gebhart/patrepeval huggingface dataset:
A novel epitope-presenting thermostable scaffold for the development of highly specific insulin-like growth factor-1/2 antibodies (2019)

High sequence and structural homology between mature human insulin-like growth factors IGF-1 and IGF-2 makes serological discrimination by immunodiagnostic IGF tests a challenging task. There is an urgent need for highly specific IGF-1 and IGF-2 antibodies, yet only a short sequence element, <i>i.e.</i> the IGF loop, provides enough difference in sequence to discriminate between the two molecules. We sought to address this unmet demand by investigating novel chimeric immunogens as carriers for recombinant peptide motif grafting. We found <i>Thermus thermophilus</i> sensitive to lysis D (SlyD) and <i>Thermococcus gammatolerans</i> SlyD FK-506-binding protein (FKBP) domains suitable for presentation of the predefined epitopes, namely the IGF-1 and IGF-2 loops. Chimeric SlyD-IGF proteins allowed for the development of exceptionally specific IGF-1 and IGF-2 monoclonal antibodies. The selected antibodies bound with high affinity to the distinct IGF epitopes displayed on the protein scaffolds, as well as on the mature human IGF isoforms. The respective SlyD scaffolds display favorable engineering properties in that they are small, monomeric, and cysteine-free and can be produced in high yields in a prokaryotic host, such as <i>Escherichia coli</i> In conclusion, FKBP domains from thermostable SlyD proteins are highly suitable as a generic scaffold platform for epitope grafting.
Novel synthetic amino acid copolymers that inhibit autoantigen-specific T cell responses and suppress experimental autoimmune encephalomyelitis (2002)

Copolymer 1 (Cop 1, Copaxone [Teva Marion Partners, Kansas City, Missouri, USA]), a random amino acid copolymer of tyrosine (Y), glutamic acid (E), alanine (A), and lysine (K), reduces the frequency of relapses by 30% in relapsing-remitting multiple sclerosis (MS) patients.In the present study, novel random four-amino acid copolymers, whose design was based on the nature of the anchor residues of the immunodominant epitope of myelin basic protein (MBP) 85-99 and of the binding pockets of MS-associated HLA-DR2 (DRB1*1501), have been synthesized by solid-phase chemistry.Poly (Y, F, A, K) (YFAK) inhibited binding of the biotinylated MBP 86-100 epitope to HLA-DR2 molecules more efficiently than did either unlabeled MBP 85-99 or any other copolymer including Cop 1.Moreover, YFAK and poly (F, A, K) (FAK) were much more effective than Cop 1 in inhibition of MBP 85-99-specific HLA-DR2-restricted T cell clones.Most importantly, these novel copolymers suppressed experimental autoimmune encephalomyelitis, induced in the susceptible SJL/J (H-2 s ) strain of mice with the encephalitogenic epitope PLP 139-151, more efficiently than did Cop 1.Thus, random synthetic copolymers designed according to the binding motif of the human immunodominant epitope MBP 85-99 and the binding pockets of HLA-DR2 might be more beneficial than Cop 1 in treatment of MS.
A novel monoclonal antibody targeting coxsackie virus and adenovirus receptor inhibits tumor growth in vivo (2017)

To create a new anti-tumor antibody, we conducted signal sequence trap by retrovirus-meditated expression method and identified coxsackie virus and adenovirus receptor (CXADR) as an appropriate target. We developed monoclonal antibodies against human CXADR and found that one antibody (6G10A) significantly inhibited the growth of subcutaneous as well as orthotopic xenografts of human prostate cancer cells in vivo. Furthermore, 6G10A also inhibited other cancer xenografts expressing CXADR, such as pancreatic and colorectal cancer cells. Knockdown and overexpression of CXADR confirmed the dependence of its anti-tumor activity on CXADR expression. Our studies of its action demonstrated that 6G10A exerted its anti-tumor activity primarily through both antibody-dependent cellular cytotoxicity and complement-dependent cytotoxicity. Moreover, 6G10A reacted with human tumor tissues, such as prostate, lung, and brain, each of which express CXADR. Although we need further evaluation of its reactivity and safety in human tissues, our results show that a novel anti-CXADR antibody may be a feasible candidate for cancer immunotherapy.
Web-Based Telerehabilitation for the Upper (2002)

