gebhart/patrepeval huggingface dataset:
New Hybrid Algorithm for Maintaining Multivariate Quantitative Calibrations of a Near-Infrared Spectrometer (2002)

Our newly developed prediction-augmented classical least-squares/partial least-squares (PACLS/PLS) hybrid algorithm can correct for the presence of unmodeled sources of spectral variation such as instrument drift by explicitly incorporating known or empirically derived information about the unmodeled spectral variation. We have tested the ability of the new hybrid algorithm to maintain a multivariate calibration in the presence of instrument drift using a near-infrared (NIR) spectrometer (7500–11 000 cm −1 ) to quantitate dilute aqueous solutions containing glucose, ethanol, and urea. The spectral variations required to update the multivariate models for both short- and long-term drift were obtained using a single representative midpoint sample whose spectrum was repeatedly measured during collection of calibration data and during collection of separate validation sample spectra on three subsequent days. The performance of the PACLS/PLS model for maintaining a calibration was compared to PLS with subset recalibration, a method that has previously been applied to maintenance and transfer of calibration. Without drift corrections, both PACLS/PLS and PLS had poor predictive ability on sample spectra collected on subsequent days. Unlike previous maintenance of calibration studies that corrected for long-term drift only, the PACLS/PLS and PLS models demonstrated the best predictive abilities when short-term drift was also corrected. The PACLS/PLS hybrid model outperformed PLS with subset recalibration for near real-time predictions when instrument drift was determined from the repeat samples closest in time to the measurement of the unknown. Near real-time standard errors of prediction (SEPs) for the hybrid model were comparable to the cross-validated SEPs obtained with the original calibration model.
Built-in self-test of FPGA interconnect (2002)

We introduce the first BIST approach for testing the programmable routing network in FPGAs. Our method detects opens in, and shorts among, wiring segments, and also faults affecting the programmable switches that configure the FPGA interconnect. As a result, the BIST technique provides complete testing of interconnect faults.
A Hybrid, Variational 3D Smoother For Orphaned Shell Meshes. (2002)

In the present paper, a hybrid , variational, user-controlled, 3D mesh smoothing algorithm is proposed for orphaned shell meshes. The smoothing model is based on a variational combination of energy and equi-potential minimization theories. A variety of smoothing techniques for predicting a new location for the node-to-smooth are employed. Each node is moved according to a specific smoothing algorithm so as to keep element included angles, skew and distortion to a minimum. The variational smoother selection logic is based on nodal valency and element connectivity pattern of the node to smooth. Results show its consistency with both quadrilateral and quad-dominant meshes with a significant gain over conventional Laplacian schemes in terms of mesh quality, stability, user control and flexibility.
nD-dBPN: new self-routing permutation networks based on the de Bruijn digraphs (2002)

A new class of self-routing permutation networks based on the de Bruijn digraphs is proposed. The new networks are modular and scalable, and have an optimal crosspoint complexity. Compared to the crossbar switches of the same size, nD-dBPN uses less cross-points, and operates faster. With its optimal configuration, the new network uses O (N log N) cross-points compared to O (N/sup 2/) cross-points of the crossbar switches. The 2D-dBPN has the same crosspoint complexity as the 3-stage Clos network, but it has a constant control complexity compared to /spl Omega/(N/sup 3/2/) of the Clos network.
Ordered Nanostructures Made Using Chaperonin Polypeptides (2004)

