gebhart/patrepeval huggingface dataset:
Research paper Isolation of trans-acting genes that enhance soluble expression of scFv antibodies in the E. coli cytoplasm by lambda phage display (2007)

Functional antibody fragments with native disulfide bonds can be expressed in Escherichia coli trxB gor mutant strains having an oxidizing cytoplasm that allows the formation of disulfide bonds. However, expression yields in the cytoplasm are generally lower than those obtained by secretion into the periplasm. We developed a novel methodology for the screening of genomic DNA fragments that enhance expression yields of scFvs in the cytoplasm of trxB gor cells by capitalizing on bacteriophage lambda display. The anti-digoxin 26.10 scFv was displayed on λ as a fusion to the coat protein gpD. A genomic E. coli library was cloned into λgt11 downstream from the lac promoter and used to lysogenize cells transformed with a plasmid encoding the scFv–gpD fusion. Following induction of expression of the cloned gene fragments, phage was prepared and screened for improved functional display via panning against immobilized hapten. Phage exhibiting improved display was isolated after two rounds. One of the isolated clones, encoding the N-terminal domain of the alpha-subunit of RNA polymerase (α-NTD), was shown to increase the yield of scFv expressed in soluble form in the cytoplasm. © 2007 Elsevier B.V. All rights reserved.
Concise Synthesis of 2,6‐Disubstituted Morpholines by Cyclization of Epoxy Alcohols (2007)

Abstract A novel, straightforward and high yielding synthesis of enantiomerically pure 2,6‐disubstituted morpholines was developed by acid‐catalyzed cyclization of epoxy alcohols. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2007)
Figure S2 from A Threshold of Systemic MAGE-A Gene Expression Predicting Survival in Resected Non–Small Cell Lung Cancer (2023)

&lt;p&gt;Analysis of solely bone marrow aspirates&lt;/p&gt;
Correction to Discovery of N-(4-[18F]Fluoro-5-methylpyridin-2-yl)isoquinolin-6-amine (JNJ-64326067), a New Promising Tau Positron Emission Tomography Imaging Tracer (2020)

status: Published
Analysis of the localization of STE6/CFTR chimeras in a Saccharomyces cerevisiae model for the cystic fibrosis defect CFTRΔF508 (1996)

The use of yeast as a model system to study mammalian proteins is attractive, because yeast genetic tools can be utilized if a suitable phenotype is created. STE6, the Saccharomyces cerevisiae a-factor mating pheromone transporter, and CFTR, the mammalian cystic fibrosis transmembrane conductance regulator, are both members of the ATP binding cassette (ABC) superfamily. Teem et al. (1993) described a yeast model for studying a mutant form of the cystic fibrosis protein, CFTR delta F508. The model involved expression of a chimeric molecule in which a portion of yeast STE6 was replaced with the corresponding region from mammalian CFTR. The STE6/CFTR chimera complemented a ste6 mutant strain for mating, indicating that it could export a-factor. However, mating efficiency was dramatically reduced upon introduction of delta F508, providing a yeast phenotype for this mutation. In human cells, the delta F508 mutation results in retention of CFTR in the endoplasmic reticulum (ER), and possibly in reduction of its chloride-channel activity. Here we examine the basis for the differences in STE6 activity promoted by the wild-type and mutant STE6/CFTR chimeras. By analysis of protein stability and subcellular localization, we find that the mutant chimera is not ER-retained in yeast. We conclude that the molecular basis for the reduced mating of the STE6/CFTR delta F508 chimera must reflect a reduction in its capacity to transport a-factor, rather than mistrafficking. Thus, STE6/CFTR delta F508 in yeast appears to be a good genetic model to probe certain aspects of protein function, but not to study protein localization.
Synthesis of Molybdenum Perfluorophenylimido 2-Adamantylidene Complexes (2021)

