gebhart/patrepeval huggingface dataset:
A Mutant of Arabidopsis Deficient in Desaturation of Palmitic Acid in Leaf Lipids (1989)

The overall fatty acid composition of leaf lipids in a mutant of Arabidopsis thaliana was characterized by elevated amounts of palmitic acid and a decreased amount of unsaturated 16-carbon fatty acids as a consequence of a single nuclear mutation. Quantitative analysis of the fatty acid composition of individual lipids suggested that the mutant is deficient in the activity of a chloroplast omega9 fatty acid desaturase which normally introduces a double bond in 16-carbon acyl chains esterified to monogalactosyldiacylglycerol (MGD). The mutant exhibited an increased ratio of 18- to 16-carbon fatty acids in MGD due to a change in the relative contribution of the prokaryotic and eukaryotic pathways of lipid biosynthesis. This appears to be a regulated response to the loss of chloroplast omega9 desaturase and presumably reflects a requirement for polyunsaturated fatty acids for the normal assembly of chloroplast membranes. The reduction in mass of prokaryotic MGD species involved both a reduction in synthesis of MGD by the prokaryotic pathway and increased turnover of MGD molecular species which contain 16:0.
The ovalbumin gene: structural sequences in native chicken DNA are not contiguous. (1978)

The sequence organization of the structural ovalbumin gene and flanking sequences in native chicken DNA was studied by restriction mapping and filter hybridization using a nick-translated probe generated from pOV230, a recombinant plasmid that contains a full-length ovalbumin DNA synthesized from ovalbumin mRNA. The structural sequences of the ovalbumin gene in native chicken DNA were found to be noncontiguous because at least two restriction endonucleases that do not cut the structural sequence do cleave the natural gene into multiple fragments by cleaving within nonstructural sequences interspersed between the structural sequences. The observation that all ovalbumin DNA-containing sequences were contained within a single DNA fragment generated by BamHI digestion of total chicken DNA has allowed us to construct an inclusive restriction map of the natural ovalbumin gene which contains at least two "insert regions." These regions may be further subdivided into alternating structural and insert sequences. Both insert regions were located within the peptide-coding regions of the gene and the sizes of these insert regions were estimated to be approximately 1.0 and 1.5 kilobase pairs, respectively.
Nanopore‐Spanning Lipid Bilayers for Controlled Chemical Release (2008)

A hybrid organic/inorganic chemical delivery system with lipid bilayer seals is demonstrated. Semiconductor fabrication methods are used to produce chemical reservoirs with sub-micrometer pore openings. These openings are selectively sealed by depositing of lipid bilayers. The seals are leak-free and stable for weeks. When desired, the reservoirs can be opened with a standard microscope lamp. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Effect of Cilastatin on Renal Handling of Vancomycin in Rats (1998)

To provide insights into the possibility of reducing the nephrotoxicity of vancomycin (VCM) by cilastatin, the effect of cilastatin on the renal handling of VCM, as well as on glomerular filtration rate (GFR) and plasma protein binding of VCM, were studied using rats. After a bolus intravenous (iv) dose of VCM (100 mg/kg), concomitant cilastatin administration (100 mg/kg, iv) resulted in a significant increase in the total VCM clearance and significant decrease in the kidney uptake clearance of VCM, defined as kidney VCM concentration vs AUC ratio. Moreover, after a 3-h continuous iv infusion of VCM (18 or 90 mg/h/kg), significant decrease in the kidney uptake clearance of VCM was observed with concomitant cilastatin iv infusion (300 mg/h/kg). On the other hand, GFR and VCM plasma protein binding did not show any significant change with cilastatin. From the observation that cilastatin decreased the kidney uptake clearance of VCM and enhanced its urinary excretion, it was suggested that cilastatin inhibited the reabsorption of VCM in the renal proximal tubular cells. Thus, it may be possible that cilastatin alleviates the nephrotoxicity of VCM due to reduced accumulation and accelerated renal excretion of VCM.
Synthesis of 24a-Substituted Milbemycin A4 Derivatives and Their Acaricidal Activity against Tetranychus uvticae (1997)