A recently invented method of fabricating periodic or otherwise ordered nanostructures involves the use of chaperonin polypeptides. The method is intended to serve as a potentially superior and less expensive alternative to conventional lithographic methods for use in the patterning steps of the fabrication of diverse objects characterized by features of the order of nanometers. Typical examples of such objects include arrays of quantum dots that would serve as the functional building blocks of future advanced electronic and photonic devices. A chaperonin is a double-ring protein structure having a molecular weight of about 60 plus or minus 5 kilodaltons. In nature, chaperonins are ubiquitous, essential, subcellular structures. Each natural chaperonin molecule comprises 14, 16, or 18 protein subunits, arranged as two stacked rings approximately 16 to 18 nm tall by approximately 15 to 17 nm wide, the exact dimensions depending on the biological species in which it originates. The natural role of chaperonins is unknown, but they are believed to aid in the correct folding of other proteins, by enclosing unfolded proteins and preventing nonspecific aggregation during assembly. What makes chaperonins useful for the purpose of the present method is that under the proper conditions, chaperonin rings assemble themselves into higher-order structures. This method exploits such higher-order structures to define nanoscale devices. The higher-order structures are tailored partly by choice of chemical and physical conditions for assembly and partly by using chaperonins that have been mutated. The mutations are made by established biochemical techniques. The assembly of chaperonin polypeptides into such structures as rings, tubes, filaments, and sheets (two-dimensional crystals) can be regulated chemically. Rings, tubes, and filaments of some chaperonin polypeptides can, for example, function as nano vessels if they are able to absorb, retain, protect, and release gases or chemical reagents, including reagents of medical or pharmaceutical interest. Chemical reagents can be bound in, or released from, such structures under suitable controlled conditions. In an example of a contemplated application, a two-dimensional crystal of chaperonin polypeptides would be formed on a surface of an inorganic substrate and used to form a planar array of nanoparticles or quantum dots. Through genetic engineering of the organisms used to manufacture the chaperonins, specific sites on the chaperonin molecules and, thus, on the two-dimensional crystals can be chemically modified to react in a specific manner so as to favor the deposition of the material of the desired nanoparticles or quantum dots. A mutation that introduces a cysteine residue at the desired sites on a chaperonin of Sulfolobus shibatae was used to form planar arrays of gold nanoparticles (see figure).
Systemic Delivery of siRNA by Chimeric Capsid Protein: Tumor Targeting and RNAi Activity <i>in Vivo</i> (2012)

Recently, we reported that a chimeric capsid protein assembled into a macromolecular container-like structure with capsid shell and the resulting siRNA/capsid nanocarrier complexes efficiently suppressed RFP gene expression in the cell culture system. To extend RNAi to the in vivo applications, we here demonstrated that the siRNA/capsid nanocarrier complexes could have tumor-specific targeting ability in vivo as well as the increased stability of siRNA during body circulation. When systemically administered, our siRNA/capsid nanocarrier complexes delivered siRNA to tumor tissues and efficiently suppressed RFP gene expression in tumor-bearing mice. The enhanced longevity of siRNA in vivo could be explained by shielding effect derived from the capsid shell, where the encapsulated siRNAs are protected from nucleases in plasma. The multivalent RGD peptides on shell surface, as a result of self-assembling of capsid protein subunits, showed efficient delivery of siRNA to the tumor tissues in vivo, due to the RGD-mediated binding to integrin receptors overexpressed on tumor cells. Moreover, the prolonged in vivo circulation time of our siRNA/capsid nanocarrier complexes increased the potential to serve as siRNA carriers for optimal in vivo RNAi. These results provide an alternative approach to systemically deliver siRNA to the tumor sites as well as to enhance the stability of siRNA in vivo. Therefore, our results revealed the promising potential of our capsid nanocarrier system as a therapeutic siRNA carrier for cancer treatment.
Kinematic Analysis and Prototyping of a Partially Decoupled 4-DOF 3T1R Parallel Manipulator (2006)

A four-degree-of-freedom (DOF) 3T1R parallel manipulator is presented in this paper. This manipulator generates the family of so-called Schönflies motions, SCARA motions or 3T1R motions, in which the moving platform can translate in all directions and rotate around an axis of a fixed direction. The kinematic analysis of this architecture is presented, including the study of the constraint singular configurations, kinematic singular configurations, and the determination of the workspace. A prototype (the Quadrupteron) is also presented and demonstrated. The characteristics of the proposed prototype are (a) there is no constraint singularity, (b) its input-output equations are partially decoupled, (c) its kinematic singular configurations can be expressed using an equation in the angle of rotation of the moving platform and are thus easy to avoid at the design stage, and (d) its forward displacement analysis requires the solution of a univariate quadratic equation and can therefore be solved efficiently.
On Parameter Optimization and Reach Enhancement for the Improved Soft-Aided Staircase Decoder (2021)

