gebhart/patrepeval huggingface dataset:
Effect of adding and removing N-glycosylation recognition sites on the thermostability of barley  -glucosidase (2004)

The thermostability of alpha-glucosidase is important because the conversion of starch to fermentable sugars during the industrial production of beer and fuel ethanol typically occurs at relatively high temperatures (60-75 degrees C). Barley (Hordeum vulgare) alpha-glucosidase is unstable at these elevated temperatures; however, the alpha-glucosidase from sugar beet (Beta vulgaris) is stable at these temperatures. An alignment of the deduced amino acid sequences of barley and sugar beet alpha-glucosidases revealed considerable differences in the number and position of N-glycosylation recognition sites (NGRS). Other researchers have shown that additions or removals of NGRS resulted in either the stabilization or destabilization of the enzymes at elevated temperatures. NGRS present in the barley sequence and absent in the sugar beet sequence were removed via site-directed mutagenesis from the barley protein. Recognition sites absent in the barley sequence and present in the sugar beet sequence were added via mutagenesis into the barley alpha-glucosidase. Two mutations significantly increased thermostability, one mutation significantly decreased thermostability and five mutations had little effect on alpha-glucosidase thermostability.
Autonomous predistortion calibration of an RF power amplifier (2011)

A novel built-in calibration mechanism for a nonlinear digitally-controlled power amplifier (DPA), or its combination with an external power amplifier (PA), is proposed. It allows construction of a digital predistortion mechanism, which is configured based on data collected entirely through processing of internal digital signals in an all-digital PLL (ADPLL)-based transmitter. The proposed technique is suitable not only for characterizing the amplitude and phase transfer function non- linearities and configuring the internal predistortion accordingly, but may also be useful for built-in self-test (BIST) purposes. The proposed technique has been implemented and successfully validated in a commercial single-chip GSM/EDGE radio.
Negative Interference in Cardiac Troponin I Immunoassays from a Frequently Occurring Serum and Plasma Component (2003)

Some yet unidentified, variable component, present in the blood from healthy volunteers and ACS patients, interferes with the binding of antibodies against epitopes in the central part of cTnI used in two commercial assays. Our approach to supplement the mid-fragment cTnI antibodies with antibodies in the N- and C-terminal parts of the molecule in an experimental assay represents a step in resolving this interferent.
Enantioselective Syntheses of Heteroyohimbine Natural Products: A Unified Approach through Cooperative Catalysis (2015)

Abstract Alstonine and serpentine are pentacyclic indoloquinolizidine alkaloids (referred to as “anhydronium bases”) containing three contiguous stereocenters. Each possesses interesting biological activity, with alstonine being the major component of a plant‐based remedy to treat psychosis and other nervous system disorders. This work describes the enantioselective total syntheses of these natural products with a cooperative hydrogen bonding/enamine‐catalyzed Michael addition as the key step.
Microprocessor based measurements of the range of motion of a human body joint (1988)

The design and development of a microprocessor-based apparatus capable of measuring the range of motion associated with the elbow joint is presented. The apparatus not only makes accurate angular measurements possible, but also allows the measurement of the velocity and acceleration associated with the motion. Thus, six different parameters associated with the motion of the elbow joint can be measured in real-time: the angular displacement and its velocity and acceleration with the forearm in flexion-extension, and the rotational displacement and its velocity and acceleration with the forearm in supination-pronation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Fermentable sugars by chemical hydrolysis of biomass (2010)

Abundant plant biomass has the potential to become a sustainable source of fuels and chemicals. Realizing this potential requires the economical conversion of recalcitrant lignocellulose into useful intermediates, such as sugars. We report a high-yielding chemical process for the hydrolysis of biomass into monosaccharides. Adding water gradually to a chloride ionic liquid-containing catalytic acid leads to a nearly 90% yield of glucose from cellulose and 70-80% yield of sugars from untreated corn stover. Ion-exclusion chromatography allows recovery of the ionic liquid and delivers sugar feedstocks that support the vigorous growth of ethanologenic microbes. This simple chemical process, which requires neither an edible plant nor a cellulase, could enable crude biomass to be the sole source of carbon for a scalable biorefinery.
New Steering System of Automated People Mover (2005)

