gebhart/patrepeval huggingface dataset:
Metabolic design in amino acid producing bacterium<i>Corynebacterium glutamicum</i> (1995)

The Gram-positive bacterium Corynebacterium glutamicum is used for the industrial production of amino acids, e.g. of l-glutamate and l-lysine. In the last 10 years, genetic engineering and amplification of relevant structural genes have become fascinating methods for the construction of strains with desired genotypes. By cloning and expressing the various genes of the l-lysine pathway in C. glutamicum we could demonstrate that an increase of the flux of l-aspartate semialdehyde to l-lysine could be obtained in strains with increased dehydrodipicolinate synthase activity. By combined overexpression of deregulated aspartate kinase and dihydrodipicolinate synthase, the l-lysine secretion could be increased (10–20%). Recently we detected that in C. glutamicum two pathways exist for the synthesis of dl-diaminopimelate and l-lysine. Mutants defective in one pathway are still able to synthesize enough l-lysine for growth, but the l-lysine secretion is reduced to 50–70%. Using NMR spectroscopy, we could calculate how much of the l-lysine secreted into the medium is synthesized via each pathway. Amplification of the feedback inhibition-insensitive homoserine dehydrogenase and homoserine kinase in a high l-lysine overproducing strain enabled channelling of the carbon flow from the intermediate aspartate semialdehyde towards homoserine, resulting in a high accumulation of l-threonine. For a further flux from l-threonine to l-isoleucine the allosteric control of threonine dehydratase must be eliminated. In addition to all steps considered so far to be important for amino acid overproduction, the secretion into the culture medium also has to be noted. Recently it could be demonstrated that l-glutamate, l-lysine and l-isoleucine are not secreted via passive diffusion but via specific active carrier systems. Analysis of lysine-overproducing C. glutamicum strains indicates that this secretion carrier has a strong influence on the overproduction of this amino acid. Thus, for the construction of strong amino acid overproducing strains by using the gene cloning techniques, the overexpression of the genes for the export systems also seems necessary.
External-field-free magnetic biosensor (2014)

In this paper, we report a magnetic nanoparticle (MNP) detection scheme without the presence of any external magnetic field. The proposed magnetic sensor uses a patterned groove structure within the sensor so that no external magnetic field is needed to magnetize the MNPs. An example is given based on a giant magnetoresistance (GMR) sensing device with a spin valve structure. For this structure, the detection of MNPs located inside the groove and near the free layer is demonstrated under no external magnetic field. Micromagnetic simulations are performed to calculate the signal to noise level of this detection scheme. A maximum signal to noise ratio (SNR) of 18.6 dB from one iron oxide magnetic nanoparticle with 8 nm radius is achieved. As proof of concept, this external-field-free GMR sensor with groove structure of 200 nm × 200 nm is fabricated using a photo and an electron beam integrated lithography process. Using this sensor, the feasibility demonstration of the detection SNR of 9.3 dB is achieved for 30 μl magnetic nanoparticles suspension (30 nm iron oxide particles, 1 mg/ml). This proposed external-field-free sensor structure is not limited to GMR devices and could be applicable to other magnetic biosensing devices.
Test generation based diagnosis of device parameters for analog circuits (2001)

With the increasing complexity of manufacturing processes and the shrinking of device geometries, the performance metrics of integrated circuits (ICs) are becoming increasingly sensitive to random fluctuations in the manufacturing process. We propose a diagnosis methodology that can be used to infer the cause(s) of variations in performance of analog ICs. The methodology consists of (a) a device parameter computation technique which is used to compute the device parameters of an IC from measurements made on it and (b) a cause-effect analysis module that is used to compute the cause of the variation in performance metrics of a given set of ICs. Simulation results to demonstrate the effectiveness of the technique are presented.
Fibrodysplasia ossificans progressiva: mechanisms and models of skeletal metamorphosis (2012)