The so-called improved soft-aided bit-marking algorithm was recently proposed for staircase codes (SCCs) in the context of fiber optical communications. This algorithm is known as iSABM-SCC. With the help of channel soft information, the iSABM-SCC decoder marks bits via thresholds to deal with both miscorrections and failures of hard-decision (HD) decoding. In this paper, we study iSABM-SCC focusing on the parameter optimization of the algorithm and its performance analysis, in terms of the gap to the achievable information rates (AIRs) of HD codes and the fiber reach enhancement. We show in this paper that the marking thresholds and the number of modified component decodings heavily affect the performance of iSABM-SCC, and thus, they need to be carefully optimized. By replacing standard decoding with the optimized iSABM-SCC decoding, the gap to the AIRs of HD codes can be reduced to 0.26-1.02 dB for code rates of 0.74-0.87 in the additive white Gaussian noise channel with 8-ary pulse amplitude modulation. The obtained reach increase is up to 22% for data rates between 401 Gbps and 468 Gbps in an optical fiber channel.
Identification of a New North American Hantavirus that Causes Acute Pulmonary Insufficiency (1995)

In May 1993, a pulmonary disease syndrome with novel clinical and epidemiologic features was identified in the southwestern United States. Healthy young adults developed a febrile prodrome followed by the rapid onset of often lethal acute respiratory distress. Although an infectious disease was suspected, intensive investigations initially failed to identify the causative agent. Multiple specialized microbiology laboratories at the National Center for Infectious Diseases (Centers for Disease Control and Prevention) applied classic serologic and culture methods as well as recently developed molecular biological techniques to samples collected from field investigations of the patients. Serologic tests detected the presence of an active immune response to a hantavirus. Reverse transcription and polymerase chain reaction amplification of RNA extracted from human tissues used primers designed from sequences of known hantaviruses to demonstrate genomic sequences of a novel hantavirus. Immunohistochemistry showed the presence of hantavirus antigens in the endothelium of lung tissues from patients and provided the final pathogenetic link to this group of viruses. These methods were concordantly positive in virtually all samples available from 18 patients with compatible clinical histories identified between January and July 1993. Test results of control subjects and searches for other agents in identified cases were negative. This newly recognized hantavirus causes a novel syndrome of acute pulmonary edema and shock; the pathogenesis is related to the presence of virus antigens in the pulmonary capillaries. The virus may be an important cause of severe and fatal disease presenting as adult respiratory distress syndrome in otherwise healthy persons.
The benefit of encoder cooperation in the presence of state information (2017)

In many communication networks, the availability of channel state information at various nodes provides an opportunity for network nodes to work together, or “cooperate.” This work studies the benefit of cooperation in the multiple access channel with a cooperation facilitator, distributed state information at the encoders, and full state information available at the decoder. Under various causality constraints, sufficient conditions are obtained such that encoder cooperation through the facilitator results in a gain in sum-capacity that has infinite slope in the information rate shared with the encoders. This result extends the prior work of the authors on cooperation in networks where none of the nodes have access to state information.
A Solid Electrolyte Valve for Micro/Nano-fluidics (2009)

This paper presents a nanovalve that uses electrodeposited nanostructures on a solid-state Ag-Ge-Se electrolyte to regulate liquid flow in micro/nano-fluidic channels. The valve uses the extremely rough surface morphology of electrodeposits to manipulate hydrophobicity, thereby closing and opening the nanovalves. Electrodeposited nanostructures can be grown and retracted on the electrolyte surface by applying voltages between 5V and -20V at room temperature. The nanovalve successfully closes and opens de-ionized water (DI) flow in a 20μm tall and 500μm wide microfluidic channel. Closing and opening a single nanovalve takes 5.3 min and 3 min, respectively, with a power consumption of 0.08 mW and 0.17mW, respectively. A triple nanovalve takes 3.8min and 2.5min to close and open, representing a 28% and 17% decrease in valving time as compared to a single nanovalve.
Structural Characterization of the HIV-1 Vpr N Terminus (2003)

