gebhart/patrepeval huggingface dataset:
Inactivation of the Flagellin Gene flaA in Magnetospirillum gryphiswaldense Results in Nonmagnetotactic Mutants Lacking Flagellar Filaments (2004)

Magnetotactic bacteria synthesize magnetosomes, which cause them to orient and migrate along magnetic field lines. The analysis of magnetotaxis and magnetosome biomineralization at the molecular level has been hindered by the unavailability of genetic methods, namely the lack of a means to introduce directed gene-specific mutations. Here we report a method for knockout mutagenesis by homologous recombination in Magnetospirillum gryphiswaldense. Multiple flagellin genes, which are unlinked in the genome, were identified in M. gryphiswaldense. The targeted disruption of the flagellin gene flaA was shown to eliminate flagella formation, motility, and magnetotaxis. The techniques described in this paper will make it possible to take full advantage of the forthcoming genome sequences of M. gryphiswaldense and other magnetotactic bacteria.
Evolution of WCDMA high speed packet access and broadcast services (2007)

This paper addresses the latest approaches for improving the data rates and spectral efficiency of the high speed packet access (HSPA) mode of wideband CDMA (WCDMA). The improvements are due to advances in modulation techniques, interference suppression, and broadcast channel reception relative to previously standardized approaches. The new modulation techniques include 2x2 MIMO and 64QAM on the downlink, and 16QAM on the uplink. Interference suppression has been augmented to more accurately model multiple sources of interference. Broadcast channel reception has been restructured for the case of multimedia services. A single frequency network option has been added to allow for macro-diversity to enable comprehensive coverage with interference suppression. We discuss all these advances and evaluate the respective performance impacts based on system and/or link simulations.
The Total Synthesis of Coleophomones B, C, and D (2005)

Members of the coleophomone family of natural products all possess several intriguing and challenging architectural features, as well as exhibit unusual biological activity. They, therefore, constitute attractive targets for synthesis. In this Article, we describe the total synthesis of coleophomones B (2), C (3), and D (4). The highly strained and congested 11-membered macrocycle of coleophomones B (2) and C (3) was constructed using an impressive olefin metathesis reaction. Furthermore, both of the requisite geometric isomers of the Delta(16,17) within the macrocycle could be accessed from a common precursor, facilitating a divergence that lent the coleophomone B (2)/C (3) synthesis an unusually high degree of efficiency. The synthesis of coleophomone D (4) confirmed that it exists as a dynamic mixture of isomeric forms with a different aromatic substitution pattern from the other family members.
CYANOSIS IN INFANTS WITH NITRATES IN DRINKING WATER AS CAUSE (1949)

Five cases of idiopathic cyanosis in babies are reported. They cleared and did not recur when well water used for drinking and formula was changed, as a result of demonstrated contamination with Coliform organisms. These cases substantiate the contention of Comly that the toxic, or nitrate-containing water, is the cause of the cyanosis. This cyanosis appears as a result of the oxidation of hemoglobin into methemoglobin by the nitrites derived from nitrates present in the well water used for drinking or formula. Cyanosis cleared within a few days following removal of the infant to the hospital, away from the home water supply, but recurred within one to two weeks after returning home to the use of the contaminated water. One infant strongly suggested that milk from cows which drank the contaminated water may be the cause of moderate cyanosis when the milk supply is restricted to the single herd. One infant suggested that cyanosis may occur in a breast-fed infant, if the mother drinks the contaminated well water, or the milk from cows drinking water from that well. Many cases of cyanosis in early infancy in farm homes have been and still are being incorrectly treated for hypertrophy of the thymus gland. Cyanosis in early infancy, occurring particularly in babies living on farms one to three weeks after birth, can be cleared by using uncontaminated water.
A poxvirus-derived vector that directs high levels of expression of cloned genes in mammalian cells. (1988)

