gebhart/patrepeval huggingface dataset:
Induction of Tetraploid Derivatives of Maize Inbred Lines by Nitrous Oxide Gas Treatment (2006)

Maize (Zea mays L.) is a model organism for various genetic and physiological studies. Induction of autotetraploid lines from elite inbred lines is valuable for investigating gene dosage effects on the molecular level. We applied nitrous oxide gas at the time of fertilization (30-36 h after pollination) for 20 h on maize inbred line Oh43. The nitrous oxide gas treatment between pressures of 600-1000 kPa proved to be effective in inducing tetraploids. The treatment also significantly increased the rates of germless and shriveled kernels. Twelve inbred lines were treated with nitrous oxide gas for 20 h at either 800 or 900 kPa pressures, 30 or 36 h after pollination. Although tetraploid or tetraploid class aneuploid plants from 9 of 12 inbreds tested were successfully generated, only six genotypes produced progenies. The successful tetraploid inbred lines were from the A188, B73, H99, Oh43, Stock 6, and W22 genetic backgrounds. Aneuploids, plants with broken chromosomes and chimeras, were also found among the treated materials.
Engineering of a monomeric and low‐glycosylated form of human butyrylcholinesterase (2002)

Human butyrylcholinesterase (BChE; EC 3.1.1.8) is of particular interest because it hydrolyzes or scavenges a wide range of toxic compounds including cocaine, organophosphorus pesticides and nerve agents. The relative contribution of each N-linked glycan for the solubility, the stability and the secretion of the enzyme was investigated. A recombinant monomeric BChE lacking four out of nine N-glycosylation sites and the C-terminal oligomerization domain was stably expressed as a monomer in CHO cells. The purified recombinant BChE showed catalytic properties similar to those of the native enzyme. Tetragonal crystals suitable for X-ray crystallography studies were obtained; they were improved by recrystallization and found to diffract to 2.0 A resolution using synchrotron radiation. The crystals belong to the tetragonal space group I422 with unit cell dimensions a = b = 154.7 A, c = 124.9 A, giving a Vm of 2.73 A3 per Da (estimated 60% solvent) for a single molecule of recombinant BChE in the asymmetric unit. The crystal structure of butyrylcholinesterase will help elucidate unsolved issues concerning cholinesterase mechanisms in general.
A new technology of optimizing survey design on real‐surface model (2008)

The survey design in complex areas is a real challenge. Many factors, like unreachable areas, hard to operate areas, hard surface conditions, etc., need to be considered in the design. In this paper, a new technology of seismic data acquisition survey design is introduced to optimize the design in the complex areas. The processes of the optimization includes: 1) real‐surface simulation; 2) scouting on real‐surface model; 3) extracting features from real‐surface model; 4) optimizing survey design based on the real‐surface model. The technology depends on many high accuracy geographical data like GPS, RS, and GIS (3S). Thanks to the recent rapid progresses in the geographical industry, the high accuracy geographical data can be easily and economically obtained. Duo to the massive amount of the 3S data, the data process and management efficiency is another important factor in our technology. The optimization technology was implemented in our seismic data acquisition software system. We applied the technology in a 3D survey design project in western China, and achieved satisfactory results in terms of data quality and productivity.
Studies on the nonmevalonate terpene biosynthetic pathway: Metabolic role of IspH (LytB) protein (2002)

Isopentenyl diphosphate and dimethylallyl diphosphate serve as the universal precursors for the biosynthesis of terpenes. Although their biosynthesis by means of mevalonate has been studied in detail, a second biosynthetic pathway for their formation by means of 1-deoxy-D-xylulose 5-phosphate has been discovered only recently in plants and certain eubacteria. Earlier in vivo experiments with recombinant Escherichia coli strains showed that exogenous 1-deoxy-D-xylulose can be converted into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate by the consecutive action of enzymes specified by the xylB and ispCDEFG genes. This article describes the transformation of exogenous [U-(13)C(5)]1-deoxy-D-xylulose into a 5:1 mixture of [U-(13)C(5)]isopentenyl diphosphate and [U-(13)C(5)]dimethylallyl diphosphate by an E. coli strain engineered for the expression of the ispH (lytB) gene in addition to recombinant xylB and ispCDEFG genes.
Guanine riboswitch variants from Mesoplasma florum selectively recognize 2′-deoxyguanosine (2007)