Automated People Mover System with guide wheels and links to steer tires has been used in airport passenger transportation systems. New steering system has no contact with guide tracks. The vehicle using the new steering system can steer tires by itself. It is possible to improve ride quality and reduce weight of steering devices by using new steering system. Also, the track structure is able to make simply. This paper shows the concepts of the new steering system for Automated People Mover System.
Electrocardiographic Imaging: II. Effect of Torso Inhomogeneities on Noninvasive Reconstruction of Epicardial Potentials, Electrograms, and Isochrones (2001)

The results demonstrate that, in the clinical application, it is not necessary to include torso inhomogeneities for noninvasive reconstructions of epicardial potentials, EGMs, and activation sequences.
Electro micro-metrology (2005)

Interaction between the so-called benzodiazepine receptor (BzR) and the chemically heterogeneous class of its ligands is still one of the most challenging objects of theoretical studies. In the mid-90s our group began to collaborate with Prof. Antonio Da Settimo and coworkers to a project of synthesis and biological evaluation of indolylglyoxylamides designed as BzR ligands. Herein we review our efforts in designing these compounds and in interpreting their structureaffinity relationships. Our investigations were carried out for years by adopting the pharmacophore/topological model for BzR ligands set up by Cook's group. In an attempt to rationalize some puzzling structure-affinity relationships we speculated in 1998 that our ligands interact with the BzR by assuming one of two alternative binding modes (called "A" and "B") depending on whether or not they were substituted at the 5-position of the indole nucleus. Such a model received support from a considerable amount of experimental data accumulated throughout our researches. About a decade later, docking calculations performed on a homology-built model of the 1 BzR subtype were found in agreement with the hypothesis of mode A and mode B of binding accessible to 5-H and, respectively, 5-Cl/NO2 indole derivatives.
Intelligent load balancing for shortest path bridging (2012)

This article provides an overview of a method to enhance the load spreading algorithms used by IEEE 802.1aq Shortest Path Bridging. The technique has a number of interesting properties with respect to distributing load on the basis of a measure of anticipated link utilization. What this provides is balanced network utilization and the ability to apply subtle modifications to the distribution of the traffic matrix previously unachievable with shortest path forwarding alone. This is achieved within the framework of the existing Ethernet technology base.
Experimental and theoretical studies into the limits to peak power in GaAs-based diode lasers (2016)

An overview is presented of progress in studies to diagnose and address limits to peak power in high power diode lasers. Key terms in advanced structures include carrier losses in the p-side waveguide, self-heating effects in the quantum well, and longitudinal spatial hole-burning.
<title>Synthetic cornea: biocompatibility and optics</title> (2002)

Purpose. Experimentally find a method to provide a safe surgical technique and an inexpensive and long lasting mesoplant for the restoration of vision in patients with bilateral corneal blindness due to ocular surface and stromal diseases. Methods. Identify the least invasive and the safest surgical technique for synthetic cornea implantation. Identify the most compatible biomaterials and the optimal shape a synthetic cornea must have to last a long time when implanted in vivo. Results. Penetrating procedures were deemed too invasive, time consuming, difficult and prone to long term complications. Therefore a non-penetrating delamination technique with central trephination was developed to preserve the integrity of Descemet's membrane and the anterior segment. Even though this approach limits the number of indications, it is acceptable since the majority of patients only have opacities in the stroma. The prosthesis was designed to fit in the removed tissue plane with its skirt fitted under the delaminated stroma. To improve retention, the trephination wall was made conical with the smallest opening on the anterior surface and a hat-shaped mesoplant was made to fit. The skirt was perforated in its perimeter to allow passage of nutrients and tissues ingrowths. To simplify the fabrication procedure, the haptic and optic were made of the same polymer. The intrastromal biocompatibility of several hydrogels was found superior to current clinically used PMMA and PTFE materials. Monobloc mesoplants made of 4 different materials were implanted in rabbits and followed weekly until extrusion occurred. Some remained optically clear allowing for fundus photography. Conclusions. Hydrogel synthetic corneas can be made to survive for periods longer than 1 year. ArF excimer laser photoablation studies are needed to determine the refractive correction potential of these mesoplants. A pilot FDA clinical trial is needed to assess the mesoplant efficacy and very long-term stability.
Chiral Separations Using Dipeptide Polymerized Surfactants:  Effect of Amino Acid Order (1998)