High levels of expression of cloned genes have been obtained in mammalian cells by using poxvirus-derived insertion/expression vectors. These vectors employ the cis-acting element (CAE I) that directs the transcription of one of the most strongly expressed genes of cowpox virus. This gene (the 160K gene) encodes the 160-kDa protein that is the major component of the A-type cytoplasmic inclusions. Its counterpart in vaccinia virus (VV) is the 94K gene contained in the HindIII A fragment of the viral DNA. Two insertion vectors have been constructed; each is designed to allow cloned genes to be placed immediately downstream of a modified version of CAE I within a poxvirus genome. One vector, p1200, enables the CAE I-cloned-gene constructs to be inserted into the thymidine kinase gene of VV. This vector was used to create a VV recombinant that directed expression of the chloramphenicol acetyltransferase (CAT) gene. The other vector, p2101, enables the CAE I-cloned-gene constructs to be inserted into the VV 94K gene. The prototype of this vector was used to create a VV recombinant that directed expression of a hybrid CAT-lacZ gene. Infection of cultured human cells with these recombinants led to high levels of synthesis of either the CAT gene product or the CAT-lacZ gene product. Each of these proteins was produced in quantities that were easily detected by Coomassie blue staining of total cell proteins resolved by polyacrylamide gel electrophoresis. We estimate that these vectors are capable of directing the synthesis of milligram amounts of gene product per 10(9) mammalian cells.
Effect of Tumor Microenvironment Modulation on the Efficacy of Oncolytic Virus Therapy (2007)

A single dose of angiostatic cRGD peptide treatment before oncolytic virus treatment enhanced the antitumor efficacy of oncolytic virus.
Development and in Vitro Testing of a Miniature Robotic System for Computer-Assisted Colonoscopy (1999)

In this article we present a new concept for computer-assisted colonoscopy based on a miniature robot capable of propelling itself semiautonomously along the colon.The miniature robot is designed to perform the same functions as current colonoscopy systems-i.e., visualization and tissue sampling for biopsy-and exploits an innovative inchworm-like locomotion principle based on adhering to the colon wall by vacuum suction.The miniature robot is connected by a thin and flexible umbilical cable to an external control unit; this unit provides pneumatic actuation signals in the appropriate sequence to the miniature robot, and information on the robot's functioning to the endoscopist, who can either teleoperate or directly supervise its operation.A prototype colonoscopy system using this robot has been fabricated and tested in vim, with promising results.The proposed concept has strong potential for further development, since miniaturization and functional integration of instrumentation and tools, together with computer assistance, not only make colonoscopy more acceptable, but can also open up a wide range of new applications in endoluminal diagnosis, therapy, and surgery.
Catalytic Asymmetric Total Synthesis of (+)-Lactacystin (2006)

Total synthesis of (+)-lactacystin, a potent and selective proteasome inhibitor, was accomplished using a catalytic enantioselective Strecker reaction of a ketoimine as the initial key step. An enone-derived N-phosphinoyl ketoimine 7 was selected as a stable masked α-hydroxy ketoimine analogue. Excellent enantioselectivity (98% ee) and practical catalyst activity were produced under the optimized catalyst preparation method using 2.5 mol % Gd{N(SiMe3)2}3 as a metal source and 3.8 mol % d-glucose-derived ligand 8. This reaction was conducted on a 5 g scale. The chiral tetrasubstituted C-5 carbon efficiently controlled the stereochemistry of the other three chiral centers of lactacystin. Chelation-controlled Meerwein-type reduction of ketone 5 using i-PrMgBr (originally reported by Kang in a related substrate) selectively produced the desired secondary alcohol at the C-9 position. The C-6 hydroxy and C-7 methyl groups were introduced via a silyl conjugate addition followed by the Tamao oxidation and Donohoe methylation, respectively, in a highly stereoselective manner. A practical amount of enantiomerically pure clasto-lactacystin β-lactone (2), the biologically active form of (+)-lactacystin, can be synthesized using this route. clasto-Lactacystin β-lactone (2) was converted to (+)-lactacystin following the reported procedure.
A Model for Fibrinogen: Domains and Sequence (1985)