Several mRNA aptamers have been identified in Mesoplasma florum that have sequence and structural features resembling those of guanine and adenine riboswitches. Two features distinguish these RNAs from established purine-sensing riboswitches. All possess shortened hairpin-loop sequences expected to alter tertiary contacts known to be critical for aptamer folding. The RNAs also carry nucleotide changes in the core of each aptamer that otherwise is strictly conserved in guanine and adenine riboswitches. Some aptamers retain the ability to selectively bind guanine or adenine despite these mutations. However, one variant type exhibits selective and high-affinity binding of 2'-deoxyguanosine, which is consistent with its occurrence in the 5' untranslated region of an operon containing ribonucleotide reductase genes. The identification of riboswitch variants that bind nucleosides and reject nucleobases reveals that natural metabolite-sensing RNA motifs can accrue mutations that expand the diversity of ligand detection in bacteria.
ACVR1 R206H cooperates with H3.1K27M in promoting diffuse intrinsic pontine glioma pathogenesis (2019)

Diffuse intrinsic pontine glioma (DIPG) is an incurable pediatric brain tumor, with approximately 25% of DIPGs harboring activating ACVR1 mutations that commonly co-associate with H3.1K27M mutations. Here we show that in vitro expression of ACVR1 R206H with and without H3.1K27M upregulates mesenchymal markers and activates Stat3 signaling. In vivo expression of ACVR1 R206H or G328V with H3.1K27M and p53 deletion induces glioma-like lesions but is not sufficient for full gliomagenesis. However, in combination with PDGFA signaling, ACVR1 R206H and H3.1K27M significantly decrease survival and increase tumor incidence. Treatment of ACVR1 R206H mutant DIPGs with exogenous Noggin or the ACVR1 inhibitor LDN212854 significantly prolongs survival, with human ACVR1 mutant DIPG cell lines also being sensitive to LDN212854 treatment. Together, our results demonstrate that ACVR1 R206H and H3.1K27M promote tumor initiation, accelerate gliomagenesis, promote a mesenchymal profile partly due to Stat3 activation, and identify LDN212854 as a promising compound to treat DIPG.
Novel Small Molecule Nonpeptide Aminopeptidase N Inhibitors with a Cyclic Imide Skeleton (1999)

A novel series of small molecule nonpeptide aminopeptidase N (APN) inhibitors with a N-phenylphthalimide or N-phenylhomophthalimide skeleton were prepared. Evaluation of their protease inhibitory activities revealed that (i) some N-phenylphthalimide analogs are potent APN inhibitors, but they are also inhibitors of another protease, dipeptidylpeptidase IV (DPP-IV), and (ii) some N-phenylhomophthalimide analogs, including 2-(2,6-diethylphenyl)-1,2,3,4-tetrahydroisoquinoline-1,3-dione (PIQ-22), are potent and specific inhibitors of APN without DPP-IV-inhibitory activity. The structure-activity relationship studies of N-phenylphthalimides and N-phenylhomophthalimides are reviewed. PIQ-22 showed potent tumor-cell invasion-inhibitory activity.
Enzyme supplementation of a poultry diet containing rye and wheat (1989)

A total of 360 1-d-old broiler chickens were fed on a diet based on rye and wheat in equal proportions without or with supplementation of increasing levels (0.11, 0.22, 0.44 and 0.88 g/kg) of a technical enzyme preparation containing pentosanase and beta-glucanase activities. In vitro investigations revealed that the enzyme preparation solubilized pentosans, increasing the relative viscosity of buffer extracts from enzyme-supplemented diets. Enzyme supplementation generally improved body-weight by approximately 27% at day 15 and 15% at day 27, increased feed intake by 15 and 8% respectively, and improved feed conversion efficiency by 10 and 5% respectively. There was also a decreased occurrence of sticky droppings. Enzyme supplementation increased the digestibility of organic matter, crude protein (nitrogen x 6.25) and starch measured in the last third of the small intestine, and of organic matter and crude fat measured in excreta. Solubilization of insoluble pentosans by the enzyme included led to negative digestibility values for soluble pentosans in the small intestine at the higher levels of supplementation. Most of the dietary fibre degradation observed occurred before the middle section of the small intestine, with some degradation of soluble fibre in the caeca and colon. The solubilization and disruption of feed endosperm cell walls by enzyme supplementation probably was primarily responsible for the observed improvements in digestibility and production results.
Complex associations (1994)

