gebhart/patrepeval huggingface dataset:
Control over the fibrillization yield by varying the oligomeric nucleation propensities of self-assembling peptides (2020)

Self-assembling peptides are an exemplary class of supramolecular biomaterials of broad biomedical utility. Mechanistic studies on the peptide self-assembly demonstrated the importance of the oligomeric intermediates towards the properties of the supramolecular biomaterials being formed. In this study, we demonstrate how the overall yield of the supramolecular assemblies are moderated through subtle molecular changes in the peptide monomers. This strategy is exemplified with a set of surfactant-like peptides (SLPs) with different β-sheet propensities and charged residues flanking the aggregation domains. By integrating different techniques, we show that these molecular changes can alter both the nucleation propensity of the oligomeric intermediates and the thermodynamic stability of the fibril structures. We demonstrate that the amount of assembled nanofibers are critically defined by the oligomeric nucleation propensities. Our findings offer guidance on designing self-assembling peptides for different biomedical applications, as well as insights into the role of protein gatekeeper sequences in preventing amyloidosis.
Initialization of the BIMBO self-test method using binary inputs and outputs (2007)

This paper deals with the initialization of the BIMBO method, a deterministic identification method based on binary observation, for the (self-) test of integrated electronic and electromechanical systems, such as MEMS. Finding an adequate starting point for the parameter estimation algorithm may be crucial, depending on the chosen model parameterization. We show how this starting point may be obtained using only binary inputs and outputs and a few straightforward calculations. The practical implementation of this method only requires a one-bit digital-to-analog converter (DAC) and a one-bit analog-to-digital converter (ADC). This makes the proposed approach very amenable to integration and leads to no additional cost compared to the BIMBO method. We describe the method from a theoretical point of view, discuss its implementation and illustrate it in some idealized cases.
Design methodology and microdiagnostics development for a self-checking microprocessor (1989)

The conventional design of electronic circuits is intolerant to operational faults. Self-checking logic is aimed at online fault detection and can hence be incorporated to achieve reliable operation. In this paper, the design of a self-checking microprocessor is discussed. Self-checking strategies for different functional units are selectively and judiciously applied, and also modified wherever necessary, for the design of the register section, the arithmetic & logic unit and the control unit. A self-checking microprogrammed control unit, capable of supporting normal instruction execution concurrently with diagnostics, is developed. The design methodology has been applied to Intel's 8085A microprocessor as a case study to make it self-testing. Overheads involved have also been estimated.
A genome-wide screen for human salicylic acid (SA)-binding proteins reveals targets through which SA may influence development of various diseases (2019)

Salicylic acid (SA) is the major metabolite and active ingredient of aspirin; both compounds reduce pain, fever, and inflammation. Despite over a century of research, aspirin/SA's mechanism(s) of action is still only partially understood. Here we report the results of a genome-wide, high-throughput screen to identify potential SA-binding proteins (SABPs) in human HEK293 cells. Following photo-affinity crosslinking to 4-azidoSA and immuno-selection with an anti-SA antibody, approximately 2,000 proteins were identified. Among these, 95 were enriched more than 10-fold. Pathway enrichment analysis with these 95 candidate SABPs (cSABPs) revealed possible involvement of SA in multiple biological pathways, including (i) glycolysis, (ii) cytoskeletal assembly and/or signaling, and (iii) NF-κB-mediated immune signaling. The two most enriched cSABPs, which corresponded to the glycolytic enzymes alpha-enolase (ENO1) and pyruvate kinase isozyme M2 (PKM2), were assessed for their ability to bind SA and SA's more potent derivative amorfrutin B1 (amoB1). SA and amoB1 bound recombinant ENO1 and PKM2 at low millimolar and micromolar concentrations, respectively, and inhibited their enzymatic activities in vitro. Consistent with these results, low millimolar concentrations of SA suppressed glycolytic activity in HEK293 cells. To provide insights into how SA might affect various human diseases, a cSABP-human disorder/disease network map was also generated.
Generating spectral-efficient duobinary data format from silicon ring resonator modulators (2008)

Two types of ultra-small silicon microring-based duobinary modulators are proposed and compared. Required drive voltage is as low as 0.77 volt. at 10 Gb/s. Extinction ratio is ≫ 15 dB.
Transkriptionelle und Post-Transkriptionelle Regulation von Mcl–1 durch die p53-Familie (2012)