Addition of 2-adamantylMgBr in diethyl ether to Mo(NArF)2(Cl)2(DME) (ArF = C6F5) gave Mo(NArF)2(Ad)2 (2, Ad = 2-adamantyl, DME = 1,2-dimethoxyethane). Addition of HCl and 2,2′-bipyridyl (bipy) to 2 gave Mo(NArF)(Adene)Cl2(bipy) (3a, Adene = 2-adamantylidene) while addition of triflic acid to 2 in the presence of DME gave Mo(NArF)(Adene)(OTf)2(DME) (3b). Compound 3b was used to prepare Mo(NArF)(Adene)(ORF9)2 (4), Mo(NArF)(Adene)(ORF9)2(THF) (4(THF)), Mo(NArF)(Adene)(ORF9)2(Piv) (4(Piv); Piv = pivalonitrile), Mo(NArF)(Adene)(OTf)(OHMT)(THF) (5(THF); OHMT = O-2,6-Mesityl2C6H3), Mo(NArF)(Adene)(OTf)(OHMT)(Piv) (5(Piv)), Mo(NArF)(Adene)(OHMT)(Pyr)(Piv) (6(Piv); Pyr = pyrrolide), and Mo(NArF)(Adene)(Me2Pyr)2 (7; Me2Pyr = 2,5-dimethylpyrrolide). X-ray structural studies of nine Adene compounds show that the difference in the Mo—Cα—Cβ bond angles in the Adene ligand is small in 18e 3a and 3b and most significant (32°) in 14e 4. Preliminary studies show that compounds 4–7 are initiators for homocoupling of 1-decene and polymerization of cyclooctene and 5,6-dicarbomethoxynorbornadiene.
Coordinated Regulation of Toll-Like Receptor and NOD2 Signaling by K63-Linked Polyubiquitin Chains (2007)

K63 polyubiquitin chains spatially and temporally link innate immune signaling effectors such that cytokine release can be coordinated. Crohn's disease is a prototypical inflammatory disorder in which this process may be faulty as the major Crohn's disease-associated protein, NOD2 (nucleotide oligomerization domain 2), regulates the formation of K63-linked polyubiquitin chains on the I kappa kinase (IKK) scaffolding protein, NEMO (NF-kappaB essential modifier). In this work, we study these K63-linked ubiquitin networks to begin to understand the biochemical basis for the signaling cross talk between extracellular pathogen Toll-like receptors (TLRs) and intracellular pathogen NOD receptors. This work shows that TLR signaling requires the same ubiquitination event on NEMO to properly signal through NF-kappaB. This ubiquitination is partially accomplished through the E3 ubiquitin ligase TRAF6. TRAF6 is activated by NOD2, and this activation is lost with a major Crohn's disease-associated NOD2 allele, L1007insC. We further show that TRAF6 and NOD2/RIP2 share the same biochemical machinery (transforming growth factor beta-activated kinase 1 [TAK1]/TAB/Ubc13) to activate NF-kappaB, allowing TLR signaling and NOD2 signaling to synergistically augment cytokine release. These findings suggest a biochemical mechanism for the faulty cytokine balance seen in Crohn's disease.
Nonlinear State Estimation with FMI: Tutorial and Applications (2020)

One of the key uses enabled by the functional mockup interface (FMI) standard is the ability to combine Modelica models governed by differential-algebraic equations with measurement data to systematically estimate unmeasured quantities in physical systems. While it is clear how this might be done in theory, many implementation challenges can make this difficult in practice. This paper provides a tutorial connecting the mathematical formulation of two different estimators, the extended Kalman filter (EKF) and the ensemble Kalman filter (EnKF), to an FMIbased Modelica implementation of these estimators. The efficacy of these methods are demonstrated on an example of a small motor model and a larger thermodynamic model of a building, and some of the advantages and disadvantages of this FMI-based approach to estimation are discussed, as well as limitations of FMI associated with constraint management for these estimation methods. The code for the motor example is publicly available and is attached to this publication.
Familial Cerebral Amyloid Angiopathies and Dementia (2000)

Amyloidosis is a disorder of protein conformation leading to aggregation. The term defines a diverse group of proteins normally present in body fluids as soluble precursors that can be deposited as insoluble amyloid fibrils in different tissues producing organ dysfunction and cell death. These fibrils are composed of self-assembled, low molecular weight mass peptides adopting beta-pleated sheet structure, the conformation responsible for their physicochemical properties and tinctoreal characteristics. So far, 20 different proteins have been identified as subunits of amyloid fibrils (Westermark et al., 1999). Collectively, they are products of normal genes; however, several amyloid precursors contain abnormal amino acid substitutions that can impose an unusual potential for self-aggregation. The molecular mass of the amyloid peptides is within the 4 to 30-kDa range, with heterogeneity at the amino- and carboxyl-terminal portions found in most amyloid proteins. Increased levels of amyloid precursors, either in the circulation or locally in sites of deposition, are usually the result of overexpression or defective clearance, or both. Of the 20 amyloid proteins identified, few of them are known to cause amyloid deposition in the central nervous system, which in turn results in cognitive deficits, dementia, stroke, cerebellar and extrapyramidal signs, or a combination of them.
Anticancer and Some Biological Activities of Thiazinotrienomycin B. (2000)