Fibrodysplasia ossificans progressiva (FOP; MIM #135100) is a debilitating genetic disorder of connective tissue metamorphosis. It is characterized by malformation of the great (big) toes during embryonic skeletal development and by progressive heterotopic endochondral ossification (HEO) postnatally, which leads to the formation of a second skeleton of heterotopic bone. Individuals with these classic clinical features of FOP have the identical heterozygous activating mutation (c.617G>A; R206H) in the gene encoding ACVR1 (also known as ALK2), a bone morphogenetic protein (BMP) type I receptor. Disease activity caused by this ACVR1 mutation also depends on altered cell and tissue physiology that can be best understood in the context of a high-fidelity animal model. Recently, we developed such a knock-in mouse model for FOP (Acvr1(R206H/+)) that recapitulates the human disease, and provides a valuable new tool for testing and developing effective therapies. The FOP knock-in mouse and other models in Drosophila, zebrafish, chickens and mice provide an arsenal of tools for understanding BMP signaling and addressing outstanding questions of disease mechanisms that are relevant not only to FOP but also to a wide variety of disorders associated with regenerative medicine and tissue metamorphosis.
Theoretical and experimental investigations of a polyalkylated-thieno[3,2-b]thiophene semiconductor (2008)

Theoretical and experimental investigations were performed for the organic semiconductor poly(3,6-dialkylthieno[3,2-b]thiophene-co-thieno[3,2-b]thiophene) (PATT). The properties of PATT were investigated with density functional calculations, x-ray diffraction, and differential scanning calorimetry. In PATT the backbone is constructed such that its alkyl side-chain separations are intermediate between those exhibited by poly(3-hexylthiophene) and poly(2,5-bis(3- alkylthiophen-2-yl)thieno[3,2-b]thiophene). An objective is to test whether such an intermediate side-chain separation leads to increased bonding strength between layers and perhaps promotes improved crystalline order and hole mobility. Measurements of hole mobility in solution processed thin film transistors employing PATT as the semiconductor indicate a mobility of 0.024 cm2/V s. Density functional calculations predict that the planar conjugated backbone of PATT is tilted. The driving force for tilting, a structural feature exhibited by many organic semiconductors, is shown to be electrostatic energy reduction.
Power-Gating Schemes for Ultra-Thin SOI (UTSOI) Circuits in Hybrid SOI-Epitaxial CMOS Structures (2006)

Several novel schemes of implementing MTCMOS circuits in hybrid UTSOI-epitaxial CMOS structures are proposed and analyzed through comprehensive circuit simulations. The schemes offer intrinsic high circuit density and facilitate header/footer body biasing techniques for performance enhancement and leakage reduction. The effectiveness in improving active-mode performance, and reducing virtual supply bounce and standby leakage power is demonstrated
Slit-enabled linear-array photoacoustic tomography with near isotropic spatial resolution in three dimensions (2015)

Due to its unique capability of visualizing optical absorption in deep tissues, photoacoustic tomography is increasingly used in biomedical imaging. Among various types of transducer arrays, the linear array is perhaps the most widely used in photoacoustic tomography because it is commercially available and readily allows ultrasound imaging. However, the three-dimensional imaging capability of a linear array is limited due to its poor elevational resolution. While various scanning schemes have been proposed to address this problem, they all suffer from long scanning time to the best of our knowledge. To address this issue, we introduce slit-enabled three-dimensional photoacoustic tomography. The metal slit, placed at the array focus, causes the incoming photoacoustic waves to diffract along the elevation direction and, hence, significantly improves the elevation detection aperture and resolution. We tested the new system in both phantoms and animals. The slit improves the elevation resolution by 10 times without compromising scanning time.
Somatostatin analogs with improved oral bioavailability. (1986)

Cyclic hexapeptide analogs of somatostatin with insulin, glucagon, and growth hormone (GH) release inhibitory potencies of 50-200 times those of somatostatin have been synthesized. Replacement of the Phe-7 residue with histidine has resulted in increased oral bioavailability and duration of action. Metabolic degradation of L-Trp containing analogs upon oral administration has also been overcome by incorporation of histidine. The all L-amino acid containing analog cyclo(NMePhe-His-Trp-Lys-Val-Ala) shows oral bioavailability comparable to D-Trp containing analogs.
Optimal, Systematic, $q$-Ary Codes Correcting All Asymmetric and Symmetric Errors of Limited Magnitude (2010)

