The results presented in this study show that CE/ECD-FT-ICR MS can be employed for peptide characterization in mixtures of standard peptides and in peptides resulting from the enzymatic digestion of proteins. Furthermore, the technique has potential for the identification and localization of post-translational modifications in peptides and proteins.
Extrasynaptic acetylcholine signaling through a muscarinic receptor regulates cell migration (2020)

Acetylcholine (ACh) promotes various cell migrations in vitro, but there are few investigations into this nonsynaptic role of ACh signaling in vivo. Here we investigate the function of a muscarinic receptor on an epithelial cell migration in <i>Caenorhabditis elegans</i> We show that the migratory gonad leader cell, the linker cell (LC), uses an M1/M3/M5-like muscarinic ACh receptor GAR-3 to receive extrasynaptic ACh signaling from cholinergic neurons for its migration. Either the loss of the GAR-3 receptor in the LC or the inhibition of ACh release from cholinergic neurons resulted in migratory path defects. The overactivation of the GAR-3 muscarinic receptor caused the LC to reverse its orientation through its downstream effectors Gαq/<i>egl-30</i>, PLCβ/<i>egl-8</i>, and TRIO/<i>unc-73</i> This reversal response only occurred in the fourth larval stage, which corresponds to the developmental time when the GAR-3::yellow fluorescent protein receptor in the membrane relocalizes from a uniform to an asymmetric distribution. These findings suggest a role for the GAR-3 muscarinic receptor in determining the direction of LC migration.
Staged Versus One-time Complete Revascularization With Percutaneous Coronary Intervention for Multivessel Coronary Artery Disease Patients Without ST-Elevation Myocardial Infarction (2013)

Patients with coronary artery disease without STEMI do not have significantly lower 3-year mortality rates with staged PCI than when they undergo CR in the index admission.
Biomimetic Tough Gels with Weak Bonds Unravel the Role of Collagen from Fibril to Suprafibrillar Self‐Assembly (2021)

Biological tissues rich in type I collagen exhibit specific hierarchical fibrillar structures together with remarkable mechanical toughness. However, the role of collagen alone in their mechanical response at different structural levels is not fully understood. Here, it is proposed to rationalize such challenging interplay from a materials science perspective through the subtle control of this protein self-assembly in vitro. It is relied on a spray-processing approach to readily use the collagen phase diagram and set a palette of biomimetic self-assembled collagen gels in terms of suprafibrillar organization. Their mechanical responses unveil the involvement of mechanisms occurring either at fibrillar or suprafibrillar scales. Noticeably, both modulus at early stage of deformations and tensile toughness probe the suprafibrillar organization, while durability under cyclic loading and stress relaxation reflect mechanisms at the fibril level. By changing the physicochemical environment, the interfibrillar interactions are modified toward more biomimetic mechanical responses. The possibility of making tissue-like materials with versatile compositions and toughness opens perspectives in tissue engineering.
9p24.1 alterations and programmed cell death 1 ligand 1 expression in early stage unfavourable classical Hodgkin lymphoma: an analysis from the German Hodgkin Study Group NIVAHL trial (2021)

High programmed cell death 1 ligand 1 (PD-L1) protein expression and copy number alterations (CNAs) of the corresponding genomic locus 9p24.1 in Hodgkin- and Reed-Sternberg cells (HRSC) have been shown to be associated with favourable response to anti-PD-1 checkpoint inhibition in relapsed/refractory (r/r) classical Hodgkin lymphoma (cHL). In the present study, we investigated baseline 9p24.1 status as well as PD-L1 and major histocompatibility complex (MHC) class I and II protein expression in 82 biopsies from patients with early stage unfavourable cHL treated with anti-PD-1-based first-line treatment in the German Hodgkin Study Group (GHSG) NIVAHL trial (ClinicalTrials.gov Identifier: NCT03004833). All evaluated specimens showed 9p24.1 CNA in HRSC to some extent, but with high intratumoral heterogeneity and an overall smaller range of alterations than reported in advanced-stage or r/r cHL. All but two cases (97%) showed PD-L1 expression by the tumour cells in variable amounts. While MHC-I was rarely expressed in >50% of HRSC, MHC-II expression in >50% of HRSC was found more frequently. No obvious impact of 9p24.1 CNA or PD-L1 and MHC-I/II expression on early response to the highly effective anti-PD-1-based NIVAHL first-line treatment was observed. Further studies evaluating an expanded panel of potential biomarkers are needed to optimally stratify anti-PD-1 first-line cHL treatment.
Power loss analysis with high primary current in magnetic energy harvesters (2015)