Electron microscopy of rotary-shadowed fibrinogen demonstrates that the molecules modified for crystallization by limited cleavage with a bacterial protease retain the major features of the native structure. This evidence, together with image processing and x-ray analysis of the crystals and of fibrin, has been used to develop a three-dimensional low resolution model for the molecule. The data indicate that the two large end domains of the molecule would be composed of the carboxyl-terminus of the B beta chain (proximal) and gamma chain (distal), respectively; the carboxyl-terminus of the A alpha chain would fold back to form an additional central domain. On this basis, the carboxyl-terminal region of each of the three chains of fibrinogen is folded independently into a globular domain.
Mechanical Maceration Divergently Shifts Protein Degradability in Condensed‐Tannin vs. o‐Quinone Containing Conserved Forages (2008)

Conditioning and conservation methods may interact with polyphenols to alter forage crude protein (CP) solubility and degradability. In this study, forages with ∼200 g CP kg −1 dry matter were roll conditioned or macerated, conserved as hay or silage, and then analyzed for CP fractions. Shifting from roll conditioning to maceration of polyphenol‐free alfalfa ( Medicago sativa L.) reduced buffer soluble protein (SP) with little effect on protease rumen‐undegradable protein (RUP) and intestinal available protein (IAP, RUP minus acid‐detergent insoluble CP). In birdsfoot trefoil ( Lotus corniculatus L.), condensed tannin (CT) and maceration independently reduced SP and increased RUP to yield up to 62% more IAP in hay and 145% more IAP in silage than alfalfa. Based on results with trefoil, roll‐conditioned forage with 70 to 120 g CT kg −1 CP or macerated forage with more modest CT levels should meet a 350 g RUP kg −1 CP target to support 35 kg d −1 milk yield by cattle. In roll‐conditioned red clover ( Trifolium pratense L.), o ‐quinones formed by polyphenol oxidase reduced SP and increased RUP to yield 50% more IAP in hay and 88% more IAP in silage than alfalfa. Surprisingly, maceration reduced SP, RUP, and IAP in clover. Following maceration, RUP and IAP in conserved clover and trefoil responded similarly to CT, suggesting that maceration disabled o ‐quinone protection of protein substrates. Although red clover has high RUP, low reported milk yields indicate o ‐quinones might depress IAP.
Complex translational regulation of BACE1 involves upstream AUGs and stimulatory elements within the 5' untranslated region (2007)

BACE1 is the protease responsible for the production of amyloid-beta peptides that accumulate in the brain of Alzheimer's disease (AD) patients. BACE1 expression is regulated at the transcriptional, as well as post-transcriptional level. Very high BACE1 mRNA levels have been observed in pancreas, but the protein and activity were found mainly in brain. An up-regulation of the protein has been described in some AD patients without a change in transcript levels. The features of BACE1 5' untranslated region (5' UTR), such as the length, GC content, evolutionary conservation and presence of upstream AUGs (uAUGs), indicate an important regulatory role of this 5' UTR in translational control. We demonstrate that, in brain and pancreas, almost all of the native BACE1 mRNA contains the full-length 5' UTR. RNA transfection and in vitro translation show that translation is mainly inhibited by the presence of the uAUGs. We provide a mutational analysis that highlight the second uAUG as the main inhibitory element while mutations of all four uAUGs fully de-repress translation. Furthermore, we have evidence that a sequence within the region 222-323 of the BACE1 5' UTR has a stimulatory effect on translation that might depend on the presence of trans-acting factors.
Fermentation performance and intracellular metabolite patterns in laboratory and industrial xylose-fermenting Saccharomyces cerevisiae (2002)