Systematic q-ary ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">q</i> > 2) codes capable of correcting all asymmetric errors of maximum magnitude <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">l</i> , where l ¿ q - 2, are given. These codes are shown to be optimal. Further, simple encoding/decoding algorithms are described. The proposed code can be modified to design codes correcting all symmetric errors of maximum magnitude <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">l</i> , where <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">l</i> ¿ ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">q</i> -2)/2.
Porphyromonas gingivalis proteinases in periodontitis, a review. (1996)

Porphyromonas gingivalis has been closely associated with the initiation and progression of some forms of periodontal diseases and its proteolytic enzymes have been implicated in invasion, tissue destruction and evasion of host antibacterial defenses. Recently, the primary focus of research has been on cysteine proteinases, referred to as gingipain R and gingipain K which are produced in large quantities and are directly involved in pathological events during development and progression of periodontitis, contributing to clinical hallmarks of the disease including: flow of gingival crevicular fluid, neutrophil accumulation and bleeding on probing. Gingipain R exists as 110-, 95-, 70- to 90- and 50-kDa proteins, the first two being a complex of the 50-kDa catalytic subunit with hemagglutinin/adhesins, with or without an added membrane anchorage peptide. The other forms are single-chain enzymes. The predominant form of gingipain K in P. gingivalis strains is a complex of a 60-kDa catalytic protein with hemagglutinin/adhesins. Molecular cloning and structural characterization of the gingipain R and gingipain K genes has shown that they code for 1704 and 1722 amino-acid residue preproenzymes, respectively. Although both structures show no similarity within the preprofragment and only limited identity within the catalytic domain (27%) they are essentially identical within the putative hemagglutinin/adhesin domain. Furthermore, on the basis of gene structure it is now apparent that various soluble and membrane bound forms of gingipains are derived through proteolytic processing of the preproenzymes, and it can be assumed that the Arg-X-specific enzyme is responsible for this processing.
A Differential Binary Message-Passing LDPC Decoder (2007)

In this paper, we propose a binary message-passing algorithm for decoding low-density parity-check (LDPC) codes. The algorithm substantially improves the performance of purely hard-decision iterative algorithms with a small increase in the memory requirements and the computational complexity. We associate a reliability value to each nonzero element of the code's parity-check matrix, and differentially modify this value in each iteration based on the sum of the extrinsic binary messages from the check nodes. For the tested random and finite-geometry LDPC codes, the proposed algorithm can achieve performance as close as 1.3 dB and 0.7 dB to that of belief propagation (BP) at the error rates of interest, respectively. This is while, unlike BP, the algorithm does not require the estimation of channel signal to noise ratio. Low memory and computational requirements and binary message-passing make the proposed algorithm attractive for high-speed low-power applications.
Reading 1D Barcodes with Mobile Phones Using Deformable Templates (2010)

Camera cellphones have become ubiquitous, thus opening a plethora of opportunities for mobile vision applications. For instance, they can enable users to access reviews or price comparisons for a product from a picture of its barcode while still in the store. Barcode reading needs to be robust to challenging conditions such as blur, noise, low resolution, or low-quality camera lenses, all of which are extremely common. Surprisingly, even state-of-the-art barcode reading algorithms fail when some of these factors come into play. One reason resides in the early commitment strategy that virtually all existing algorithms adopt: The image is first binarized and then only the binary data are processed. We propose a new approach to barcode decoding that bypasses binarization. Our technique relies on deformable templates and exploits all of the gray-level information of each pixel. Due to our parameterization of these templates, we can efficiently perform maximum likelihood estimation independently on each digit and enforce spatial coherence in a subsequent step. We show by way of experiments on challenging UPC-A barcode images from five different databases that our approach outperforms competing algorithms. Implemented on a Nokia N95 phone, our algorithm can localize and decode a barcode on a VGA image (640 × 480, JPEG compressed) in an average time of 400-500 ms.
Production of high oleic rice grains by suppressing the expression of the OsFAD2-1 gene (2013)