A series of 24a-substituted milbemycin A4 derivatives were synthesized from 24a-hydroxymilbemycin A4, which had been obtained by the microbial oxidation of milbemycin A4. The acaricidal activity of each synthesized derivative against Tetranychus urticae was tested and some of the derivatives showed higher activity than parent milbemycin A4. Among them, 24a-methylmilbemycin A4 (22) was the most active derivative, with 100% mortality of the mite at a concentration of 1 ppm and 50% mortality at a concentration of 0.1 ppm.
Identification of Chlamydophila Pneumoniae in an Emerald Tree Boa, Corallus Caninus (2004)

Tissues were evaluated from emerald tree boas, Corallus caninus, from a collection in which chlamydiosis was diagnosed. To determine the strain of chlamydia infecting these snakes, tissue samples from 5 frozen snakes were tested by a quantitative TaqMan polymerase chain reaction (PCR) test and a PCR sequence analysis test. Of the 22 samples tested, 9 were categorized as either positive or weakly positive with the TaqMan test, and 6 yielded an amplicon using a serial PCR test that amplified a portion of the 23S ribosomal RNA gene. A PCR product suitable for sequencing was obtained from the heart of one of the snakes. Sequence analysis showed that the snake had been infected with Chlamydophila pneumoniae. These findings show that C. pneumoniae can infect emerald tree boas, broadening the range of reptiles known to be infected by this primarily human pathogen.
DNA Elements Are Asymmetrically Joined During the Site-Specific Recombination of Kappa Immunoglobulin Genes (1985)

Immunoglobulin K genes are constructed during lymphocyte differentiation by the joining of two DNA elements, VK and JK, to form both a VKJK coding unit and a reciprocal recombination product. The two products formed in single VK-to-JK joining events can be directly isolated through the use of a retrovirally introduced recombination substrate. The structural analysis of a number of recombinants and the derivation of secondary recombination products define some of the basic features of the mechanism of immunoglobulin gene assembly.
Pharmacological aspects of Nerium indicum Mill: A comprehensive review (2014)

Phytomedicine is the oldest medical practice known to man. Since the dawn of mankind, various plant resources are used to cure different diseases and also for a long and healthy life. The ancient knowledge of plant based medicine has transferred from generations to generations and accumulated as ethnopharmacological knowledge among different ethnic groups. India is the spanning bed of traditional phytomedicinal system where Ayurveda was born out of the knowledge of traditional medicine. In various other countries of South-Eastern Asia, South America, and in Arabian countries, still today, a great number of people rely primarily on phytomedicines to cure diseases. In the complementary and alternative medicinal systems, Nerium indicum is one such plant which is famed for its therapeutic efficiency in different diseases globally. In the present time, when the pharmaceutical companies are concentrating more toward the plant based traditional medicines to avoid the side-effects and resistance against synthetic drugs, N. indicum has proved its efficiency in different disease models. Therefore, this review comprehensively covers the medicinal and pharmacological activities of different parts of the plant N. indicum.
Controlled-intensity detection peaks in a binary joint transform correlator (1994)

In multiobject pattern recognition the height of the correlation peaks should be controlled when the power spectrum of ajoint transform correlator is binarized. In this paper a method to predetermine the value of detection peaks is demonstrated. The technique is based on a frequency-variant threshold in order to remove the intraclass terms and on a suitable factor to normalize the binary joint power spectrum. Digital simulations and experimental hybrid implementation of this method were carried out.
Rapid fabrication of lightweight silicon-carbide mirrors (2002)

Silicon carbide (SiC) has long been recognized as an attractive mirror material due to its superior mechanical and thermal properties when compared to conventional optical materials. However, the material properties of SiC which make the material attractive from a design standpoint have often precluded its use when low cost and rapid delivery of an optical mirror were required. This paper describes an approach that was developed by Zygo Corporation, working in conjunction with POCO Graphite Inc. for the rapid fabrication of lightweight silicon carbide optics. This approach utilizes a SiC substrate produced by POCO Graphite Inc. using a non-traditional process coupled with deterministic finishing techniques developed by Zygo. Using this approach, we are now capable of producing high quality prototype components (&lambda;/10 PV figure, 10 &Aring; rms. micro roughness) of SiC within a few weeks, rather than the traditional period of months. Applications include lightweight scan mirrors, stage mirrors for lithography positioning tools, as well as similar applications where high stiffness and low weight are significant performance parameters. MRF polishing results comparing SiC to conventional optical materials are also presented.
PCR Amplification from a Homolog of thebEMating-Type Gene as a Sensitive Assay for the Presence ofUstilago scitamineaDNA (1996)