Chiral separations using various polymerized dipeptide surfactants in electrokinetic capillary chromatography (EKC) are investigated. The two main dipeptide surfactants used in this study were sodium N-undecylenyl-L-valine-L-leucine (L-SUVL), and sodium N-undecylenyl-L-leucine-L-valine (L-SULV). These studies were performed in order to determine if the order of amino acids in dipeptide surfactants is important in terms of chiral recognition and separations. Both the monomer and the polymer of these two surfactants were compared for the separation of two model atropisomers, (+/-)-1,1-bi-2-naphtol (BOH) and (+/-)-1,1'-bi-2-naphthyl-2,2'-diyl hydrogen phosphate (BNP). Some advantages and disadvantages of the polymer relative to the monomer are discussed. Four other surfactants, the polymers of sodium N-undecylenyl-L-leucine-L-leucine (L-SULL), sodium N-undecylenyl-L-valine-L-valine (L-SUVV), sodium N-undecylenyl-L-valine (L-SUV), and sodium N-undecylenyl-L-leucine (L-SUL), were also used in this study, and their performance was compared to that of poly(L-SULV). These data show conclusively that the order of amino acids in dipeptide surfactants has a dramatic effect on chiral recognition. Our investigations indicate that poly-(L-SULV) provides the best enantioselectivity among the four dipeptide and two single amino acid surfactants for the separation of BNP and BOH. The advantages of poly-(L-SULV) are demonstrated via the ultrafast separation of the enantiomers of BNP and BOH in less than 1 min.
Low-Temperature Catalytic Process To Produce Hydrocarbons From Sugars (2005)

Disclosed is a method of producing hydrogen from oxygenated hydrocarbon reactants, such as methanol, glycerol, sugars (e.g. glucose and xylose), or sugar alcohols (e.g. sorbitol). The method takes place in the condensed liquid phase. The method includes the steps of reacting water and a water-soluble oxygenated hydrocarbon in the presence of a metal-containing catalyst. The catalyst contains a metal selected from the group consisting of Group VIIIB transitional metals, alloys thereof, and mixtures thereof. The disclosed method can be run at lower temperatures than those used in the conventional steam reforming of alkanes.
Hybrid vectorial and tensorial Compressive Sensing for hyperspectral imaging (2015)

Hyperspectral imaging has a wide range of applications; however, due to the high dimensionality of the data involved, the complexity and cost of hyperspectral imagers can be prohibitive. Exploiting redundancies along the spatial and spectral dimensions of a hyperspectral image of a scene has created new paradigms that do away with the limitations of traditional imaging systems. While Compressive Sensing (CS) approaches have been proposed and simulated with success on already acquired hyperspectral imagery, most of the existing work relies on the capability to simultaneously measure the spatial and spectral dimensions of the hyperspectral cube. Most real-life devices, however, are limited to sampling one or two dimensions at a time, which renders a significant portion of the existing work unfeasible. In this paper we propose a novel CS framework that is a hybrid between traditional vectorized approaches and recently proposed tensorial approaches, and that is compatible with real-life devices both in terms of the acquisition and reconstruction requirements.
Applying assist features to improve two dimensional feature process robustness (2005)