Cancers are caused by complex combinations of somatic mutations in genes controlling cell growth and differentiation.
Control of tumor growth in animals by infusion of an angiogenesis inhibitor. (1980)

Angiogenesis and tumor growth were inhibited in two different animal models by regional infusion of a partially purified cartilage extract. In rabbits bearing corneal implants of V2 carcinoma and receiving the inhibitor, vascular growth rates were < 3% of those in control animals receiving either Ringer's solution or bovine trypsin inhibitor (Trasylol). Subconjunctival B16 melanoma implants in mice receiving the inhibitor weight < 2.5% of implants in mice receiving Ringer's solution, Trasylol, or albumin. Histologic study of major organs and standard blood tests revealed no toxic effects in any of the animals. The inhibitor did not retard the growth of either tumor cell type in tissue culture at concentrations as high as 1 mg/ml. These results suggest that the cartilage factor does not interfere with the growth of the tumor cell population directly but that it prevents tumor growth by inhibiting angiogenesis.
A Highly Efficient and Adaptable Solar-Energy Harvesting Circuit for Batteryless IoT Devices (2018)

In this paper a new on-chip 2nd generation solar energy harvesting DC-DC converter has been proposed for a battery-less Internet of Things (IoTs) Devices. The propose circuit is design to maximize the transfer efficiency and stability as well as enough high power supply to the back-end loads. Altogether the proposed circuit consists of a cross-coupled charge pump, a maximum power point tracking (MPPT) circuit, a timing control circuit and regulator. The range of input voltage is from 0.5V to 3V. Required boosted output voltage is in the range of 1V to 3.3V. The maximum transfer efficiency is more than 60% and the maximum throughout power is 200μW. A gated clock frequency modulation circuit has been designed and employed in the maximum power point tracking (MPPT) unit to lock the input resistance of the charge pump. In addition, to provide a stable voltage to the load a low dropout (LDO) regulator circuit is used. The experimental results show that the maximum power conversion efficiency (PCE) is 78% at 52μW input power condition.
Relationship of HfO2 Material Properties and Transistor Performance (2006)

We report on the relationship between the materials science of a HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /TiN stack and transistor performance. Atomic layer deposited (ALD) HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> can be scaled to a physical thickness of 1.2 nm resulting in EOT 1.0 nm. In scaling HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> the interfacial SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> layer (IL) is also scaled and the extent of HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> crystallization is reduced. Reduced HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> crystallinity is coincident with reduced threshold voltage instability (10 mV) and increased electron mobility (82% Univ. SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ). For these stable, high mobility devices, we find that HfO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> can coordinate N as Hf-N without excessive nitridation of the IL
Two Band Model Interpretation of the p to n Transition in Ternary Tetradymite Topological Insulators (2015)

The requirement for large bulk resistivity in topological insulators has led to the design of complex ternary and quaternary phases with balanced donor and acceptor levels. A common feature of the optimized phases is that they lie close to the p to n transition. The tetradymite Bi2Te3_xSex system exhibits minimum bulk conductance at the ordered composition Bi2Te2Se. By combining local and integral measurements of the density of states, we find that the point of minimum electrical conductivity at x=1.0 where carriers change from hole-like to electron-like is characterized by conductivity of the mixed type. Our experimental findings, which are interpreted within the framework of a two band model for the different carrier types, indicate that the mixed state originates from different type of native defects that strongly compensate at the crossover point.
<title>Feature spacing trajectory representation and processing for active vision</title> (1996)