This paper presents an analysis of a magnetic energy harvester operating from a high power primary device with substantial current consumption. The existing `transfer window alignment (TWA)' technique that can significantly boost the amount of harvested power from magnetic fields is revisited with a high primary current scenario, revealing that any shifting of the transfer window from passive rectification can be suboptimal once the primary side current goes beyond a certain level. This is caused by undesirable development of flux due to parasitic elements in the circuits. A new model to predict such an issue is first derived, and its simulation results are provided. The estimation of the critical level in the primary side current is explored, and the optimal strategy of a magnetic energy harvester that operates with a wide range of primary current is discussed.
Rational coupled dynamics network manipulation rescues disease-relevant mutant cystic fibrosis transmembrane conductance regulator (2014)

Many cellular functions necessary for life are tightly regulated by protein allosteric conformational change, and correlated dynamics between protein regions has been found to contribute to the function of proteins not previously considered allosteric. The ability to map and control such dynamic coupling would thus create opportunities for the extension of current therapeutic design strategy. Here, we present an approach to determine the networks of residues involved in the transfer of correlated motion across a protein, and apply our approach to rescue disease-causative mutant cystic fibrosis transmembrane regulator (CFTR) ion channels, ΔF508 and ΔI507, which together constitute over 90% of cystic fibrosis cases. We show that these mutations perturb dynamic coupling within the first nucleotide-binding domain (NBD1), and uncover a critical residue that mediates trans-domain coupled dynamics. By rationally designing a mutation to this residue, we improve aberrant dynamics of mutant CFTR as well as enhance surface expression and function of both mutants, demonstrating the rescue of a disease mutation by rational correction of aberrant protein dynamics.
Compensation of nonlinear phase noise impairments through optical phase conjugation in long-haul transmission systems (2005)

Differential-quadrature phase-shift-keying (DQPSK) can, unlike on-off-keying (OOK), be impaired by nonlinear phase noise (NPN). It has been shown that optical phase conjugation (OPC) is an effective compensation scheme for NPN resulting from the ASE of EDFAs (ASE-NPN). In this paper we discuss the influence of NPN resulting from modulator imperfections (MJ-NPN). We show that MI-NPN can be compensated for through OPC, though shifts the optimum location of the OPC towards the middle of the transmission link.
Hole Mobility in Accumulation Mode Metal–Oxide–Semiconductor Field-Effect Transistors (2012)

The paper deals with the investigation of the mobility in accumulation mode p-channel metal–oxide–semiconductor field-effect transistors (p-MOSFETs). The mobility extracted following the conventional methodology used for the inversion mode p-MOSFETs is actually incorporating a component related to the silicon-on-insulator (SOI) layer. Thus, a very simple and efficient technique to remove the contribution coming from the SOI layer has been proposed. This ultimately led to the extraction of the hole mobility of the accumulation layer. Its study carried out for several doping concentrations revealed a universal behavior similar to the one of the inversion layer. To finish, the contribution of the SOI layer to the measured mobility has been done and revealed a linear trend with the doping concentration. As a result, a simple and very efficient modeling of the mobility in the accumulation mode p-MOSFETs, incorporating the contribution of both the channel and bulk regions, has been achieved.
<i>Burkholderia</i> of Plant-Beneficial Group are Symbiotically Associated with Bordered Plant Bugs (Heteroptera: Pyrrhocoroidea: Largidae) (2015)