Stroke is a leading cause of disability in the United States and yet little technology is currently available for individ- uals with stroke to practice and monitor rehabilitation therapy on their own. This paper provides a detailed design description of a telerehabilitation system for arm and hand therapy following stroke. The system consists of a Web-based library of status tests, therapy games, and progress charts, and can be used with a variety of input devices, including a low-cost force-feedback joystick capable of assisting or resisting in movement. Data from home-based usage by a chronic stroke subject are presented that demonstrate the feasibility of using the system to direct a therapy program, mechanically assist in movement, and track improve- ments in movement ability.
Revolver is a New Class of Transposon-like Gene Composing the Triticeae Genome (2008)

Revolver discovered in the Triticeae plant is a novel class of transposon-like gene and a major component of the large cereal genome. An 89 bp segment of Revolver that is enriched in the genome of rye was isolated by deleting the DNA sequences common to rye and wheat. The entire structure of Revolver was determined by using rye genomic clones, which were screened by the 89 bp probe. Revolver consists of 2929-3041 bp with an inverted repeated sequence on each end and is dispersed through all seven chromosomes of the rye genome. Revolver is transcriptionally active, and the isolated full-length cDNA (726 bp) reveals that Revolver harbors a single gene consisting of three exons (342, 88, and 296 bp) and two introns (750 and 1237 bp), and encodes 139 amino acid residues of protein, which shows similarity to some transcriptional regulators. Revolver variants ranging from 2665 to 4269 bp, in which 5' regions were destructed, indicate structural diversities around the first exon. Revolver does not share identity with any known class I or class II autonomous transposable elements of any living species. DNA blot analysis of Triticeae plants shows that Revolver has existed since the diploid progenitor of wheat, and has been amplified or lost in several species during the evolution of the Triticeae.
Collagen Prolyl 4-Hydroxylase as a Therapeutic Target (2018)

Collagen is the dominant protein of the extracellular matrix. Its distinguishing feature is a three-stranded helix of great tensile strength. (2 S,4 R)-4-Hydroxyproline residues are essential for the stability of this triple helix. These residues arise from the post-translational modification of (2 S)-proline residues by collagen prolyl 4-hydroxylases (CP4Hs), which are members of the Fe(II)- and α-ketoglutarate (AKG)-dependent dioxygenase family. Here, we provide a framework for the inhibition of CP4Hs as the basis for treating fibrotic diseases and cancer metastasis. We begin with a summary of the structure and enzymatic reaction mechanism of CP4Hs. Then, we review the metal ions, metal chelators, mimetics of AKG and collagen strands, and natural products that are known to inhibit CP4Hs. Our focus is on inhibitors with potential utility in the clinic. We conclude with a prospectus for more effective inhibitors.
Engineering lepidopteran insect cells for sialoglycoprotein production by genetic transformation with mammalian  1,4-galactosyltransferase and  2,6-sialyltransferase genes (2001)

Recombinant mammalian glycoproteins produced by the baculovirus-insect cell expression system usually do not have structurally authentic glycans. One reason for this limitation is the virtual absence in insect cells of certain glycosyltransferases, which are required for the biosynthesis of complex, terminally sialylated glycoproteins by mammalian cells. In this study, we genetically transformed insect cells with mammalian beta 1,4-galactosyltransferase and alpha 2,6-sialyltransferase genes. This produced a new insect cell line that can express both genes, serve as hosts for baculovirus infection, and produce foreign glycoproteins with terminally sialylated N-glycans.
COMMUNICATION TO THE EDITOR Production of Mannitol and Lactic Acid by Fermentation With Lactobacillus intermedius NRRL B-3693 † (2003)

Lactobacillus intermedius B-3693 was selected as a good producer of mannitol from fructose after screening 72 bacterial strains. The bacterium produced mannitol, lactic acid, and acetic acid from fructose in pH- controlled batch fermentation. Typical yields of manni- tol, lactic acid, and acetic acid from 250 g/L fructose were 0.70, 0.16, and 0.12 g, respectively per g of fructose. The fermentation time was greatly dependent on fructose concentration but the product yields were not dependent on fructose level. Fed-batch fermentation decreased the time of maximum mannitol production from fructose (300 g/L) from 136 to 92 h. One-third of fructose could be replaced with glucose, maltose, galactose, mannose, raf- finose, or starch with glucoamylase (simultaneous sac- charification and fermentation), and two-thirds of fruc- tose could be replaced with sucrose. L. intermedius B-3693 did not co-utilize lactose, cellobiose, glycerol, or xylose with fructose. It produced lactic acid and ethanol but no acetic acid from glucose. The bacterium produced 21.3 ± 0.6 g lactic acid, 10.5 ± 0.3 g acetic acid, and 4.7 ± 0.0 g ethanol per L of fermentation broth from dilute acid (15% solids, 0.5% H2SO4, 121°C, 1 h) pretreated enzyme (cellulase, -glucosidase) saccharified corn fiber hydro- lyzate. © 2003 Wiley Periodicals, Inc. *Biotechnol Bioeng 82: 864-871, 2003.
A blocking monoclonal antibody reveals dimerization of intracellular domains of ALK2 associated with genetic disorders (2023)