Die transkriptionell aktiven (TA-) Isoformen der p53-Familie induzieren Apoptose, wohingegen die dominant negativen (DN-) Isoformen die TA-vermittelte Apoptose inhibieren. Wir konnten zeigen, dass die Imbalance der TA- und DN-Isoformen der p53-Familie bei Überwiegen der DN-Isoformen zu Entstehung, Progression und Therapieresistenz des Hepatozellulären Karzinoms (HCC) führt. Darüber hinaus konnten wir zeigen, dass die Expression von Myeloid cell leukemia–1 (Mcl–1), ein anti-apoptotisches Mitglied der Bcl–2 Familie, mit einer verminderten Apoptosesensitivität und Chemoresistenz im HCC einhergeht.
Complete Polarimeter for Retinal Tissue Visualization (2005)

A Laser Diagnostic Technologies GDx Nerve Fiber Analyzer was modified to provide a complete Mueller Matrix polarization image of retinal tissue. Preliminary results demonstrate that interesting retardance, diattenuation, and depolarization features can be visualized.
Relevance Subject Machine: A Novel Person Re-identification Framework (2017)

We propose a novel method called the Relevance Subject Machine (RSM) to solve the person re-identification (re-id) problem. RSM falls under the category of Bayesian sparse recovery algorithms and uses the sparse representation of the input video under a pre-defined dictionary to identify the subject in the video. Our approach focuses on the multi-shot re-id problem, which is the prevalent problem in many video analytics applications. RSM captures the essence of the multi-shot re-id problem by constraining the support of the sparse codes for each input video frame to be the same. Our proposed approach is also robust enough to deal with time varying outliers and occlusions by introducing a sparse, non-stationary noise term in the model error. We provide a novel Variational Bayesian based inference procedure along with an intuitive interpretation of the proposed update rules. We evaluate our approach over several commonly used re-id datasets and show superior performance over current state-of-the-art algorithms. Specifically, for ILIDS-VID, a recent large scale re-id dataset, RSM shows significant improvement over all published approaches, achieving an 11.5% (absolute) improvement in rank 1 accuracy over the closest competing algorithm considered.
Scalability in IP-oriented Networks (Guest Editorial) (2003)

Presents the guest editorial for this issue of the publication.
Batch-Fabricated Substrate-Embedded Ka Band Self-Biased Circulators Using Screen-Printed Strontium Hexaferrite/PDMS Composite (2021)

In this work, we report a K <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">a</inf> band self-biased microwave circulator using a strontium hexaferrite (SrM) / polydimethylsiloxane (PDMS) nanocomposite fabricated with a low-temperature (70 °C), packaging-compatible, screen-printing process. The magnetic composite shows a ferromagnetic resonance frequency (FMR) of 44.3 GHz. A millimeter wave circulator completely embedded in a Rogers 5880 substrate with a thickness of 254 µm and a total area of 33 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> is designed, fabricated, and characterized. At an operational frequency of 37.2 GHz, the measured insertion loss (IL) and isolation (IS) of the circulator are 5.4 dB and 22.2 dB, respectively. The measurement results match with the simulation results from High Frequency Structure Simulator (HFSS) and compare favorably with those of other magnetic circulators from literature.
Selective Mechanical Transfer of Graphene from Seed Copper Foil Using Rate Effects (2015)

A very fast, dry transfer process based on mechanical delamination successfully effected the transfer of large-area, CVD grown graphene on copper foil to silicon. This has been achieved by bonding silicon backing layers to both sides of the graphene-coated copper foil with epoxy and applying a suitably high separation rate to the backing layers. At the highest separation rate considered (254.0 μm/s), monolayer graphene was completely transferred from the copper foil to the target silicon substrate. On the other hand, the lowest rate (25.4 μm/s) caused the epoxy to be completely separated from the graphene. Fracture mechanics analyses were used to determine the adhesion energy between graphene and its seed copper foil (6.0 J/m(2)) and between graphene and the epoxy (3.4 J/m(2)) at the respective loading rates. Control experiments for the epoxy/silicon interface established a rate dependent adhesion, which supports the hypothesis that the adhesion of the graphene/epoxy interface was higher than that of the graphene/copper interface at the higher separation rate, thereby providing a controllable mechanism for selective transfer of graphene in future nanofabrication systems such as roll-to-roll transfer.
Strategies to Stabilize Cell Penetrating Peptides forIn VivoApplications (2015)