Sub-resolution assist features are an important tool for improving process robustness for one-dimensional pattern features at advanced manufacturing process nodes. However, sub-resolution assist feature development efforts have not generally considered optimization for process robustness with two-dimensional pattern features. This generally arises both from conservatively placing SRAFs to avoid the possibility of imaging, and from a desire to simplify SRAF placement rules. By studying two-dimensional features using a manufacturing sensitivity model, one can gain insight into the capabilities of SRAFs regarding two-dimensional pattern features. These insights suggest new methodologies for shaping assist features to enhance two-dimensional feature robustness. In addition, a manufacturing sensitivity model form can be employed to optimize the placement of multiple competing SRAFs in localized two-dimensional regions. Initial studies demonstrate significant pullback reduction for two-dimensional features once SRAF placement has been optimized using the manufacturing sensitivity model form.
Faithful bipartite ROM reciprocal tables (2002)

We describe bipartite reciprocal tables that employ separate table lookup of the positive and negative portions of a borrow-save reciprocal value. The fusion of the parts includes a rounding so the output reciprocals are guaranteed correct to a unit in the last place, and typically provide a round-to-nearest reciprocal for over 90% of input arguments. The output rounding can be accomplished in conjunction with multiplier recoding yielding practically no cost in logic complexity or time in employing bipartite tables. We demonstrate these tables to be 2 to 4 times smaller than conventional 4-bit reciprocal tables. For 10-16 bit reciprocal table lookup the compression grows from a factor of 4 to over 16, making possible the use of larger seed reciprocals than previously considered cost effective.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Extending the p-cycle concept to path segment protection for span and node failure recovery (2003)

The paper introduces an extension to the method of p-cycles for network protection. The p-cycle concept is generalized to protect path segments of contiguous working flow, not only spans that lie on the cycle or directly straddle the p-cycle. The original span protecting use of the p-cycle technique is extend to include path protection or protection of any flow segment along a path. It also gives an inherent means of protecting working flows that transit a failed node. We use integer linear programming to study the new concept and determine its inherent capacity requirements relative to prior p-cycle designs and other types of efficient mesh-survivable networks. Results show that path-segment-protecting p-cycles ("flow p-cycles") have capacity efficiency near that of the shared backup path-protection (SBPP) scheme currently favored for optical networking. Because its protection paths are fully preconnected and because it protects path segments (not entire paths), it has the potential for both higher speed and higher availability than SBPP. We also develop capacity optimization models to support 100% restoration of transiting flows through failed nodes. Only a very small additional spare capacity is needed to achieve both 100% span and intermediate node-failure restorabilities, and a very high transiting traffic restorability can be accomplished for node failure restorability given spare capacity only for span-failure protection. An immediate practical application is to suggest the use of flow p-cycles to protect transparent optical express flows through a regional network.
Tracking the Antibody Immunome in Type 1 Diabetes Using Protein Arrays (2016)

We performed an unbiased proteome-scale profiling of humoral autoimmunity in recent-onset type 1 diabetes (T1D) patients and nondiabetic controls against ∼10 000 human proteins using a Nucleic Acid Programmable Protein Array (NAPPA) platform, complemented by a knowledge-based selection of proteins from genes enriched in human pancreas. Although the global response was similar between cases and controls, we identified and then validated six specific novel T1D-associated autoantibodies (AAbs) with sensitivities that ranged from 16 to 27% at 95% specificity. These included AAbs against PTPRN2, MLH1, MTIF3, PPIL2, NUP50 (from NAPPA screening), and QRFPR (by targeted ELISA). Immunohistochemistry demonstrated that NUP50 protein behaved differently in islet cells, where it stained both nucleus and cytoplasm, compared with only nuclear staining in exocrine pancreas. Conversely, PPIL2 staining was absent in islet cells, despite its presence in exocrine cells. The combination of anti-PTPRN2, -MLH1, -PPIL2, and -QRFPR had an AUC of 0.74 and 37.5% sensitivity at 95% specificity. These data indicate that these markers behave independently and support the use of unbiased screening to find biomarkers because the majority was not predicted based on predicted abundance. Our study enriches the knowledge of the "autoantibody-ome" in unprecedented breadth and width.
<i>In Situ</i> Intercalation Replacement and Selective Functionalization of Graphene Nanoribbon Stacks (2012)