Heterologous genes for xylose utilization were introduced into an industrial Saccharomyces cerevisiae, strain A, with the aim of producing fuel ethanol from lignocellulosic feedstocks. Two transformants, A4 and A6, were evaluated by comparing the performance in 4-l anaerobic batch cultivations to both the parent strain and a laboratory xylose-utilizing strain: S. cerevisiae TMB 3001. During growth in a minimal medium containing a mixture of glucose and xylose (50 g/l each), glucose was preferentially consumed. During the first growth phase on glucose, the specific growth rates were 0.26, 0.32, 0.27 and 0.30 h(-1) for strains TMB 3001, A (parental strain), A4, and A6, respectively. The specific ethanol productivities were 0.04, 0.13, 0.04 and 0.03 g/g.per hour, for TMB 3001, A, A4 and A6, respectively. The specific xylose consumption rates were 0.06, 0.21 and 0.14 g/g.per hour, respectively for strains TMB 3001, A4 and A6. Xylose consumption resulted mainly in the formation of xylitol, with biomass and ethanol being minor products. The metabolite profile of intermediates in the pentose phosphate pathway and key glycolytic intermediates were determined during growth on glucose and xylose, respectively. The metabolite pattern differed depending on whether glucose or xylose was utilized. The levels of intracellular metabolites were higher in the industrial strains than in the laboratory strain during growth on xylose.
Pigment epithelium-derived factor: neurotrophic activity and identification as a member of the serine protease inhibitor gene family. (1993)

Cultured pigment epithelial cells of the fetal human retina secrete a protein, pigment epithelium-derived factor (PEDF), that induces a neuronal phenotype in cultured human retinoblastoma cells. Morphological changes include the induction of an extensive neurite meshwork and the establishment of corona-like cellular aggregates surrounding a central lumen. The differentiated cells also show increases in the expression of neuron-specific enolase and the 200-kDa neurofilament subunit. Amino acid and DNA sequence data demonstrate that PEDF belongs to the serine protease inhibitor (serpin) family. The PEDF gene contains a typical signal-peptide sequence, initiator methionine codon, and polyadenylylation signal and matches the size of other members of the serpin superfamily (e.g., alpha 1-antitrypsin). It lacks homology, however, at the putative serpin reactive center. Thus, PEDF could exert a paracrine effect in the embryonic retina, influencing neuronal differentiation by a mechanism that does not involve classic inhibition of serine protease activity.
Highly linear Al/sub 0.3/Ga/sub 0.7/N-Al/sub 0.05/Ga/sub 0.95/N-GaN composite-channel HEMTs (2005)

We report an Al/sub 0.3/Ga/sub 0.7/N-Al/sub 0.05/Ga/sub 0.95/N-GaN composite-channel HEMT with enhanced linearity. By engineering the channel region, i.e., inserting a 6-nm-thick AlGaN layer with 5% Al composition in the channel region, a composite-channel HEMT was demonstrated. Transconductance and cutoff frequencies of a 1 ×100 μm HEMT are kept near their peak values throughout the low- and high-current operating levels, a desirable feature for linear power amplifiers. The composite-channel HEMT exhibits a peak transconductance of 150 mS/mm, a peak current gain cutoff frequency (f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> ) of 12 GHz and a peak power gain cutoff frequency (f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> ) of 30 GHz. For devices grown on sapphire substrate, maximum power density of 3.38 W/mm, power-added efficiency of 45% are obtained at 2 GHz. The output third-order intercept point (OIP3) is 33.2 dBm from two-tone measurement at 2 GHz.
Individual RNA Base Recognition in Immobilized Oligonucleotides Using a Protein Nanopore (2012)

Protein nanopores are under investigation as key components of rapid, low-cost platforms to sequence DNA molecules. Previously, it has been shown that the α-hemolysin (αHL) nanopore contains three recognition sites, capable of discriminating between individual DNA bases when oligonucleotides are immobilized within the nanopore. However, the direct sequencing of RNA is also of critical importance. Here, we achieve sharply defined current distributions that enable clear discrimination of the four nucleobases, guanine, cytosine, adenine, and uracil, in RNA. Further, the modified bases, inosine, N(6)-methyladenosine, and N(5)-methylcytosine, can be distinguished.
Journey of remdesivir from the inhibition of hepatitis C virus to the treatment of COVID-19 (2022)