In the era of biomedicines and engineered carrier systems, cell penetrating peptides (CPPs) have been established as a promising tool for therapeutic application. Likewise, other therapeutic peptides, successful in vivo application of CPPs will strongly depend on peptide stability, the bottleneck for this type of biodegradable molecules. In this review, the authors describe the current knowledge of the in vivo degradation for known CPPs and the different strategies available to provide a higher resistance to metabolic degradation while preserving cell penetration efficiency. Peptide stability can be improved by different means, either modifying the structure to make it unrecognizable to proteases, or preventing access of proteolytic enzymes by applying conformation restriction or shielding strategies.
Zur Rolle von EDA‐Komplexen bei kationischen Polymerisationen. VI[1]. Wechselwirkung von Halogenidionen mit organischen aπ‐Elektronenacceptoren (1979)

The Role of Donor‐Acceptor Complexes in Cationic Polymerisations. The Interaction of Halide Ions with Organic aπ‐Acceptors The anions of salts of the type Kat + X − (Kat +  Li + , Na + , Et 4 N + ; X −  Cl − , Br − , I − ) form donor‐acceptor complexes with organic a π‐acceptors. The long‐wave charge‐transfer absorption show a bathochrome shift with higher periodic numbers of X − and increasing electron affinity of the acceptors Acc. Strong acceptors form radical ions very rapidly with X  I and slowly with X  Br. Cl. The interactions in the system Kat + X − → Acc are influenced by solvents in a very complex way. As acceptors they interact preferably with the halide ion X − and, hence, reduce its donicity for the competing acceptor Acc. As donors they change the dissociation of the ion pair Kat + X − by solvation of the cation Kat + and influence in that indirect way also the donicity of X − for the acceptor Acc.
Biomineralization of a Self-Assembled Extracellular Matrix for Bone Tissue Engineering (2008)

Understanding how biomineralization occurs in the extracellular matrix (ECM) of bone cells is crucial to the understanding of bone formation and the development of a successfully engineered bone tissue scaffold. It is still unclear how ECM mechanical properties affect protein-mineral interactions in early stages of bone mineralization. We investigated the longitudinal mineralization properties of MC3T3-E1 cells and the elastic modulus of their ECM using shear modulation force microscopy, synchrotron grazing incidence X-ray diffraction (GIXD), scanning electron microscopy, energy dispersive X-ray spectroscopy, and confocal laser scanning microscopy (CLSM). The elastic modulus of the ECM fibers underwent significant changes for the mineralizing cells, which were not observed in the nonmineralizing cells. On substrates conducive to ECM network production, the elastic modulus of mineralizing cells increased at time points corresponding to mineral production, whereas that of the nonmineralizing cells did not vary over time. The presence of hydroxyapatite in mineralizing cells and the absence thereof in the nonmineralizing ones were confirmed by GIXD, and CLSM showed that a restructuring of actin occurred only for mineral-producing cells. These results show that the correct and complete development of the ECM network is required for osteoblasts to mineralize. This in turn requires a suitably prepared synthetic substrate for bone development to succeed in vitro.
Inflammatory bowel disease and hereditary nonpolyposis colorectal cancer: Is there a genetic link? (1998)

GASTROENTEROLOGY 1998;114:608-609
Nanophotonics Over Macroscopic Scales and its Associated Fabrication Challenges (2014)

In nanophotonics, we create material-systems which are structured at length-scales smaller than the wavelength of light. When light propagates inside such effective materials, numerous novel and exciting phenomena can emerge, enabling a variety of novel applications. However, in order to make use of these opportunities for many real-world applications of interest, one has to have the ability to implement nanophotonic structures over large scales. Printing techniques are often useful for implementation of such structures, especially when the wavelength of interest is sufficiently long. In this talk, I will present some of our recent theoretical and experimental progress in exploring these opportunities, as well as novel physics phenomena that emerges in this process.
Compact organic vapor jet printing print head (2023)