A new feature space trajectory (FST) description of 3D distorted views of an object is advanced for active vision applications. In an FST, different distorted object views are vertices in feature space. A new eigen-feature space and Fourier transform features are used. Vertices for different adjacent distorted views are connected by straight lines so that an FST is created as the viewpoint changes. Each different object is represented by a distinct FST. An object to be recognized is represented as a point in feature space; the closest FST denotes the class of the object, and the closest line segment on the FST indicates its pose. A new neural network is used to efficiently calculate distances. We discuss its uses in active vision. Apart from an initial estimate of object class and pose, the FST processor can specify where to move the sensor to: confirm class and pose, to grasp the object, or to focus on a specific object part for assembly or inspection. We advance initial remarks on the number of aspect views needed and which aspect views are needed to represent an object. We note the superiority of our eigenspace for discrimination, how it can provide shift invariance, and how the FST overcomes problems associated with other classifiers.
Complex Regulation by Apetala2 Domain-Containing Transcription Factors Revealed through Analysis of the Stress-Responsive TdCor410b Promoter from Durum Wheat (2013)

Expression of the wheat dehydrin gene Cor410b is induced several fold above its non-stressed levels upon exposure to stresses such as cold, drought and wounding. Deletion analysis of the TdCor410b promoter revealed a single functional C-repeat (CRT) element. Seven transcription factors (TFs) were shown to bind to this CRT element using yeast one-hybrid screens of wheat and barley cDNA libraries, of which only one belonged to the DREB class of TFs. The remaining six encoded ethylene response factors (ERFs) belong to three separate subfamilies. Analysis of binding selectivity of these TFs indicated that all seven could bind to the CRT element (GCCGAC), and that three of the six ERFs could bind both to the CRT element and the ethylene-responsive GCC-box (GCCGCC). The TaERF4 subfamily members specifically bound the CRT element, and did not bind either the GCC-box or DRE element (ACCGAC). Molecular modeling and site-directed mutagenesis identified a single residue Pro42 in the Apetala2 (AP2) domain of TaERF4-like proteins that is conserved in monocotyledonous plants and is responsible for the recognition selectivity of this subfamily. We suggest that both DREB and ERF proteins regulate expression of the Cor410b gene through a single, critical CRT element. Members of the TaERF4 subfamily are specific, positive regulators of Cor410b gene expression.
ChemInform Abstract: High Oxidation State Transition Metal Complexes Ligated with N‐Heterocyclic Carbenes (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Contamination rates of optical surfaces at 157 nm in the presence of hydrocarbon impurities (2002)

Photodeposition rates for ten hydrocarbon species have been measured on CaF<SUB>2</SUB> substrates under 157-nm irradiation in the presence of ppm scale levels of oxygen. The species are representative of hydrocarbon based compounds observed in outgassing studies of common build materials used in 157-nm based lithographic systems. Photodeposition rates have also been measured for a subset of the hydrocarbon species on a MgF<SUB>2</SUB> thin film, six anti-reflective dielectric stacks, and fluorine doped fused silica for comparison with the results on CaF<SUB>2</SUB> substrates. Two contamination processes are observed. One is the formation of an equilibrium layer on the surfaces. The other is a quasi-permanent contamination which is most pronounced at elevated levels of contaminant.
A New Calibration Method for Sampling Clock Skew in Time-interleaved ADC (2008)

A sampling clock skew calibration method with a new calibration signal addition circuit is presented in this paper. The clock skew is detected using a calibration signal, and the calibration is done by adjustment of sample clock delay. The new calibration signal addition circuit consisting of small capacitors and a few switches has little interference to the input signal, and makes it possible for the proposed calibration method to operate at background.
Proteolytic activation defines distinct lymphangiogenic mechanisms for VEGFC and VEGFD (2016)

Lymphangiogenesis is supported by 2 homologous VEGFR3 ligands, VEGFC and VEGFD. VEGFC is required for lymphatic development, while VEGFD is not. VEGFC and VEGFD are proteolytically cleaved after cell secretion in vitro, and recent studies have implicated the protease a disintegrin and metalloproteinase with thrombospondin motifs 3 (ADAMTS3) and the secreted factor collagen and calcium binding EGF domains 1 (CCBE1) in this process. It is not well understood how ligand proteolysis is controlled at the molecular level or how this process regulates lymphangiogenesis, because these complex molecular interactions have been difficult to follow ex vivo and test in vivo. Here, we have developed and used biochemical and cellular tools to demonstrate that an ADAMTS3-CCBE1 complex can form independently of VEGFR3 and is required to convert VEGFC, but not VEGFD, into an active ligand. Consistent with these ex vivo findings, mouse genetic studies revealed that ADAMTS3 is required for lymphatic development in a manner that is identical to the requirement of VEGFC and CCBE1 for lymphatic development. Moreover, CCBE1 was required for in vivo lymphangiogenesis stimulated by VEGFC but not VEGFD. Together, these studies reveal that lymphangiogenesis is regulated by two distinct proteolytic mechanisms of ligand activation: one in which VEGFC activation by ADAMTS3 and CCBE1 spatially and temporally patterns developing lymphatics, and one in which VEGFD activation by a distinct proteolytic mechanism may be stimulated during inflammatory lymphatic growth.
In Vivo Characterization of a Series of18F-Diaryl Sulfides (18F-2-(2′-((Dimethylamino)Methyl)-4′-(Fluoroalkoxy)Phenylthio)Benzenamine) for PET Imaging of the Serotonin Transporter (2009)

