gebhart/patrepeval huggingface dataset:
Structural Basis and Targeting of the Interaction between Fibroblast Growth Factor-inducible 14 and Tumor Necrosis Factor-like Weak Inducer of Apoptosis (2013)

Deregulation of the TNF-like weak inducer of apoptosis (TWEAK)-fibroblast growth factor-inducible 14 (Fn14) signaling pathway is observed in many diseases, including inflammation, autoimmune diseases, and cancer. Activation of Fn14 signaling by TWEAK binding triggers cell invasion and survival and therefore represents an attractive pathway for therapeutic intervention. Based on structural studies of the TWEAK-binding cysteine-rich domain of Fn14, several homology models of TWEAK were built to investigate plausible modes of TWEAK-Fn14 interaction. Two promising models, centered on different anchoring residues of TWEAK (tyrosine 176 and tryptophan 231), were prioritized using a data-driven strategy. Site-directed mutagenesis of TWEAK at Tyr(176), but not Trp(231), resulted in the loss of TWEAK binding to Fn14 substantiating Tyr(176) as the anchoring residue. Importantly, mutation of TWEAK at Tyr(176) did not disrupt TWEAK trimerization but failed to induce Fn14-mediated nuclear factor κ-light chain enhancer of activated B cell (NF-κB) signaling. The validated structural models were utilized in a virtual screen to design a targeted library of small molecules predicted to disrupt the TWEAK-Fn14 interaction. 129 small molecules were screened iteratively, with identification of molecules producing up to 37% inhibition of TWEAK-Fn14 binding. In summary, we present a data-driven in silico study revealing key structural elements of the TWEAK-Fn14 interaction, followed by experimental validation, serving as a guide for the design of small molecule inhibitors of the TWEAK-Fn14 ligand-receptor interaction. Our results validate the TWEAK-Fn14 interaction as a chemically tractable target and provide the foundation for further exploration utilizing chemical biology approaches focusing on validating this system as a therapeutic target in invasive cancers.
Packaging Architecture for Fluidic Components in Microfluidic PCBs (2016)

We present a novel packaging architecture for fluidic surface mount components in microfluidic printed circuit boards (PCB)s. The package incorporates sacrificial layers to protect the fluid cavities and inlets/outlets to the component during mounting and integration on a microfluidic circuit board. In this paper we describe the general scheme to package and integrate microfluidic components such as valves, pumps, mixers, etc. in microfluidic PCBs. We also report the use of dry film photoresist as a possible protective sealant for fluidic openings on the package. As an example microfluidic packaged surface mount component, we introduce an optofluidic cell counter that can be soldered directly on a PCB and connected to a microfluidic system.
Spectral Dictionaries (2008)

Database search tools identify peptides by matching tandem mass spectra against a protein database. We study an alternative approach when all plausible de novo interpretations of a spectrum (spectral dictionary) are generated and then quickly matched against the database. We present a new MS-Dictionary algorithm for efficiently generating spectral dictionaries and demonstrate that MS-Dictionary can identify spectra that are missed in the database search. We argue that MS-Dictionary enables proteogenomics searches in six-frame translation of genomic sequences that may be prohibitively time-consuming for existing database search approaches. We show that such searches allow one to correct sequencing errors and find programmed frameshifts.
A second promoter provides an alternative target for therapeutic up-regulation of utrophin in Duchenne muscular dystrophy (1999)

Duchenne muscular dystrophy (DMD) is an inherited muscle-wasting disease caused by the absence of a muscle cytoskeletal protein, dystrophin. We have previously shown that utrophin, the autosomal homologue of dystrophin, is able to compensate for the absence of dystrophin in a mouse model of DMD; we have therefore undertaken a detailed study of the transcriptional regulation of utrophin to identify means of effecting its up-regulation in DMD muscle. We have previously isolated a promoter element lying within the CpG island at the 5' end of the gene and have shown it to be synaptically regulated in vivo. In this paper, we show that there is an alternative promoter lying within the large second intron of the utrophin gene, 50 kb 3' to exon 2. The promoter is highly regulated and drives transcription of a widely expressed unique first exon that splices into a common full-length mRNA at exon 3. The two utrophin promoters are independently regulated, and we predict that they respond to discrete sets of cellular signals. These findings significantly contribute to understanding the molecular physiology of utrophin expression and are important because the promoter reported here provides an alternative target for transcriptional activation of utrophin in DMD muscle. This promoter does not contain synaptic regulatory elements and might, therefore, be a more suitable target for pharmacological manipulation than the previously described promoter.
Bistable Alignment of Nematic Liquid Crystals Around Microscopic Posts (2004)