Mutations in activin receptor-like kinase 2 (ALK2) can cause the pathological osteogenic signaling seen in some patients with fibrodysplasia ossificans progressiva and other conditions such as diffuse intrinsic pontine glioma. Here, we report that intracellular domain of wild-type ALK2 readily dimerizes in response to BMP7 binding to drive osteogenic signaling. This osteogenic signaling is pathologically triggered by heterotetramers of type II receptor kinases and ALK2 mutant forms, which form intracellular domain dimers in response to activin A binding. We develop a blocking monoclonal antibody, Rm0443, that can suppress ALK2 signaling. We solve the crystal structure of the ALK2 extracellular domain complex with a Fab fragment of Rm0443 and show that Rm0443 induces dimerization of ALK2 extracellular domains in a back-to-back orientation on the cell membrane by binding the residues H64 and F63 on opposite faces of the ligand-binding site. Rm0443 could prevent heterotopic ossification in a mouse model of fibrodysplasia ossificans progressiva that carries the human R206H pathogenic mutant.
Advanced-Database for the Development of Ni-Base Superalloys (2009)

We constructed a database for Ni-base Superalloys development. The database includes many data related to Superalloy development in areas of chemical composition in alloy design, casting and heat treatment in processing, and results of creep tests, thermal fatigue tests, oxidation tests, and so on. This distributed-type database includes small database systems for each category of data, such that it is possible to retrieve required data from an individual category. The system, which performs all data retrieval, is arranged upstream of these small databases and refers to the data according to its relation from all small databases. While enhancing data security, the system enables effective and reliable retrieval. Using the database, evaluation and analysis can be performed using huge volumes of data related to Superalloy development.
CXCR7 Protein Is Not Expressed on Human or Mouse Leukocytes (2010)

Since the discovery that CXCR7 binds to CXCL12/SDF-1α, the role of CXCR7 in CXCL12-mediated biological processes has been under intensive scrutiny. However, there is no consensus in the literature on the expression of CXCR7 protein by peripheral blood cells. In this study we analyzed human and mouse leukocytes and erythrocytes for CXCR7 protein expression, using a competitive CXCL12 binding assay as well as by flow cytometry and immunohistochemistry using multiple CXCR7 Abs. CXCR7(-/-) mice were used as negative controls. Together, these methods indicate that CXCR7 protein is not expressed by human peripheral blood T cells, B cells, NK cells, or monocytes, or by mouse peripheral blood leukocytes. CXCR7 protein is, however, expressed on mouse primitive erythroid cells, which supply oxygen to the embryo during early stages of development. These studies therefore suggest that, whereas CXCR7 protein is expressed by primitive RBCs during murine embryonic development, in adult mammals CXCR7 protein is not expressed by normal peripheral blood cells.
Urinary-Cell mRNA Profile and Acute Cellular Rejection in Kidney Allografts (2013)

A molecular signature of CD3ε mRNA, IP-10 mRNA, and 18S rRNA levels in urinary cells appears to be diagnostic and prognostic of acute cellular rejection in kidney allografts. (Funded by the National Institutes of Health and others.).
Structure and activity of botulinum neurotoxin X (2023)

Botulinum neurotoxins (BoNTs) are the most potent toxins known and are used to treat an increasing number of medical disorders. All BoNTs are naturally co-expressed with a protective partner protein (NTNH) with which they form a 300 kDa complex, to resist acidic and proteolytic attack from the digestive tract. We have previously identified a new botulinum neurotoxin serotype, BoNT/X, that has unique and therapeutically attractive properties. We present the cryo-EM structure of the BoNT/X-NTNH/X complex at 3.1 Å resolution. Unexpectedly, the BoNT/X complex is stable and protease resistant at both neutral and acidic pH and disassembles only in alkaline conditions. Using the stabilizing effect of NTNH, we isolated BoNT/X and showed that it has very low potency both <i>in vitro</i> and <i>in vivo</i> . Given the high catalytic activity and translocation efficacy of BoNT/X, low activity of the full toxin is likely due to the receptor-binding domain, which presents weak ganglioside binding and exposed hydrophobic surfaces.
Bronchoprotector Properties of Calcitonin Gene–related Peptide in Guinea Pig and Human Airways: Effect of Pulmonary Inflammation (1999)