This compound series was found to have potential for producing a suitable (18)F-radiolabeled PET radiotracer for SERT. Compound 4, the pentoxy derivative, had the lowest brain uptake and target-to-nontarget ratio. Compound 3, the butoxy derivative, had a lower target-to-nontarget ratio than compounds 1 (ethoxy derivative) and 2 (propoxy derivative). Compounds 1 and 2 both hold promise as SERT radioimaging agents, but because of cost limitations, only compound 2 will be evaluated in further studies.
Synthetic regulatory reconstitution reveals principles of mammalian Hox cluster regulation (2022)

Precise <i>Hox</i> gene expression is crucial for embryonic patterning. Intra-<i>Hox</i> transcription factor binding and distal enhancer elements have emerged as the major regulatory modules controlling <i>Hox</i> gene expression. However, quantifying their relative contributions has remained elusive. Here, we introduce "synthetic regulatory reconstitution," a conceptual framework for studying gene regulation, and apply it to the <i>HoxA</i> cluster. We synthesized and delivered variant rat <i>HoxA</i> clusters (130 to 170 kilobases) to an ectopic location in the mouse genome. We found that a minimal <i>HoxA</i> cluster recapitulated correct patterns of chromatin remodeling and transcription in response to patterning signals, whereas the addition of distal enhancers was needed for full transcriptional output. Synthetic regulatory reconstitution could provide a generalizable strategy for deciphering the regulatory logic of gene expression in complex genomes.
Matching Vector Codes. (2010)

An (r, δ, ɛ)-locally decodable code encodes a k-bit message x to an N-bit codeword C(x), such that for every i ∈ [k], the i-th message bit can be recovered with probability 1 − ɛ, by a randomized decoding procedure that queries only r bits, even if the codeword C(x) is corrupted in up to δN locations. Recently a new class of locally decodable codes, based on families of vectors with restricted dot products has been discovered. We refer to those codes as Matching Vector (MV) codes. Several families of (r, δ, Θ(rδ))-locally decodable MV codes have been obtained. While codes in those families were shorter than codes of earlier generations, they suffered from having large values of ɛ = Ω(rδ), which meant that r-query MV codes could only handle error-rates below 1 r. Thus larger query complexity gave shorter length codes but at the price of less error-tolerance. No MV codes of super-constant number of queries capable of tolerating a constant fraction of errors were known to exist. In this paper we present a new view of matching vector codes and uncover certain similarities between MV codes and classical Reed Muller codes. Our view allows us to obtain deeper insights into the power and limitations of MV codes. Specifically, 1. We show that existing families of MV codes can be enhanced to tolerate a large constant fraction of errors, independent of the number of queries. Such enhancement comes at a price of a moderate increase in the number of queries; 2. Our construction yields the first families of matching vector codes of super-constant query complexity that can tolerate a constant fraction of errors. Our codes are shorter than Reed Muller LDCs for all values of r ≤ log k/(log log k) c, for some constant c; 3. We show that any MV code encodes messages of length k to codewords of length at least k2 Ω( √ log k). Therefore MV codes do not improve upon Reed Muller LDCs for r ≥ (log k) Ω ( √ log k)
Closing the Part D Coverage Gap and Out-of-Pocket Costs for Multiple Sclerosis Drugs (2020)

Medicare Part D beneficiaries can pay thousands of dollars yearly out of pocket for DMTs. Closing the Part D coverage gap did not reduce out-of-pocket costs for patients because of simultaneous increases in DMT prices.