Abstract With conventional nematic liquid crystal displays there is only one orientation of the material that is stable without an applied field. In order to maintain an image the pixels have to be continually refreshed, placing an upper limit on the pixel count. Overcoming this requires having some memory within each pixel. To avoid putting an expensive transistor within every pixel one can design the display to be inherently bistable. Here we describe how micron-scale posts on a substrate can stabilize multiple orientations. By engineering the posts we have demonstrated a bistable display with long term memory. Keywords: BistabilityLiquid CrystalMicrostructureNematic
Electrical design for lateral junction photonic crystal lasers (2013)

We model conduction and free-carrier injection in laterally doped GaAs p-i-n diodes formed in one and twodimensional photonic crystal (PC) nanocavities. Finite element simulations show that the lateral geometry exhibits high electrical conductivity for a wide range of PC parameters and allows for precise control over current flow, enabling efficient carrier injection despite fast surface recombination. Thermal simulations indicate that the temperature increase during steady-state operation is only 3.3K in nanobeams and 0.29K in L3 defect nanocavities. The results affirm the suitability of lateral doping in PC devices and indicate criteria for further design optimization.
Conservative signal processing architectures for asynchronous, distributed optimization part I: General framework (2014)

This paper presents a framework for designing a class of distributed, asynchronous optimization algorithms, realized as signal processing architectures utilizing various conservation principles. The architectures are specifically based on stationarity conditions pertaining to primal and dual variables in a class of generally nonconvex optimization problems. The stationarity conditions, which are closely related to the principles of stationary content and co-content that can be derived using Tellegen's theorem in electrical networks, are in particular transformed via a linear change of coordinates to obtain a set of linear and nonlinear maps that form the basis for implementation. The resulting algorithms specifically operate by processing a linear superposition of primal and dual decision variables using the associated maps, coupled using synchronous or asynchronous delay elements to form a distributed system. A table is provided containing specific example elements that can be assembled to form various optimization algorithms directly from the corresponding problem statements.
A hydrothermal atomic force microscope for imaging in aqueous solution up to 150 °C (1998)

We present the design of a contact atomic force microscope (AFM) that can be used to image solid surfaces in aqueous solution up to 150 °C and 6 atm. The main features of this unique AFM are: (1) an inert gas pressurized microscope base containing stepper motor for coarse advance and the piezoelectric tube scanner; (2) a chemically inert membrane separating these parts from the fluid cell; (3) a titanium fluid cell with fluid inlet–outlet ports, a thermocouple port, and a sapphire optical window; (4) a resistively heated ceramic booster heater for the fluid cell to maintain the temperature of solutions sourced from a hydrothermal bomb; and (5) mass flow control. The design overcomes current limitations on the temperature and pressure range accessible to AFM imaging in aqueous solutions. Images taken at temperature and pressure are presented, demonstrating the unit-cell scale (&lt;1 nm) vertical resolution of the AFM under hydrothermal conditions.
Application of Gram-Schmidt algorithm to optimum radar signal processing (1984)

The paper deals with the application of Gram-Schmidt decorrelation algorithm to the clutter cancellation and useful signal enhancement in radar signal processing. The proposed system architecture is an adaptive implementation of the well known optimum processor. The performance of the selected approach is evaluated and compared with that of the optimum one. As a general result, the adaptation time is a few tens of range cells and the losses are negligible. Finally, the hardware complexity is briefly considered
High performance micro-machined inductors on CMOS substrate (2005)