The 96-residue human immunodeficiency virus (HIV) accessory protein Vpr serves manifold functions in the retroviral life cycle including augmentation of viral replication in non-dividing host cells, induction of G2 cell cycle arrest, and modulation of HIV-induced apoptosis. Using a combination of dynamic light scattering, circular dichroism, and NMR spectroscopy the N terminus of Vpr is shown to be a unique domain of the molecule that behaves differently from the C-terminal domain in terms of self-association and secondary structure folding. Interestingly, the four highly conserved proline residues in the N terminus are predicted to have a high propensity for cis/trans isomerism. Thus the high resolution structure and folding of a synthetic N-terminal peptide (Vpr1-40) and smaller fragments thereof have been investigated. 1H NMR data indicate Vpr1-40 possesses helical structure between residues 17-32, and for the first time, this helix, which is bound by proline residues, was observed even in aqueous solution devoid of any detergent supplements. In addition, NMR data revealed that all of the proline residues undergo a cis/ trans isomerism to such an extent that approximately 40% of all Vpr molecules possess at least one proline in a cis conformation. This phenomenon of cis/trans isomerism, which is unprecedented for HIV-1 Vpr, not only provides an explanation for the molecular heterogeneity observed in the full-length molecule but also indicates that in vivo the folding and function of Vpr should depend on a cis/trans-proline isomerase activity, particularly as two of the proline residues in positions 14 and 35 show considerable amounts of cis isomers. This prediction correlates well with our recent observation (Zander, K., Sherman, M. P., Tessmer, U., Bruns, K., Wray, V., Prechtel, A. T., Schubert, E., Henklein, P., Luban, J., Neidleman, J., Greene, W. C., and Schubert, U. (2003) J. Biol. Chem. 278, 43170-43181) of a functional interaction between the major cellular isomerase cyclophilin A and Vpr, both of which are incorporated into HIV-1 virions.
Spin valves using insulating cobalt ferrite exchange-spring pinning layers (2002)

Cobalt ferrite, CoFe2O4, thin films are explored as pinning layers for read sensor applications. High ΔR/R values, 12.8%, and high pinning fields, 1500 Oe, are observed. Unlike other coercivity based pinning layers, the soft properties of the free layer are not compromised. The properties of the cobalt ferrite layers are strongly dependent on the microstructure, which, in turn, depends on the reactive sputtering process.
Enabling layer 2 pathlet tracing through context encoding in software-defined networking (2014)

Troubleshooting Software-Defined Networks requires a structured approach to detect mistranslations between high-level intent (policy) and low-level forwarding behavior, and a flexible on-demand packet tracing tool is highly desirable on the data plane. In this paper, we introduce a Layer 2 path tracing utility named PathletTracer. PathletTracer offers an interface for users to specify multiple Layer 2 paths to inspect. Based on the Layer 2 paths of interests, PathletTracer then accounts paths with identifiable IDs, and installs a set of flow table entries into switches to imprint path IDs on the packets going through. PathletTracer re-uses some fields in packet headers such as the ToS octet for recording path IDs. To efficiently carry imprints using limited bits, PathletTracer uses an encoding algorithm motivated by the calling context encoding scheme in the software engineering domain. With k bits for encoding, PathletTracer is able to trace more than 2k paths simultaneously.
Performance enhancement of a dye-sensitized solar cell by peripheral aromatic and heteroaromatic functionalization in di-branched organic sensitizers (2018)

Suppression of back reaction and enhanced photoinduced intramolecular electron transfer through peripheral functionalization of triphenylamino based dibranched donor–acceptor dyes.
Extended Dynamic Range From a Combined Linear-Logarithmic CMOS Image Sensor (2006)