If a planned path reaches a dead-end, one can simply stop. Or one can turn around, walk back to the last intersection and take another path, or one can consider taking few paths in parallel. The last scenario is reflective of the journey of remdesivir, the first antiviral for the treatment of COVID-19, that was approved by FDA less than 10 months after the isolation of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. As of January 2022, 10 million COVID-19 patients have been treated with remdesivir worldwide, but the journey of this molecule started more than a decade earlier with the search for a cure of hepatitis C virus. The development path of remdesivir before the emergence of COVID-19 represents a valuable example of a preemptive pandemic preparedness, but the pursuit of this path would not have been possible without sustaining support of John C. Martin, whom we will sorely miss for his piercing vision, uncompromising leadership, and genuine compassion for patients suffering around the world.
Trans-dominant inhibition of poly(ADP-ribosyl)ation potentiates carcinogen induced gene amplification in SV40-transformed Chinese hamster cells. (1996)

Poly(ADP-ribose) polymerase (PARP) is an evolutionally conserved nuclear protein present in most eukaryotic species and catalyzes the formation of ADP-ribose polymers covalently attached to proteins. PARP is strongly activated by DNA single- or double-strand breaks and is thought to be involved in cellular responses to DNA damage. Based on the SV40-transformed Chinese hamster cell line CO60, we had established stable transfectants that overexpress the PARP DNA-binding domain conditionally. DNA-binding domain overexpression led to trans-dominant inhibition of poly(ADP-ribosyl)ation and sensitized the cells to genotoxic agents. Using the amplification of chromosomally integrated SV40 DNA as an indicator system, we show here that trans-dominant PARP inhibition potentiates genetic instability induced by N-methyl-N'-nitro-N-nitrosoguanidine treatment of cells.
A novel invertebrate GABAA receptor‐like polypeptide Sequence and pattern of gene expression (1993)

A full-length complementary DNA has been isolated, from the fresh-water mollusc Lymnaea stagnalis, that encodes a polypeptide (which we have named zeta) that exhibits between 30% and 40% identity to vertebrate GABAA and glycine receptor subunit sequences. The locations of seven introns have been determined in the corresponding gene and six of these occur at similar relative positions as those found in vertebrate GABAA receptor genes. RNase protection studies have revealed that the transcript for this Lymnaean polypeptide is present at highest levels in the adult nervous system but that it can also be detected in peripheral tissues.
The Synthesis and Reactions of Some Substituted β-Lactams (1951)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Synthesis and Reactions of Some Substituted β-LactamsJohn C. Sheehan and Ajay Kumar BoseCite this: J. Am. Chem. Soc. 1951, 73, 4, 1761–1765Publication Date (Print):April 1, 1951Publication History Published online1 May 2002Published inissue 1 April 1951https://pubs.acs.org/doi/10.1021/ja01148a095https://doi.org/10.1021/ja01148a095research-articleACS PublicationsRequest reuse permissionsArticle Views209Altmetric-Citations25LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Heteroaggregation of ceramic colloids in suspensions (2016)

The colloidal route is an important methodology in ceramic processing. A key step of the colloidal route is the aggregation of colloids in suspension. This often involves colloids of different types, in a process which is known as heteroaggregation. Here we review the recent developments in ceramic heteroaggregation, focusing on the physical mechanisms that cause it and on the structural properties of the resulting aggregates. Structural properties are analysed both on the local scale, at the level of nearest-neighbour contacts between colloids and on the long-range scale, at which percolating aggregates form, leading to gelification. Both experimental and simulation results are reviewed. The effects of the structure of the aggregates on the subsequent steps of ceramic processing are discussed.
Studies on the Conversion of Proinsulin to Insulin (1971)

Proinsulin can be rapidly and quantitatively cleaved by a combination of pancreatic trypsin and carboxypeptidase B in vitro to yield intact insulin, the C-peptide, and free arginine and lysine. No significant dealanylation or further degradation of the insulin occurs under the specified conditions. This in vitro system appears to provide a useful model for studies of the in vivo converting enzyme system localized in the β-cells of the islets of Langerhans.