Using a combination of micromachining and three-dimensional (3-D) processing technologies, we have designed, fabricated, and tested inductors on CMOS grade Si substrate (10/spl sim/20 /spl Omega/-cm resistivity) which exhibit very high quality factor and high resonant frequency. A 1.2 nH inductor in this process achieves a record high quality factor of /spl sim/140 at 12GHz, with Q > 100 for frequencies between 8 to 20GHz. The technology to fabricate these inductors is based on one step deposition and electroplating of a stressed layered metal combination of Cr and Au and is fully compatible with CMOS technology.
Prevention of Recurrent Calcium Stone Formation with Potassium Citrate Therapy in Patients with Distal Renal Tubular Acidosis (1985)

Distal renal tubular acidosis is a common cause of intractable calcium nephrolithiasis. We examined the effect of oral potassium citrate therapy in 9 patients with incomplete distal renal tubular acidosis diagnosed on the basis of an abnormal response to an oral ammonium chloride load. Patients were studied during a control phase and after 3 months of potassium citrate treatment (60 to 80 mEq. daily). Potassium citrate caused a significant increase in urinary pH and urinary citrate, and a decrease in urinary calcium. The urinary relative saturation ratio of calcium oxalate significantly decreased during treatment, while that of brushite did not change. Potassium citrate also was shown to inhibit new stone formation. During a mean treatment period of 34 months none of the 9 patients had new stones, although 39.3 plus or minus 79.7 (standard deviation) stones per patient formed during the 3 years preceding treatment. The results support the potential clinical advantage of potassium citrate therapy in patients with distal renal tubular acidosis and recurrent calcium nephrolithiasis.
A Binary DNA Probe for Highly Specific Nucleic Acid Recognition (2006)

A new concept for nucleic acid probe design is reported. The extremely high selectivity of the probe is predetermined by cooperative hybridization of the two relatively short (10 nucleotide) DNA hairpin fragments to the analyte. A binary DNA probe fluorescently reports the presence of 0.5% of the analyte in excess amount of a single base substituted oligodeoxyribonucleotide and distinguishes single nucleotide substitutions at any position of a 20-mer oligonucleotide at room temperature.
Bottom-up fabrication of a multi-component nanopore sensor that unfolds, processes and recognizes single proteins (2020)

Abstract Transmembrane channels and pores have many biotechnological applications, notably in the single-molecule sequencing of DNA. Small synthetic nanopores have been designed using amphipathic peptides, or by assembling computationally designed transmembrane helices. The fabrication of more complex transmembrane devices has yet to be reported. In this work, we fabricated in two steps a multi-protein transmembrane device that addresses some of the main challenges in nanopore protein sequencing. In the first step, artificial nanopores are created from soluble proteins with toroid shapes. This design principle will allow fabricating a variety of nanopores for single-molecule analysis. In the second step one α-subuinit of the 20S proteasome from Thermoplasma acidophilum is genetically integrated into the artificial nanopore, and a 28-component nanopore-proteasome is co-assembled in E. coli cells. This multi-component molecular machine opens the door to two new approaches in protein sequencing, in which selected substrate proteins are unfolded, fed to into the proteasomal chamber and then identified by the nanopore sensor either as intact or fragmented polypeptides. The ability to integrate molecular devices directly onto a nanopore sensors allows creating next-generation protein sequencing devices, and will shed new lights on the fundamental processes of biological nanomachines.
Dual linear ion trap/orthogonal acceleration time‐of‐flight mass spectrometer with improved precursor ion selectivity (2005)