A first device is provided. The first device includes a print head, and a first gas source hermetically sealed to the print head. The print header further includes a first layer comprising a plurality of apertures, each aperture having a smallest dimension of 0.5 to 500 microns. A second layer is bonded to the first layer. The second layer includes a first via in fluid communication with the first gas source and at least one of the apertures. The second layer is made of an insulating material.
Performance of Polarimetric Beamformers for Phased Array Radio Telescopes (2011)

The results of four recently introduced beamforming schemes for phased array systems are discussed, each of which is capable to provide high sensitivity and accurate polarimetric performance of array-based radio telescopes. Ideally, a radio polarimeter should recover the actual polarization state of the celestial source, and thus compensate for unwanted polarization degradation effects which are intrinsic to the instrument. In this paper, we compare the proposed beamforming schemes through an example of a practical phased array system (APERTIF prototype) and demonstrate that the optimal beamformer, the max-SLNR beamformer, the eigenvector beamformer, and the bi-scalar beamformer are sensitivity equivalent but lead to different polarization state solutions, some of which are sub-optimal.
Raw data for "20Gbps silicon lateral MOS-Capacitor electro-optic modulator" (2017)

This dataset contains the raw data used for the figures in the paper Kapil Debnath, David J. Thomson, Weiwei Zhang, Ali Z Khokhar, Callum Littlejohns, James Byers, Lorenzo Mastronardi, Muhammad K. Husain, Fredric Y. Gardes, Graham T. Reed, and Shinichi Saito '20Gbps silicon lateral MOS-Capacitor electro-optic modulator' in CLEO Laser Science to Photonic Applications 2018. Conference on Lasers and Electro-optics 2018, San Jose, United States, 13-18 May.Abstract: This work presents an experimental demonstration of a 500µm long MZI carrier accumulation type modulator based on lateral MOS-capacitor integration on a silicon platform. A modulation efficiency (VπLπ) of 1.53V-cm, moderate modulation speed of 20Gbit-s-1 and extinction ratio of 3.65dB have been obtained.
Power-aware operand delivery (2007)

Based on operand delivery, existing microprocessors can be categorized into architected register file (ARF) or physical register file (PRF) machines, both with or without payload RAM (PL). Though many previous generation microprocessors use a PRF without PL, the trend of newer microprocessors targeting lower power environments seem to be moving towards ARF with PL. We quantitatively analyze power consumption of different machine styles: ARF with PL, ARF without PL, PRF with PL, and PRF only machine. Our result shows that PRF without PL consumes the least amount of power and is fundamentally the best approach for building power-aware out-of-order microprocessors.
Transport limits in high-speed quantum well lasers (1992)

Quantum well (QW) lasers have been shown to have a larger differential gain than bulk lasers, but the modulation bandwidths reported in QW lasers have only recently been comparable with those of bulk lasers.1-3 This has led to proposals that the carrier transport across the separate confinement heterostructure (SCH) of the laser may have an adverse affect on the modulation bandwidth of quantum well lasers.4,5
HIV-1 Conserved Mosaics Delivered by Regimens with Integration-Deficient DC-Targeting Lentiviral Vector Induce Robust T Cells (2017)

To be effective against HIV type 1 (HIV-1), vaccine-induced T cells must selectively target epitopes, which are functionally conserved (present in the majority of currently circulating and reactivated HIV-1 strains) and, at the same time, beneficial (responses to which are associated with better clinical status and control of HIV-1 replication), and rapidly reach protective frequencies upon exposure to the virus. Heterologous prime-boost regimens using virally vectored vaccines are currently the most promising vaccine strategies; nevertheless, induction of robust long-term memory remains challenging. To this end, lentiviral vectors induce high frequencies of memory cells due to their low-inflammatory nature, while typically inducing only low anti-vector immune responses. Here, we describe construction of novel candidate vaccines ZVex.tHIVconsv1 and ZVex.tHIVconsv2, which are based on an integration-deficient lentiviral vector platform with preferential transduction of human dendritic cells and express a bivalent mosaic of conserved-region T cell immunogens with a high global HIV-1 match. Each of the two mosaic vaccines was individually immunogenic. When administered together in heterologous prime-boost regimens with chimpanzee adenovirus and/or poxvirus modified vaccinia virus Ankara (MVA) vaccines to BALB/c and outbred CD1-Swiss mice, they induced a median frequency of over 6,000 T cells/10<sup>6</sup> splenocytes, which were plurifunctional, broadly specific, and cross-reactive. These results support further development of this vaccine concept.
An Integrated System for Transmission Electron Microscopy. (2000)