Ustilago scitaminea, the causal agent of sugarcane (Saccharum spp.) smut, has a bipolar mating system in that the haploid stage of the life cycle has sporidia of two mating types (designated plus and minus). Only haploid sporidia of complementary mating types can fuse to form the infectious, mycelial dikaryon. With the use of primers based on the U. maydis bE mating-type gene, DNA segments from sporidia were polymerase chain reaction (PCR)-amplified from both minus and plus mating types of U. scitaminea. These DNA fragments were sequenced and found to be approximately 70% identical in nucleotide sequence to the corresponding region of the bE gene in U. maydis and U. hordei. The mating behavior of U. scitaminea is similar to that of other bipolar Ustilago spp. This and the similarity in DNA sequence between the b genes suggests that mating-type genes of U. scitaminea are similar in structure and function to those of other Ustilago spp. previously studied. Use of one of the cloned fragments as a probe in Southern analysis of U. scitaminea revealed specific hybridization to single BamHI fragments of different sizes in the two mating types, confirming mating type-specific differences at this locus. Primers made to the cloned sequence have been used to amplify by PCR a DNA fragment of the predicted size from a 2,000:1 mixture of sugarcane and U. scitaminea dikaryon DNA.
Limitations of a Molecular Clock Applied to Considerations of the Origin of HIV-1 (1998)

A recent report has provided information that helps to determine the age of a common viral ancestor of the AIDS epidemic. Korber et al . examine the strengths as well as limitations of molecular clock analysis and the implications of the findings for planning vaccines and forecasting the future of the epidemic.
The Three-Dimensional Structure of the Human Pi Class Glutathione Transferase P1-1 in Complex with the Inhibitor Ethacrynic Acid and Its Glutathione Conjugate, (1997)

The potent diuretic drug ethacrynic acid has been tested in clinical trials as an adjuvant in chemotherapy. Its target is the detoxifying enzyme glutathione transferase which is often found overexpressed in cancer tissues. We have solved the crystal structures of human pi class glutathione transferase P1-1 in complex with the inhibitor ethacrynic acid and its glutathione conjugate. Ethacrynic acid is found to bind in a nonproductive mode to one of the ligand binding sites of the enzyme (the H site) while the glutathione binding site (G site) is occupied by solvent molecules. There are no structural rearrangements of the G site in the absence of ligand. The structure indicates that bound glutathione is required for ethacrynic acid to dock into the H site in a productive binding mode. The binding of the ethacrynic acid-glutathione conjugate shows that the contacts of the glutathione moiety with the protein are identical to those observed in crystal structures of the enzyme with other glutathione-based substrates and inhibitors. The ethacrynic acid moiety of the conjugate binds in the H site in a fashion that has not been observed in crystal structures of other glutathione-based inhibitor complexes. The crystal structures implicate Tyr 108 as an electrophilic participant in the Michael addition of glutathione to ethacrynic acid.
CD39L2, a Gene Encoding a Human Nucleoside Diphosphatase, Predominantly Expressed in the Heart (2000)