The composition of rice (Oryza sativa L.) grain fatty acids (18% palmitic acid, 36% oleic acid and 37% linoleic acid) is suboptimal for rice storage and utilisation of rice bran oil as food grade oil or a source of biodiesel. Genetic manipulation of fatty acid composition in rice bran oil to increase oleic acid levels at the expense of linoleic acid and palmitic acid would not only add extra value to the rice, but also enhance health benefits for consumers. Four putative rice microsomal Δ12-fatty acid desaturase (OsFAD2) genes were identified as potentially important target genes to achieve this improvement. Reverse transcription-PCR analysis indicated that OsFAD2-1 was the most highly expressed gene in rice grains. RNA interference (RNAi) suppression of the expression of OsFAD2-1 resulted in an increase of oleic acid and a reduction of linoleic and palmitic acids in T3 grains. The research here showed that in the rice grains, the OsFAD2-1 enzyme was an effective target for raising oleic acid levels at the expense of the oxidatively unstable linoleic acid and the cholesterol-raising palmitic acid.
An emitter switched thyristor with base resistance control (1993)

An MOS-gated emitter-switched thyristor structure with base resistance control, which combines the best features of both the emitter-switched thyristor (EST) and the base-resistance-controlled thyristor (BRT), is reported. With this structure, it is possible to obtain turn-off (dynamic) current densities above the static latch-up current density of the parasitic thyristor in the EST, while preserving its unique current saturation capability. It has been experimentally demonstrated for 600 V forward blocking devices that the maximum controllable current density under dynamic conditions is a function of both the gate bias and the dimensions of the N/sup +/ floating emitter. Turn-off measurements have demonstrated that the new structure has a maximum controllable current density of over 2.5 times that for the EST structure without base resistance control.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
<title>Differential phase measurements by partial coherence interferometry</title> (1999)

In the past ten years, partial coherence interferometry has been developed and applied to high precision measurements of various biological and technical materials. This technique was extended to a high resolution, non contact imaging technique: optical coherence tomography (OCT). Recently, OCT was extended to perform polarization sensitive measurements and imaging. In this case, small phase variations caused by birefringence are measured and imaged. Small phase differences between adjacent beams can also be caused by other circumstances, e.g. by slight variations of geometric path length or refractive index. We present a method to measure these phase differences as a function of longitudinal and lateral position in the object. This method allows to determine the path length gradient with a resolution on the order of 10<SUP>-5</SUP>. Furthermore, we report first results obtained in simple test objects and present first differential phase contrast OCT tomograms.
Improvement in estimation of time of arrival (TOA) from timing advance (TA) (2002)

Wireless systems reporting TOA (time of arrival), the propagation time from the mobile station (MS) to the base station (BS), may use this information to assist with automatic location identification (ALI). The TA (timing advance), used in TDMA systems, may be used as an approximation for TOA. The MS/BS system measures TOA with a certain raw measurement error. The TA is assigned from this to one of a finite set of discrete values, resulting in a multinomial distribution of results. We assume that the user does not have access to the original TOA measurement and must attempt to reverse the process and estimate the TOA from the TA. The resultant error in the estimated TOA might be large if, by random error, the wrong TA bin has been selected. A simple solution to improve the accuracy of the TOA information thus obtained from the system is to take an average of two or more consecutive TA values. Paradoxically, the mean square error of this average is best at a value of the raw TOA measurement error that is not too small. This is a consequence of the fact that we cannot construct an estimator that is consistent in the statistical sense due to the finite TA bin size. We must also take into account the effects of the RF path and the possible motion of the mobile. We discuss the solution for any system with TA information. We also discuss the significance of multipath and its impact on the estimation of TOA. Simulations for the particular case of GSM are used to illustrate the results.
Subtractive design: A novel approach to heatsink improvement (2016)