Calcitonin gene-related peptide (CGRP), a neuropeptide released from sensory nerves during axonal reflexes, has strong bronchoprotector properties in rat isolated airways. In this study, we examined this ability of CGRP to prevent agonist-induced contraction in guinea pig and human airways and determined whether inflammatory reaction affects its function. CGRP administered intravenously (0.38 to 114 microgram/kg) in anesthesized guinea pig had no effect per se on airway resistance but caused a dose-related inhibition of substance P (SP; 13.5 microgram/kg)-induced bronchoconstriction (60% at 114 microgram/kg). Similarly, CGRP (10(-)9 to 10(-)6 M) prevented in a concentration-dependent manner the contraction elicited by SP (5 x 10(-)8 M) in guinea pig isolated main bronchi and parenchymal strips, the inhibition caused by CGRP being more pronounced in distal than in proximal airways (47 and 20%, respectively, at 10(-)6 M). The breaking effect of CGRP on SP-induced constriction was however significantly reduced (p < 0.05) in guinea pig actively sensitized to ovalbumin (OA) and the loss in its potency was of similar magnitude (> 40%) whether it was administered in vivo or in vitro. A same phenomenon was observed in human isolated peripheral bronchi. CGRP (10(-)6 M) reduced by more than 75% the extent of the contraction evoked by 10(-)6 M of carbamylcholine and its protector effect was totally abolished in bronchi showing clear morphological manifestation of inflammatory reaction. It is concluded that CGRP acts as a potent bronchoprotector agent on both guinea pig and human airways but its ability to limit the extent of airway responsiveness is strongly impaired in inflammatory conditions.
Evaluation of Fusion Beat Detection with a New Ventricular Automatic Capture Algorithm in ICDs (2005)

This study evaluated a newly developed automatic capture verification scheme for implantable cardioverter defibrillators (ICDs) regarding discrimination of capture, fusion, and noncapture beats, with an emphasis on fusion detection. The algorithm uses evoked response detection based on a sensing vector from right ventricular shocking coil to Can. Patients undergoing ICD implant or replacement were enrolled in this study. An external system was used for pacing and data acquisition. To provoke ventricular fusion beats, VVI patients were paced close to the rate of their intrinsic rhythm and DDD patients were paced close at their intrinsic PR interval. Surface ECG and wideband filtered intracardiac electrograms were recorded for off-line analysis. Each paced beat was independently classified visually by surface ECG and by the automatic detection algorithm. The algorithm performance was then evaluated by comparing the classification results. Twenty-seven patients (22 males, 5 females; 63.8 +/- 12.5 years) were analyzed. Device and lead demographics were: 18 DDD/9 VVI; 16 dedicated bipolar, 11 integrated bipolar leads; 18 acute, 9 chronic (3.7 +/- 2.0 years) leads. In total, 2064 beats were analyzed, including 1,477 fusion beats and 587 capture beats. Fusion detection sensitivity and specificity were 99.5% and 99.0%, respectively. Seven true-fusion beats (0.5%) were classified as capture and 6 capture beats (1.0%) were identified as fusions. Capture or fusion beats were never detected as non-capture beats. It is concluded that the algorithm was effective in detecting fusion beats. It could potentially be used in ICD applications that need accurate fusion detection.
Silicon–germanium avalanche photodiodes with direct control of electric field in charge multiplication region (2019)

A CMOS-compatible avalanche photodiode (APD) with high speed and high sensitivity is a critical component of a low-cost, high-data-rate, and energy-efficient optical communication link. A novel waveguide-coupled silicon–germanium APD detector with three electric terminals was demonstrated with breakdown voltage of −6  V, bandwidth of 18.9 GHz, DC photocurrent gain of 15, open-eye diagram at a data rate of 35 Gb/s, and sensitivity of −11.4  dBm at a data rate of 25 Gb/s. This three-terminal APD allows high-yield fabrication in the standard CMOS process and provides robust high-sensitivity operation under small voltage supply.
Esterified lignin coating as water vapor and oxygen barrier for fiber-based packaging (2013)