E-NTPDases are extracellular enzymes that hydrolyze nucleotides. The human E-NTPDase gene family currently consists of five reported members (CD39, CD39L1, CD39L2, CD39L3, and CD39L4). Both membrane-bound and secreted family members have been predicted by encoded transmembrane and leader peptide motifs. In this report, we demonstrate that the human CD39L2 gene is expressed predominantly in the heart. In situ hybridization results from heart indicate that the CD39L2 message is expressed in muscle and capillary endothelial cells. We also show that the CD39L2 gene encodes an extracellular E-NTPDase. Flow cytometric experiments show that transiently expressed CD39L2 is present on the surface of COS-7 cells. Transfected cells also produce recombinant glycosylated protein in the medium, and this process can be blocked by brefeldin A, an inhibitor of the mammalian secretory pathway. The enzymology of CD39L2 shows characteristic features of a typical E-NTPDase, but with a much higher degree of specificity for NDPs over NTPs as enzymatic substrates. The kinetics of the ADPase activity exhibit positive cooperativity. The predominance of CD39L2 expression in the heart supports a functional role in regulating platelet activation and recruitment in this organ.
Human fibroblast collagenase contains an amino acid sequence homologous to the zinc-binding site of Serratia protease. (1987)

Analysis of sequence alignments between the recently published sequence of human fibroblast collagenase and a computer file of published protease sequences has revealed a previously unrecognized homology to the 11 amino acids flanking the zinc-binding site of Serratia protease, a bacterial metalloprotease. There is also strong homology among several bacterial metalloproteases at this site. This finding implies that zinc binding by many proteins may have structural requirements which are apparent even in primary structure and which have been evolutionarily conserved or convergently evolved. This consensus sequence could be used as a marker for recognizing other members of the metalloprotease family.
The path to next generation biofuels: successes and challenges in the era of synthetic biology (2010)

Volatility of oil prices along with major concerns about climate change, oil supply security and depleting reserves have sparked renewed interest in the production of fuels from renewable resources. Recent advances in synthetic biology provide new tools for metabolic engineers to direct their strategies and construct optimal biocatalysts for the sustainable production of biofuels. Metabolic engineering and synthetic biology efforts entailing the engineering of native and de novo pathways for conversion of biomass constituents to short-chain alcohols and advanced biofuels are herewith reviewed. In the foreseeable future, formal integration of functional genomics and systems biology with synthetic biology and metabolic engineering will undoubtedly support the discovery, characterization, and engineering of new metabolic routes and more efficient microbial systems for the production of biofuels.
Temperature-independent narrowband optical filterat 1.3 µm wavelength by an athermal waveguide (1996)

The authors report the realisation of a temperature independent narrowband optical filter at 1.3 µm wavelength. A ring resonator has been designed and fabricated using an athermal waveguide, in which the optical path length is independent of temperature. The temperature coefficient of the central wavelength was successfully reduced to 7 × 10-4 nm/K (7% of that of a conventional filter).
Interstitial Cystitis and Painful Bladder Syndrome (2007)

Although interstitial cystitis accounts for a small percent of health care visits, its economic burden is substantial. Because of misdiagnosis, the true burden of interstitial cystitis/painful bladder syndrome on the health care system in the United States is probably underestimated in administrative data that rely only on physician coding to identify the disorder. The greatest part of the disease burden is likely not captured in this economic analysis.
[Progress in stem cells and regenerative medicine]. (2015)

Stem cells have the ability to differentiate into all types of cells in the body and therefore have great application potential in regenerative medicine, in vitro disease modelling and drug screening. In recent years, stem cell technology has made great progress, and induced pluripotent stem cell technology revolutionizes the whole stem cell field. At the same time, stem cell research in our country has also achieved great progress and becomes an indispensable power in the worldwide stem cell research field. This review mainly focuses on the research progress in stem cells and regenerative medicine in our country since the advent of induced pluripotent stem cell technology, including induced pluripotent stem cells, transdifferentiation, haploid stem cells, and new gene editing tools.
Crystal engineering of diamondoid networks (1994)

M. J. Zaworotko, Chem. Soc. Rev., 1994, 23, 283 DOI: 10.1039/CS9942300283
Prognostic significance of p53 mutations and 3p deletions in primary resected non-small cell lung cancer. (1993)