A number of phytophagous stinkbugs (order Heteroptera: infraorder Pentatomomorpha) harbor symbiotic bacteria in a specific midgut region composed of numerous crypts. Among the five superfamilies of the infraorder Pentatomomorpha, most members of the Coreoidea and Lygaeoidea are associated with a specific group of the genus Burkholderia, called the "stinkbug-associated beneficial and environmental (SBE)" group, which is not vertically transmitted, but acquired from the environment every host generation. A recent study reported that, in addition to these two stinkbug groups, the family Largidae of the superfamily Pyrrhocoroidea also possesses a Burkholderia symbiont. Despite this recent finding, the phylogenetic position and biological nature of Burkholderia associated with Largidae remains unclear. Based on the combined results of fluorescence in situ hybridization, cloning analysis, Illumina deep sequencing, and egg inspections by diagnostic PCR, we herein demonstrate that the largid species are consistently associated with the "plant-associated beneficial and environmental (PBE)" group of Burkholderia, which are phylogenetically distinct from the SBE group, and that they maintain symbiosis through the environmental acquisition of the bacteria. Since the superfamilies Coreoidea, Lygaeoidea, and Pyrrhocoroidea are monophyletic in the infraorder Pentatomomorpha, it is plausible that the symbiotic association with Burkholderia evolved at the common ancestor of the three superfamilies. However, the results of this study strongly suggest that a dynamic transition from the PBE to SBE group, or vice versa, occurred in the course of stinkbug evolution.
ChemInform Abstract: Synthesis and anti‐HIV Activity of GS‐9148 (2′‐Fd4AP), a Novel Nucleoside Phosphonate HIV Reverse Transcriptase Inhibitor. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Early Lessons on Bundled Payment at an Academic Medical Center (2017)

Opportunities for savings under bundled payment may be greater for lower extremity joint arthroplasty than for other conditions.
Level crossing in liquids involving intermolecular electronic to vibrational energy transfer (1990)

The A′/A state lifetime of I2 in various deuterated hydrocarbon solvents has been determined from picosecond transient absorption spectra. The lifetime observed in the deuterated solvents is 2.0 times as long as that which has been measured in the corresponding undeuterated solvent. A mechanism involving intermolecular electronic to vibration energy transfer from the electronically excited I2 to the solvent is proposed to explain this effect and the overall trend of shorter lifetime with increasing density of CH stretching modes.
Chiral acyl anion equivalents: asymmetric synthesis of 11-deoxy-ent-prostaglandin intermediates (1981)

Conjugate addition of the chiral formyl anion equivalent p-tolyl p-tolylthiomethyl sulphoxide (+)-(S)-(1) to the cyclopentenone derivative (2a) leads to the adduct (3a) in 45% yield with high diastereoselectivity. Reduction of (3a) gives the dithioacetal (4a), an interesting optically pure intermediate in the synthesis of 11-deoxy-ent-prostanoids. The high selectivity, contrasting with a lower selectivity observed using cyclopentenone, is to be ascribed to more severe steric demands in the transition state.
Tunable graphene-based infrared reflectance filter having patterned nanoantenna layer and unpatterned graphene layer (2023)

An actively tunable optical filter can control the amplitude of reflected infrared light. The filter exploits the dependence of the excitation energy of plasmons in a continuous and unpatterned sheet of graphene, on the Fermi-level, which can be controlled by conventional electrostatic gating. An exemplary filter enables simultaneous modification of two distinct spectral bands whose positions are dictated by the device geometry and graphene plasmon dispersion. Within these bands, the reflected amplitude can be varied by over 15% and resonance positions can be shifted by over 90 cm−1. Electromagnetic simulations verify that tuning arises through coupling of incident light to graphene plasmons by a nanoantenna grating structure. Importantly, the tunable range is determined by a combination of graphene properties, device structure, and the surrounding dielectrics, which dictate the plasmon dispersion. Thus, the underlying design is applicable across a broad range of infrared frequencies.
Dispersion reduction in single-mode-fibre links (1985)

By combining lengths of single-mode fibre having different dispersion characteristics it is possible to reduce the overall dispersion at a given wavelength. This can be used to extend the section-length capability of dispersion-limited high-bit-rate systems.
Shield fields (2008)

We describe a unified representation of occluders in light transport and photography using shield fields: the 4D attenuation function which acts on any light field incident on an occluder. Our key theoretical result is that shield fields can be used to decouple the effects of occluders and incident illumination. We first describe the properties of shield fields in the frequency-domain and briefly analyze the "forward" problem of efficiently computing cast shadows. Afterwards, we apply the shield field signal-processing framework to make several new observations regarding the "inverse" problem of reconstructing 3D occluders from cast shadows -- extending previous work on shape-from-silhouette and visual hull methods. From this analysis we develop the first single-camera, single-shot approach to capture visual hulls without requiring moving or programmable illumination. We analyze several competing camera designs, ultimately leading to the development of a new large-format, mask-based light field camera that exploits optimal tiled-broadband codes for light-efficient shield field capture. We conclude by presenting a detailed experimental analysis of shield field capture and 3D occluder reconstruction.