Abstract Lignin, esterified with palmitic and lauric acid chloride, has been studied for the application as coating on fiber-based packaging material. The aim was to improve the barrier properties against water vapor and oxygen of paperboard. The esterification was followed by Fourier transform infrared spectroscopy, 31 P nuclear magnetic resonance spectroscopy, and gel permeation chromatography measurements. The lignin esters were applied on paperboard and formed a continuous film. The moisture barrier property of the coated paperboards was characterized by the water vapor transmission rate (WVTR). A significant decrease in WVTR was observed, for example, 40 g m -2 (for 24 h) for a paperboard coated with 10.4 g m -2 hardwood kraft lignin palmitate. The contact angle of water on the lignin ester coatings was high and stable. For all paperboard samples coated with lignin esters, a significant decrease in oxygen transmission rate was observed. Accordingly, lignin palmitate and laurate have a high potential as a barrier materials in packaging applications.
RETRACTED: DNAzymes in Environmental Sensing (2006)

Please click here to view a statement of retraction concerning this article.
Sequestration of Amyloid β‐Peptide<sup>a</sup> (1993)

Amyloid beta-protein, or beta/A4, is a 4-kilodalton peptide that forms poorly soluble extracellular depositions of amyloid in brains and leptomeninges of patients with Alzheimer's disease (AD), Down's syndrome (DS), and hereditary cerebral hemorrhage with amyloidosis-Dutch type (HCHWA-D). beta/A4 peptide is a derivative of a large transmembrane glycoprotein (APP) and is found in the extracellular space, i.e., in the cerebrospinal fluid and serum of individuals with and without AD and in the conditioned media of many different cells grown in culture. The mechanism by which normally produced amyloid beta peptide forms extracellular aggregates in patients is unknown. One possible explanation is a failure of a mechanism for removal of the beta/A4 peptide that prevents this highly aggregating peptide from forming extracellular amyloid depositions.
Wireless power transfer with artificial magnetic conductors (2013)

In this paper, a wireless power transfer system (WPT) with magnetically coupled resonators is studied. The idea to use a reflector to enhance the coupling coefficient and the transfer efficiency is proposed and analyzed. Perfect magnetic conductor (PMC) was used in numerical calculations in order to study the performance of a reflector. In the WPT system we studied, efficiency is increased from 48% without reflector to 72% with PMC reflector. With recently developed metamaterial technologies, artificial PMCs can be designed and fabricated for such reflectors.
Hand-Motion Crane Control Using Radio-Frequency Real-Time Location Systems (2012)

Human operators have difficulty driving cranes quickly, accurately, and safely because the heavy structure of the crane responds slowly and its payload oscillates. Manipulation difficulty is increased by nonintuitive control interfaces (such as buttons, levers, and joysticks) that require substantial experience to master. This paper presents a new type of interface that allows operators to drive a crane by simply moving a hand-held radio-frequency tag through the desired path. Real-time location sensors are used to track the movements of the tag and its position is used in a feedback control loop to drive the crane. Unfortunately, crane movements usually induce large-amplitude payload oscillations. Therefore, an input-shaping control element is used to limit payload swing. Experimental results on an industrial bridge crane validate the controller performance.
Operation Improvement of The Omni-directional Power Assisted Cart (2004)

We developed an easy-to-operate, omni-directional vehicle including the power assist technology that acts for both the lon-gitudinal and rotational motions of the cart. We had two challenges during the development of this power-assisted cart. The first one was that, due to the relatively long body of the cart, it was difficult to keep the balance between lateral movement and turning movement of the cart when shifting the cart laterally. Therefore we modified the equation for calculating the cart turning speed so that the moment, which was driven by the operating force in the right/left direction, was offset. This way, we could stabilize the balance, resulting in a largely increased operating performance in the lateral direction. The second problem was that, during the one-hand pull-operation, the cart tended to run off its course to the right/left, especially during cornering. To solve this problem, we developed a positional control that detects the amount of lateral deviation by dead reckoning. Do-ing so, we could efficiently reduce the lateral deviation of the cart. We have succeeded in largely improving the operating performance by developing the above control technique.
A Method for Optimizing the Output Power of MEMS Vibrational Energy Harvester (2020)

A MEMS vibrational energy harvester is developed for infrastructures monitoring systems. The output power is maximized by appropriately choosing the load resistance in accordance with the vibration conditions of a vibration source. More than 500 μu W of output power is obtained from an actual vacuum pump used in a factory.