Typical Heatsink design includes base and fin thickness, fin height, and fin gap optimization. In situations where material cost or mass of the heat sink are also a design priority further optimization with respect to mass removal can be significant. This paper discusses a method to further improve a heat sink topology by the systematic removal of heat sink mass where the Thermal BottleNeck (BN) Number was found to be lowest.
50.4: Flexible Encapsulated Cholesteric LCDs by Polymerization Induced Phase Separation (2005)

Abstract We demonstrate a cholesteric liquid crystal‐polymer dispersion where the liquid crystal is encapsulated via polymerization induced phase separation. A polymerizable additive formulation is used to control the liquid crystal droplet size. Encapsulation prevents the flow of liquid crystal thereby preserving the bistable texture when the display is flexed.
Poly-Logarithmic Range Queries on Encrypted Data with Small Leakage (2016)

Privacy-preserving range queries allow encrypting data while still enabling queries on ciphertexts if their corresponding plaintexts fall within a requested range. This provides a data owner the possibility to outsource data collections to a cloud service provider without sacrificing privacy nor losing functionality of filtering this data. However, existing methods for range queries either leak additional information (like the ordering of the complete data set) or slow down the search process tremendously by requiring to query each ciphertext in the data collection. We present a novel scheme that only leaks the access pattern while supporting amortized poly-logarithmic search time. Our construction is based on the novel idea of enabling the cloud service provider to compare requested range queries. By doing so, the cloud service provider can use the access pattern to speed-up search time for range queries in the future. On the one hand, values that have fallen within a queried range, are stored in an interactively built index for future requests. On the other hand, values that have not been queried do not leak any information to the cloud service provider and stay perfectly secure. In order to show its practicability we have implemented our scheme and give a detailed runtime evaluation.
Message Authentication Based on Cryptographically Secure CRC without Polynomial Irreducibility Test (2017)

In this paper, we present a message authentication scheme based on cryptographically secure cyclic redundancy check (CRC). Similarly to previously proposed cryptographically secure CRCs, the presented one detects both random and malicious errors without increasing bandwidth. The main difference from previous approaches is that we use random instead of irreducible generator polynomials. This eliminates the need for irreducibility tests. We provide a detailed quantitative analysis of the achieved security as a function of message and CRC sizes. The results show that the presented scheme is particularly suitable for the authentication of short messages.
Conductive Carbon Nanotube Inks for Use with Desktop Inkjet Printing Technology (2013)

In a nationwide analysis of patients in Sweden, long-term use of OCs, particularly the combination type, was associated with an increased risk of surgery among women with established CD. Clinicians carefully should evaluate and monitor contraceptive options among women with established CD.
Preventing Wine Counterfeiting by Individual Cork Stopper Recognition Using Image Processing Technologies (2018)

Wine counterfeiting is a major problem worldwide. Within this context, an approach to the problem of discerning original wine bottles from forged ones is the use of natural features present in the product, object and/or material (using it “as is”). The proposed application uses the cork stopper as a unique fingerprint, combined with state of the art image processing techniques to achieve individual object recognition and smartphones as the authentication equipment. The anti-counterfeiting scheme is divided into two phases: an enrollment phase, where every bottle is registered in a database using a photo of its cork stopper inside the bottle; and a verification phase, where an end-user/retailer captures a photo of the cork stopper using a regular smartphone, compares the photo with the previously-stored one and retrieves it if the wine bottle was previously registered. To evaluate the performance of the proposed application, two datasets of natural/agglomerate cork stoppers were built, totaling 1000 photos. The worst case results show a 100% precision ratio, an accuracy of 99.94% and a recall of 94.00%, using different smartphones. The perfect score in precision is a promising result, proving that this system can be applied to the prevention of wine counterfeiting and consumer/retailer security when purchasing a wine bottle.