A new hybrid mass spectrometer based on dual linear ion traps (LITs) and an orthogonal acceleration time-of-flight mass spectrometer (oaTOF), that can achieve MS(n) analysis and high-mass-accuracy detection with high sensitivity, has been developed. Dual-LIT was necessary because, in a single LIT plus oaTOF combination, the LIT pressure favorable for high precursor selectivity in MS(n) analysis (less than 1 mTorr) was far different from an optimum damping pressure (50-100 mTorr) for efficient connection to the TOF mass spectrometer. A dual-LIT solved this problem of inconsistency of the optimum pressures by using the first LIT for MS(n) analysis and the second LIT for collisional damping. This dual-LIT/TOF instrument achieved high-sensitivity MS(n) analysis with high precursor-ion selectivity.
A Low-Voltage Large-Displacement Large-Force Inchworm Actuator (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Inchworm microactuators are popular in micropositioning applications for their long ranges. However, until now, they could not be considered for applications such as <emphasis emphasistype="boldital">in vivo</emphasis> biomedical applications because of their high input voltages. This paper reports on the modeling, design, fabrication, and testing of a new family of pull-in-based electrostatic inchworm microactuators which provides a solution to this problem. Actuators with only 7-V operating voltage are achieved with a <formula formulatype="inline"><tex Notation="TeX">$\pm 18\hbox{-}\mu\hbox{m}$</tex></formula> total range and a <formula formulatype="inline"><tex Notation="TeX">$\pm 30\hbox{-}\mu\hbox{N}$</tex></formula> output force. Larger operating voltage (16 V) actuators show even better results in force (<formula formulatype="inline"><tex Notation="TeX">$\pm 110\ \mu \hbox{N}$</tex></formula>) and range <formula formulatype="inline"><tex Notation="TeX">$(\pm 35\ \mu\hbox{m})$</tex></formula>. The actuator has an in-plane angular deflection conversion which provides a force-displacement tradeoff and allows us to set step sizes varying from few nanometers to few micrometers with a minor change in design. In this paper, we designed 1- and 4-<formula formulatype="inline"><tex Notation="TeX">$\mu\hbox{m}$</tex></formula> step-size devices. The actuator step size may change during the operation because of the slipping of the shuttle and the beam bending; however, our model successfully explains the reasons. One of our actuator prototypes has survived more than 25 million cycles without performance deterioration. The device is fabricated using the silicon-on-insulator-based multiuser MEMS process.<formula formulatype="inline"><tex Notation="TeX">$\hfill$</tex></formula>[2007-0146] </para>
Magnetooptical Recording with Optical Modulation and Magnetic Field Modulation (1991)

The magnetooptic recording characteristics of three types of DyFeCo films with a quadrilayer structure were measured using three recording methods: optical modulation, magnetic field modulation and the laser-off method. In the laser-off method, the laser power was lowered only while the magnetic field was changing. The transition metal (TM)-rich medium had the best carrier-to-noise (C/N) ratio when using the optical modulation method. When using magnetic field modulation, the C/N was lower than for optical modulation recording. The three media had similar characteristics when using magnetic field modulation. Adoption of the laser-off method improved the C/N and the magnetic field dependence of the C/N. In particular, the TM-rich medium exhibited the same C/N as when using optical modulation.
Acoustic measurements and modeling of air-filled, underwater resonator cavities (2013)

This paper investigates the near-resonance acoustical properties of submerged air-filled resonators intended for use in an underwater noise abatement system. These resonators are a potential alternative to encapsulated bubbles. The resonators are similar to Helmholtz resonators in shape and design, but without a neck, consisting of underwater inverted air-filled cavities with rigid walls. A finite element model was developed to investigate the acoustic behavior of the resonators near their resonance frequencies, and based on the results of the model, physical realizations of the resonators were designed and fabricated for testing. Experiments were performed with the resonators in a closed water-filled tank operated in the long wavelength limit [J. Acoust. Soc. Am. 132, 2039 (2012)], where their resonance frequencies and Q-factors were measured using the technique described by Leighton et al., [J. Acoust. Soc. Am. 112, 1366–1376 (2002)]. Comparison between the results from the measurements and modeling will be discussed. [Work supported by Shell Global Solutions.]
On the segmentation of text in videos (2002)

A new and robust multi-resolution approach of localizing and segmenting text in videos is proposed. The approach has been tested extensively on a large variety of video frame sizes such 352/spl times/240 up to 1920/spl times/1280 and a large representative set of video sequences such as home videos, newscasts, title sequences and commercials. 95% of the text bounding boxes in videos were localized correctly. 80% of all characters were segmented correctly, while 7.8% characters were damaged. 90% of the correctly segmented characters were recognized correctly by standard OCR software.
A new method for robust far-distance road course estimation in advanced driver assistance systems (2010)