A cost-effective and potentially industrially scalable, in situ functionalization procedure for preparation of soluble graphene nanoribbon (GNRs) from commercially available carbon nanotubes is presented. The physical characteristics of the functionalized product were determined using SEM, evolved gas analysis, X-ray diffraction, solid-state (13)C NMR, Raman spectroscopy, and GC-MS analytical techniques. A relatively high preservation of electrical properties in the bulk material was observed. Moreover, replacement of intercalated potassium with haloalkanes was obtained. While carbon nanotubes can be covalently functionalized, the conversion of the sp(2)-hybridized carbon atoms to sp(3)-hybridized atoms dramatically lowers their conductivity, but edge functionalized GNRs permit their heavy functionalization while leaving the basal planes intact.
Hierarchical partitioned least squares filter-bank for fingerprint enhancement (2002)

It is desirable to enhance the fingerprint image for achieving good fingerprint matching performance. In our earlier work, we have proposed a method for learning a set of partitioned least-squares filters from a given set of images and ground truth pairs. In this paper, we propose a refined approach to learn a class of hierarchical filter banks to extend our enhancement technique. The new technique is shown to obtain much better results particularly when the input image is not easily restored using our earlier technique. We evaluate the performance of our new approach to fingerprint enhancement filter design by assessing the effect of enhancement on performance of (i) fingerprint feature extraction and (ii) fingerprint matching.
Add-drop multiplexer with signal amplification ability using optical fiber grating couplers (1999)

An add-drop multiplexer (ADM) with signal amplification ability, composed of two optical fiber grating couplers (FGCs) and two Er-doped fiber amplifiers (EDFAs), is proposed and demonstrated for the first time. The ADM can amplify signal lightwaves including dropped and added ones and can effectively remove the pumping lightwaves for EDFAs from the main stream of optical fiber routing.
Optimizing data flow graphs to minimize hardware implementation (2009)

This paper describes an efficient graph-based method to optimize data-flow expressions for best hardware implementation. The method is based on factorization, common subexpression elimination (CSE) and decomposition of algebraic expressions performed on a canonical representation, Taylor Expansion Diagram. The method is generic, applicable to arbitrary algebraic expressions and does not require specific knowledge of the application domain. Experimental results show that the DFGs generated from such optimized expressions are better suited for high level synthesis, and the final, scheduled implementations are characterized, on average, by 15.5% lower latency and 7.6% better area than those obtained using traditional CSE and algebraic decomposition.
Automatic glandular and tubule region segmentation in histological grading of breast cancer (2015)

In the popular Nottingham histologic score system for breast cancer grading, the pathologist analyzes the H and E tissue slides and assigns a score, in the range of 1-3, for tubule formation, nuclear pleomorphism and mitotic activity in the tumor regions. The scores from these three factors are added to give a final score, ranging from 3-9 to grade the cancer. Tubule score (TS), which reflects tubular formation, is a value in 1-3 given by manually estimating the percentage of glandular regions in the tumor that form tubules. In this paper, given an H and E tissue image representing a tumor region, we propose an automated algorithm to detect glandular regions and detect the presence of tubules in these regions. The algorithm first detects all nuclei and lumen candidates in the input image, followed by identifying tumor nuclei from the detected nuclei and identifying true lumina from the lumen candidates using a random forest classifier. Finally, it forms the glandular regions by grouping the closely located tumor nuclei and lumina using a graph-cut-based method. The glandular regions containing true lumina are considered as the ones that form tubules (tubule regions). To evaluate the proposed method, we calculate the tubule percentage (TP), i.e., the ratio of the tubule area to the total glandular area for 353 H and E images of the three TSs, and plot the distribution of these TP values. This plot shows the clear separation among these three scores, suggesting that the proposed algorithm is useful in distinguishing images of these TSs.