Objects model phenomena and a phenomenon is usually a component. Information characterizing a component is encapsulated and accessible only by its methods. The relations between components are modeled explicitly by means of associations or references. A relation is also a phenomenon and objects can model this type of phenomena too. Components are usually related conceptually in diverse and subtle ways: Some relations are implicitly given and some are local to other more basic relations. Such kinds of relations are important for understanding the organization and cooperation of objects and may be supported in object-oriented analysis, design, and programming: An implicit association describes a relation between an object and objects local to this enclosing object, and a complex association describes an explicit relation between local objects in different enclosing objects. Such associations are described by classes and the objects have the usual properties including methods and attributes.
Successful Treatment of Candida albicans Endophthalmitis With Intravitreal Amphotericin B (1981)

• A severely debilitated 38-year-old woman had culture-proved<i>Candida albicans</i>endophthalmitis that resolved after treatment with a single intravitreal injection of 5 μg of amphotericin B and a total of only 190 mg of intravenous amphotericin B. The patient recovered visual acuity of 6/7.5 (20/25), and her electroretinogram was normal 22 months after operation. There was no evidence of a retinal toxic reaction to amphotericin B on long-term follow-up.
Identification of a mammalian nuclear factor and human cDNA-encoded proteins that recognize DNA containing apurinic sites. (1990)

Damage to DNA can have lethal or mutagenic consequences for cells unless it is detected and repaired by cellular proteins. Repair depends on the ability of cellular factors to distinguish the damaged sites. Electrophoretic binding assays were used to identify a factor from the nuclei of mammalian cells that bound to DNA containing apurinic sites. A binding assay based on the use of beta-galactosidase fusion proteins was subsequently used to isolate recombinant clones of human cDNAs that encoded apurinic DNA-binding proteins. Two distinct human cDNAs were identified that encoded proteins that bound apurinic DNA preferentially over undamaged, methylated, or UV-irradiated DNA. These approaches may offer a general method for the detection of proteins that recognize various types of DNA damage and for the cloning of genes encoding such proteins.
[Preventive effect of TJ-14, a kampo (Chinese herb) medicine, on diarrhea induced by irinotecan hydrochloride (CPT-11)]. (1994)

Diarrhea is one of dose-limiting factors of irinotecan (CPT-11) and its incidence is over 60% in patients receiving this drug. Therefore, it is important to prevent diarrhea for more effective use of CPT-11. We used Hange-shashinto (TJ-14), an ethical Kampo (Chinese herb) Medicine, to prevent diarrhea induced by CPT-11. Twenty-three patients (9 lung cancer, 4 pancreatic cancer, 2 colorectal cancer, 4 malignant lymphoma, and 4 other types of cancer) entered in this study. All patients were treated with CPT-11 in combination with oral TJ-14 (7.5 g t.i.d.) every day starting prior to CPT-11 infusion. The dose of CPT-11 was 60-100 mg/m2/w, 120-150 mg/m2/2 w or 40 mg/m2/d x 3 days/w. Three of 23 patients could not evaluate the efficacy and safety of TJ-14 since they could not take TJ-14 due to its odor and taste. The efficacy and safety of TJ-14 was not evaluated in one patient also since the patient could not continue taking TJ-14 due to vomiting induced by CPT-11. Nine patients showed an excellent response (no diarrhea or only 1 day of ECOG Grade 1 diarrhea). 9 showed a good response (Grade 1 diarrhea that disappears within 3 days) and one did not reveal response. It is suggested that TJ-14 possesses a preventive effect against diarrhea induced by CPT-11.
Ten- to 50-nm-long quasi-ballistic carbon nanotube devices obtained without complex lithography (2004)

A simple method combining photolithography and shadow (or angle) evaporation is developed to fabricate single-walled carbon nanotube (SWCNT) devices with tube lengths of approximately 10-50 nm between metal contacts. Large numbers of such short devices are obtained without the need of complex tools such as electron beam lithography. Metallic SWCNTs with lengths of approximately 10 nm, near the mean free path of l(op) approximately 15 nm for optical phonon scattering, exhibit nearly ballistic transport at high biases and can carry unprecedented 100-microA currents per tube. Semiconducting SWCNT field-effect transistors with approximately 50-nm channel lengths are routinely produced to achieve quasi-ballistic operations for molecular transistors. The results demonstrate highly length-scaled and high-performance interconnects and transistors realized with SWCNTs.
What's the Relative Risk? (1998)