A CMOS image sensor that can operate in both linear and logarithmic mode is described. Two sets of data are acquired and combined in the readout path to render a high dynamic range image. This is accomplished in real-time without the use of frame memory. A dynamic range in excess of 120 dB was achieved at 26 frames/s (352times288-array). The system addresses the problems of high fixed pattern noise (FPN), slow response time, and low signal-to-noise ratio (SNR) in logarithmic mode. FPN has been effectively reduced by single and two parameter calibration, the latter achieving FPN of 2% per decade. A novel on-chip method of deriving a reference point has been implemented. The system is fabricated in a 0.18-mum 1P4M process and achieves a pixel pitch of 5.6 mum with 7 transistors per pixel
Design Of A Low Cost Diode-Laser-Based High Spectral Resolution Lidar (HSRL) (2016)

A concept for an eye-safe, semiconductor-based high spectral resolution lidar has been developed at the National Center for Atmospheric Research. The lidar operates at a wavelength of 780 nm near several rubidium absorption peaks. A rubidium vapor cell is used to block aerosol backscatter in one channel to provide a molecular backscatter measurement for calculating extinction and backscatter ratio (calibrated backscatter).
Vaccination with VLPs Presenting a Linear Neutralizing Domain of S. aureus Hla Elicits Protective Immunity (2020)

The pore-forming cytotoxin α-hemolysin, or Hla, is a critical <i>Staphylococcus aureus</i> virulence factor that promotes infection by causing tissue damage, excessive inflammation, and lysis of both innate and adaptive immune cells, among other cellular targets. In this study, we asked whether a virus-like particle (VLP)-based vaccine targeting Hla could attenuate <i>S. aureus</i> Hla-mediated pathogenesis. VLPs are versatile vaccine platforms that can be used to display target antigens in a multivalent array, typically resulting in the induction of high titer, long-lasting antibody responses. In the present study, we describe the first VLP-based vaccines that target Hla. Vaccination with either of two VLPs displaying a 21 amino-acid linear neutralizing domain (LND) of Hla protected both male and female mice from subcutaneous Hla challenge, evident by reduction in lesion size and neutrophil influx to the site of intoxication. Antibodies elicited by VLP-LND vaccination bound both the LND peptide and the native toxin, effectively neutralizing Hla and preventing toxin-mediated lysis of target cells. We anticipate these novel and promising vaccines being part of a multi-component <i>S. aureus</i> vaccine to reduce severity of <i>S. aureus</i> infection.
Silica waveguide electrooptic modulator employing push-pull electrodes (2004)

An unpoled electrooptic material is used as the cladding on a silica waveguide interferometer to form an optical modulator operating at microwave frequencies. Two electrodes in a push-pull configuration are shown to increase modulation depth.
P‐251L: <i>Late‐News Poster</i> : Miniature Wide‐Throw‐Angle Scanning Fiber Projection Display (2008)

Abstract Advances in mobile devices have enabled internet access and viewing of images and video, but small screens constrain the experience. We have developed a novel scanning fiber optical projector that is 1.07 mm in diameter and 13 mm long, and can project images at up to a 100° throw angle.
Codelet parsing: quadratic-time, sequential, adaptive algorithms for lossy compression (2003)

The codelet parsing algorithms were proposed for lossy compression. The algorithms sequentially parse a given source sequence into phrases, say, sourcelets, and map each sourcelet to a distorted phrase, say, a codelet, such that the pre-letter distortion between the two phrases does not exceed the desired distortion. The algorithms adaptively maintain a codebook, and do not require any a priori knowledge of the source statistics. The algorithms use approximate string matching and, at each epoch, carefully select one of the many approximately matching codewords to balance between the code rates in the current epoch versus the code rate from the resulting codebooks in future epochs. The algorithms are quadratic-time in the length of the source sequence and output a distorted sequence that can be naturally losslessly compressed using the Lempel-Ziv algorithm.