An advanced method for road course estimation is presented. It is based on the state-of-the-art Kalman filter lane detection and allows for a robust sensor-based estimation of road courses in great distances. Only the parameters for the road course are estimated which results in a reduced parameter space and therewith more robustness. Instead of laterally displaced single feature points tangential structures are used as measurements in the filter model. Therefore the method is translation-invariant and applicable for all continuous differentiable road course models. As shown with video and radar input examples it is also sensor-independent and particularly suitable for sensor fusion approaches. For accuracy estimations an advanced method based on inertial navigation is used which is independent of lateral movements of the host vehicle and the road model.
Mask bias effects in e-beam cell projection lithography (1997)

We newly developed the mask bias method in electron beam (EB) cell projection lithography to improve the resolution and to increase the throughput. In this method, the open slits of EB mask are shrunk to reduce the ratio of open area in EB mask. This shrinkage decreases the Coulomb interaction effect and the proximity effect. This results that 0.14 micrometer L/S pattern can be resolved even at the maximum shot size (25 micrometer<SUP>2</SUP>) and so the writing time of 0.14 micrometer L/S pattern can be reduced by half.
Green Polymer Chemistry: Enzyme-Catalyzed Polymer Functionalization (2015)

Enzymes are “green” alternative to conventional chemical catalysts offering several advantages including high selectivity, high efficiency, ability to operate under mild conditions, recyclability and biocompatibility. This paper will first give an overview of the functionalization of natural and synthetic polymers. Subsequently our work related to the synthesis of symmetric and asymmetric telechelic polymers using Candida antarctica lipase B will be discussed. Quantitative functionalization of polyisobutylenes, polysiloxanes and poly(ethylene glycol)s (PEGs) was achieved. Multifunctional PEGs were also successfully produced. Controlled polycondensation of tetraethylene glycol and divinyl benzene yielded symmetric and asymmetric telechelic PEGs with high efficiency.
A crossbar-type high sensitivity ultraviolet photodetector array based on a one hole–one nanorod configuration via nanoimprint lithography (2011)

Single crystalline vertical ZnO nanorods were grown in a one hole-one rod configuration using a hydrothermal method with a patterned polymer template generated by nanoimprint lithography, allowing precise control over the position and density of the ZnO nanorods. An 8×8 ZnO nanorod-based ultraviolet photodetector array is demonstrated, in which a well-confined number of ZnO nanorods are sandwiched between crossbar-type platinum and indium tin oxide electrodes (e.g. 16 nanorods in a 2×2 µm2 area). A high photocurrent/dark current ratio of 3×10(3) at a reverse bias of 1.5 V under UV illumination at room temperature, a responsivity of 4381.4 A W(-1) at 365 nm, and an ultraviolet-to-visible rejection ratio of 83 are obtained and maintained, irrespective of pixel size. A uniform photoresponse is achieved in each of the pixels, indicating the scalability with this technique for fabricating an integrated UV photodetector array circuit.
Bioactivity-HiTES Unveils Cryptic Antibiotics Encoded in Actinomycete Bacteria (2019)

Bacteria harbor an immense reservoir of potentially new and therapeutic small molecules in the form of "silent" biosynthetic gene clusters (BGCs). These BGCs can be identified bioinformatically but are sparingly expressed under normal laboratory growth conditions, or not at all, and therefore do not produce significant levels of the corresponding small molecule product. Several methods have been developed for activating silent BGCs. A major limitation for nearly all methods is that they require genetic procedures and/or do not report on the bioactivity of the cryptic metabolite. We herein report "Bioactivty-HiTES", an approach that links the bioactivity of cryptic metabolites to their induction while at the same time obviating the need for genetic manipulations. Using this method, we detected induction of cryptic antibiotics in three actinomycete strains that were tested. Follow-up studies in one case allowed us to structurally elucidate two cryptic metabolites, elicited by the β-blocker atenolol in Streptomyces hiroshimensis, with selective growth-inhibitory activity against Gram-negative bacteria, notably Escherichia coli and Acinetobacter baumannii. Atenolol turned out to be a global elicitor of secondary metabolism, and characterization of additional cryptic metabolites led to the discovery of a novel naphthoquinone epoxide. Bioactivity-HiTES is a general, widely applicable procedure that will be useful in identifying cryptic bioactive metabolites in the future.