Logistic regression is used frequently in cohort studies and clinical trials. When the incidence of an outcome of interest is common in the study population (>10%), the adjusted odds ratio derived from the logistic regression can no longer approximate the risk ratio. The more frequent the outcome, the more the odds ratio overestimates the risk ratio when it is more than 1 or underestimates it when it is less than 1. We propose a simple method to approximate a risk ratio from the adjusted odds ratio and derive an estimate of an association or treatment effect that better represents the true relative risk.
The Nucleic Acids Protocols Handbook (2000)

Ralph Rapley, Ed., The Nucleic Acids Protocols Handbook (Totawa: Humana Press 2000) ISBN 978-0-89603-459-4, eISBN 978-1-59259-038-4, DOI 10.1385/1592590381
GUI creation for removal of motion artifact in PPG signals (2016)

Photoplethysmography(PPG) signals provide a valuable insight to the cardiac functioning non-invasively. Analysis of PPG signals is of great challenge as the Finger PPG sensors are subjected to various noises like motion artifact, noises from the ambient sunlight and also flow of blood in the terminal arterioles. To obtain the reliable measures from PPG signals, filtering the PPG signal from various noises becomes important. Various methods such as periodic moving average filter, SVD method, Wavelet Filters, FFT Filter, Adaptive Filters, have been proposed to remove motion artifact of PPG signals by various authors. All the filtering methods are carried out individually as a signal processing application. It would be helpful to compare the different filtering methods if all this filtering method are done under single GUI, this also helps the researcher to filter the motion artifact in the PPG signals with ease. In this work a code has been written in MATLAB for different filtering methods such as periodic moving average filter, SVD method, Wavelet Filters, FFT Filter and Adaptive Filters. The different filtering methods have been compared using SNR (Signal to Noise Ratio) values. The SNR values of SVD and AS-LMS algorithm were 2.24 and 2.39 respectively and were found to be the best signal processing methods for removal of motion artifacts in PPG signals. This new GUI has been conceived for filtering PPG signals using different signal processing methods and in making the filtering process more users friendly.
Silk-Elastin-like Hydrogel Improves the Safety of Adenovirus-Mediated Gene-Directed Enzyme−Prodrug Therapy (2010)

Recombinant silk-elastin-like protein polymers (SELPs) are well-known for their highly tunable properties on both the molecular and macroscopic hydrogel levels. One specific structure of these polymers, SELP-815K, has been investigated as an injectable controlled delivery system for the treatment of head and neck cancer via a gene-directed enzyme prodrug therapy (GDEPT) approach. Due to its pore size and gelation properties in vivo, SELP restricts the distribution and controls the release of therapeutic viruses for up to one month. It has been shown that SELP-mediated delivery significantly improves therapeutic outcome of the herpes simplex virus thymidine kinase (HSVtk)/ganciclovir (GCV) system in xenograft models of human head and neck cancer. However little is known about potential benefits of this approach with regard to toxicity in the presence of a fully intact immune system. The studies presented here were designed to assess the change in toxicity of the SELP-mediated viral delivery compared to free viral injection in a non-tumor-bearing immune competent mouse model. Toxicity was assessed at 1, 2, 4, and 12 weeks via body weight monitoring, complete blood count (CBC), and blood chemistry. It was found that in the acute and subacute phases (weeks 1-4) there is significant toxicity in groups combining the virus and the prodrug, and matrix-mediated gene delivery with SELP demonstrates a reduction in toxicity from the 2 week time point through the 4 week time point. At the end of the subchronic phase (12 weeks), signs of toxicity had subsided in both groups. Based on these results, recombinant SELPs offer a significant reduction in toxicity of virus-mediated GDEPT treatment compared to free virus injection in the acute and subacute phases.
Molecular weight distribution of chitosan isolated from Mucor rouxii under different culture and processing conditions (1992)