We evaluated the prognostic significance of p53 mutations and an allelic loss of chromosome 3p in 71 patients with non-small cell lung cancer who underwent potentially curative resection. p53 mutations were detected in 35 cases (49%), while 3p deletions were observed in 34 of 70 informative cases (49%). The presence of the p53 mutation was associated with a shortened survival in all patients (P = 0.014 by log rank test), including those in early stages of the disease (stage I or II, n = 48) (P = 0.016 by log rank test). Multivariate analysis by the Cox proportional hazards model also revealed that p53 mutation was an independent yet unfavorable prognostic factor (P = 0.013). Patients with 3p deletion tended to have a poorer prognosis, but not to a statistically significant extent.
The Low-Density Lipoprotein Receptor-Related Protein (LRP) Mediates Clearance of Coagulation Factor Xa In Vivo (1998)

Blood coagulation factor X plays a pivotal role in the clotting cascade. When administered intravenously to mice, the majority of activated factor X (factor Xa) binds to alpha 2-macroglobulin (alpha 2M) and is rapidly cleared from the circulation into liver. We show here that the low-density lipoprotein receptor-related protein (LRP) is responsible for factor Xa catabolism in vivo. Mice overexpressing a 39-kD receptor-associated protein that binds to LRP and inhibits its ligand binding activity displayed dramatically prolonged plasma clearance of 125I-factor Xa. Preadministration of alpha 2M-proteinase complexes (alpha 2M*) also diminished the plasma clearance of 125I-factor Xa in a dose-dependent fashion. The clearance of preformed complexes of 125I-factor Xa and alpha 2M was similar to that of 125I-factor Xa alone and was also inhibited by mice overexpressing a 39-kD receptor-associated protein. These results thus suggest that, in vivo, factor Xa is metabolized via LRP after complex formation with alpha 2M.
OPTIMOL: automatic Online Picture collecTion via Incremental MOdel Learning (2007)

A well-built dataset is a necessary starting point for advanced computer vision research. It plays a crucial role in evaluation and provides a continuous challenge to state-of-the-art algorithms. Dataset collection is, however, a tedious and time-consuming task. This paper presents a novel automatic dataset collecting and model learning approach that uses object recognition techniques in an incremental method. The goal of this work is to use the tremendous resources of the web to learn robust object category models in order to detect and search for objects in real-world cluttered scenes. It mimics the human learning process of iteratively accumulating model knowledge and image examples. We adapt a non-parametric graphical model and propose an incremental learning framework. Our algorithm is capable of automatically collecting much larger object category datasets for 22 randomly selected classes from the Caltech 101 dataset. Furthermore, we offer not only more images in each object category dataset, but also a robust object model and meaningful image annotation. Our experiments show that OPTIMOL is capable of collecting image datasets that are superior to Caltech 101 and LabelMe.
Diabetic foot ulcer classification system for research purposes: a progress report on criteria for including patients in research studies (2004)

Various different systems have been proposed to classify diabetic foot ulcers, but none has gained widespread acceptance. The International Working Group of the Diabetic Foot (IWGDF) developed a classification system for research purposes, which is described in this report. In this PEDIS system, all foot ulcers should be classified according to five categories: perfusion, extent/size, depth/tissue loss, infection and sensation. The methods to determine the presence and severity of these factors are described; each (sub)category is defined according to strict criteria, which are applicable worldwide. All experts involved and all members of the IWGDF reached consensus on this system, which will be validated first, before it can be formally introduced.
Synthesis of Lipidated Proteins (2016)

Protein lipidation is one of the major post-translational modifications (PTM) of proteins. The attachment of the lipid moiety frequently determines the localization and the function of the lipoproteins. Lipidated proteins participate in many essential biological processes in eukaryotic cells, including vesicular trafficking, signal transduction, and regulation of the immune response. Malfunction of these cellular processes usually leads to various diseases such as cancer. Understanding the mechanism of cellular signaling and identifying the protein-protein and protein-lipid interactions in which the lipoproteins are involved is a crucial task. To achieve these goals, fully functional lipidated proteins are required. However, access to lipoproteins by means of standard expression is often rather limited. Therefore, semisynthetic methods, involving the synthesis of lipidated peptides and their subsequent chemoselective ligation to yield full-length lipoproteins, were developed. In this Review we summarize the commonly used methods for lipoprotein synthesis and the development of the corresponding chemoselective ligation techniques. Several key studies involving full-length semisynthetic lipidated Ras, Rheb, and LC3 proteins are presented.