Abstract Macromolecular microscopy is becoming an increasingly important tool for structural biology. The development of improved capabilities for three-dimensional electron microscopy is critical for optimal progress in emerging integrative research in molecular cell biology. These techniques currently suffer from several severe disadvantages related to the tremendous time and effort required to acquire and analyze the data. For several years we have been developing software for automated and intelligent acquisition of transmission electron micrographs [1,2,3]. Our overall goal is to develop a system for rapid and routine structure determination of macromolecular assemblies from specimens preserved in vitreous ice. Ultimately we plan to develop an integrated system that can produce an electron density map of a structure within a few hours of inserting a specimen into the electron microscope. With this goal in mind it is essential that the images be acquired using a digital camera rather than film.
Epitaxy of SrTiO3 on Silicon: The Knitting Machine Strategy (2016)

International audience
ng Optical Emission Spectroscopy in (2013)

A hybrid partial least squares-suppor (PLS-SVM) model of optical emission s proposed and successfully demonstrat endpoint detection of through silicon v using the Bosch process. Accurate res TSVs with diameters of 80 µm and 25 µ
Reciprocal and real space maps for EMCD experiments (2009)

Electron magnetic chiral dichroism (EMCD) is an emerging tool for quantitative measurements of magnetic properties using the transmission electron microscope (TEM), with the possibility of nanometer resolution. The geometrical conditions, data treatment and electron gun settings are found to influence the EMCD signal. In this article, particular care is taken to obtain a reliable quantitative measurement of the ratio of orbital to spin magnetic moment using energy filtered diffraction patterns. For this purpose, we describe a method for data treatment, normalization and selection of mirror axis. The experimental results are supported by theoretical simulations based on dynamical diffraction and density functional theory. Special settings of the electron gun, so called telefocus mode, enable a higher intensity of the electron beam, as well as a reduction of the influence from artifacts on the signal. Using these settings, we demonstrate the principle of acquiring real space maps of the EMCD signal. This enables advanced characterization of magnetic materials with superior spatial resolution.
Exposure to non-therapeutic INR in a high risk cardiovascular patient: potential hazard reduction with genotype-guided warfarin (Coumadin) dosing. (2010)

A case to illustrate the utility of genetic screening in warfarin (Coumadin) management is reported. A 45 year-old woman of Puerto Rican ancestry was admitted to the emergency room twice within one month with chest pain. She was diagnosed with congestive heart failure, which was stabilized both times. At her second release, warfarin therapy was initiated at 5 mg/ day to prevent thrombus formation and was lowered to 3.75 mg/day at day 7 by her primary physician. International Normalized Ratio (INR) test results in the follow-up period at days 1, 7, and 10 of warfarin therapy were 4.5, 6.5, and 7.3, respectively-far in excess of the therapeutic range, despite the lower dosage in effect from day 7 onward. The patient achieved target INR over the next 43 days after downward adjustment of the dose to a dose of 1.5 mg/day by trial and error. DNA-typing specific for the CYP2C9*2,*3,*4,*5,*6 alleles and seven variants in the VKORC1 gene, including the VKORC1-1639 G > A polymorphism, revealed the presence of combinatorial CYP2C9*2/*3 and VKORC1-1639 G/A genotypes in this patient. Entering the patient's demographic and genotype status data into independent algorithms available in the public domain to predict effective warfarin dose yielded predicted doses which ranged from 1.5 to 1.8 mg/day. Notably, the prediction of 1.5 mg/day, which was generated by the online resource www.warfarindosing.org, coincided with the patient's actual effective warfarin dose. We conclude that the rapid rise in INR observed upon the initiation of warfarin therapy and the final effective warfarin dose of 1.5 mg/day, are attributable in some part to the presence of two minor alleles in CYP2C9, which together significantly reduce warfarin metabolism. Warfarin genotyping can therefore inform the clinician of the predicted effective warfarin dose. The results highlight the potential for warfarin genetic testing to improve patient care.