The isolation of chitosan from a fungal source offers the potential of a product with controlled physicochemical properties not obtainable by the commercial chemical conversion of crustacean chitin. A variety of culture and processing protocols using Mucor rouxii were studied for their effects on biomass yield and chitosan molecular weight. Weight-averaged molecular weight determined by gel permeation chromotography ranged from 2.0 x 10(5) to approximately 1.4 x 10(6) daltons. The chitosan yield ranged from 5% to 10% of total biomass dry weight and from 30% to 40% of the cell wall. Of the culture parameters studied, length of incubation and medium composition effected biomass production and molecular weight. Modification of the processing protocol, including the type and strength of acid, and cell wall disruption in acid prior to refluxing were used to optimize the efficiency of chitosan extraction.The degree of deacetylation of fungal and commercial chitosans was compared using infrared spectrometry, titration, and first derivative of UV absorbance spectrometry. The chitosan obtained directly from the fungal cell wall had a higher degree of deacetylation than commercial chitosan from the chemical conversion process.
Proteins Binding to Cisplatin-Damaged DNA in Human Cell Lines (1994)

Cisplatin (CDDP) is a highly effective, frequently used cancer chemotherapeutic drug employed in the treatment of several human malignancies including ovarian, testicular, and bladder cancers. A common problem encountered with cisplatin therapy is intrinsic or acquired resistance to this drug. While the mechanisms of resistance to cisplatin, and other chemotherapeutic agents, are not fully understood, one factor affecting the cellular response to CDDP may result from differences in the level of specific proteins that recognize CDDP-damaged DNA. We have developed a damaged DNA affinity precipitation technique that allows the direct visualization and characterization of cellular proteins that bind to cisplatin-damaged DNA. In the present study we have utilized this method to analyze proteins present in several mammalian cell lines that bind to cisplatin-damaged DNA. We demonstrate that HeLa cells, resistant to CDDP cytotoxicity, contain high levels of high-mobility-group proteins 1 and 2, which bind to CDDP-DNA. We also show that xeroderma pigmentosum cells of different genetic complementation groups contain variable levels of a 45-kDa protein that binds to CDDP-DNA. Thus, our results indicate that different human cell lines demonstrate qualitative and quantitative differences in the expression of cisplatin-damaged DNA binding proteins.
Dopamine autoreceptor agonists: resolution and pharmacological activity of 2,6-diaminotetrahydrobenzothiazole and an aminothiazole analog of apomorphine (1987)

The enantiomers of the aminothiazole analogues of the known dopaminergic agonists apomorphine (1) and 2-aminohydroxytetralin (2) have been prepared. The absolute configurations of the enantiomers of 2,6-diaminotetrahydrobenzothiazole have been established by X-ray crystallographic analysis. Dopamine (DA) autoreceptor agonist activities of the compounds were evaluated. Testing revealed (-)-5, the S enantiomer, to be the most active compound tested (inhibition of GBL accelerated dopamine synthesis and inhibition of alpha-methyltyrosine-induced decline of DA). In addition (-)-5 does not exhibit stereotyped behavior, suggesting a pronounced selectivity for DA autoreceptors.
Alterations in skeletal muscle gene expression of ob/ob mice by mRNA differential display. (1998)

To identify molecules that contribute to insulin resistance, we compared the patterns of gene expression in skeletal muscle of the obese ob/ob mouse, a genetic model of obesity and severe insulin resistance, with that of its thin littermate (ob/+) using the mRNA differential display method. From about 9,000 cDNAs displayed, we found 12 differentially expressed in ob/ob mice skeletal muscle that could be recovered from the differential display gels and confirmed by Northern blot analysis and sequenced. Eight mRNAs were overexpressed in ob/ob muscle: Id2 (a negative regulator of the basic helix-loop-helix family of transcription factors), fast skeletal muscle troponin T, ribosomal protein L3, the integral protein of the peroxisomal membrane 22PMP, the mammalian homolog of geranylgeranyl pyrophosphate synthase, an mRNA related to phosphatidylinositol-glycan-specific phospholipase D, and two unknown mRNAs. The level of overexpression of these mRNAs in skeletal muscle varied from a 500% increase to as little as a 25% increase. Two mRNAs were underexpressed 20-35%, including the f-subunit of mitochondrial ATP synthase and a retrovirus-related DNA. Two proteins with multiple transcripts, skeletal muscle alpha-tropomyosin and one for a repetitive sequence, showed a change in mRNA pattern of expression in the muscle of the ob/ob mouse. Because the primary genetic defect in the ob/ob mouse is known to be in the leptin gene, these data indicate how acquired alterations in gene expression of multiple classes of proteins may play a role in the complex pathogenesis of insulin resistance in obesity and diabetes.