gebhart/patrepeval huggingface dataset:
Rice NICOTIANAMINE SYNTHASE 2 expression improves dietary iron and zinc levels in wheat (2016)

Iron and zinc deficiencies negatively impact human health worldwide. We developed wheat lines that meet or exceed recommended dietary target levels for iron and zinc in the grains. These lines represent useful germplasm for breeding new wheat varieties that can reduce iron and zinc deficiency-associated health burdens in the affected populations. Micronutrient deficiencies, including iron and zinc deficiencies, have negative impacts on human health globally. Iron-deficiency; anemia affects nearly two billion people worldwide and is the cause of reduced cognitive development, fatigue and overall low productivity. Similarly, zinc deficiency causes stunted growth, decreased immunity and increased risk of respiratory infections. Biofortification of staple crops is a sustainable and effective approach to reduce the burden of health problems associated with micronutrient deficiencies. Here, we developed wheat lines expressing rice NICOTIANAMINE SYNTHASE 2 (OsNAS2) and bean FERRITIN (PvFERRITIN) as single genes as well as in combination. NAS catalyzes the biosynthesis of nicotianamine (NA), which is a precursor of the iron chelator deoxymugeneic acid (DMA) required for long distance iron translocation. FERRITIN is important for iron storage in plants because it can store up to 4500 iron ions. We obtained significant increases of iron and zinc content in wheat grains of plants expressing either OsNAS2 or PvFERRTIN, or both genes. In particular, wheat lines expressing OsNAS2 greatly surpass the HarvestPlus recommended target level of 30 % dietary estimated average requirement (EAR) for iron, and 40 % of EAR for zinc, with lines containing 93.1 µg/g of iron and 140.6 µg/g of zinc in the grains. These wheat lines with dietary significant levels of iron and zinc represent useful germplasm for breeding new wheat varieties that can reduce micronutrient deficiencies in affected populations.
Sequence and expression of Drosophila myristoyl-CoA:protein N-myristoyl transferase: evidence for proteolytic processing and membrane localisation (1997)

The enzyme N-myristoyl transferase transfers the 14 carbon fatty acid myristate to an N-terminal glycine residue in a small subset of cytoplasmic proteins. Many myristoyl proteins are components of cellular signalling pathways, some of which play important roles during embryonic development, for example protein kinase A. Thus, the function of N-myristoyl transferase is probably essential for embryogenesis and it is of some interest to study the enzyme in an organism with well understood developmental biology. In this paper we report the purification of a processed form of the Drosophila enzyme from peripheral membrane fractions of embryos by affinity chromatography to a protein containing leucine rich repeats. We have also isolated the Drosophila N-myristoyl transferase gene and determined its nucleotide sequence. The predicted amino acid sequence of the Drosophila enzyme is closely related to that of mammalian and fungal N-myristoyl transferases and residues essential for enzyme function are conserved. Our findings indicate that a fraction of Drosophila NMT is bound to the membrane and they are consistent with recent results for the human enzyme. We suggest that N-myristoyl transferase may be recruited to the membrane as part of a translational complex, perhaps by binding to p34 ribosome binding protein, a leucine rich repeat receptor of the microsomal membranes. We have also studied the expression pattern of the gene in the embryo by northern blot analysis and in situ hybridization. The transcripts appear to be uniformly distributed in the pre-cellular embryo but at later stages the RNA is barely detectable with these methods. However, from about stage 14, high levels of transcript are detected in a small number of randomly distributed cells of the central and peripheral nervous system.
Kill one bird with two stones: potential efficacy of BCR-ABL and autophagy inhibition in CML (2011)

The introduction of imatinib in the treatment of chronic myeloid leukemia (CML) represents the most successful example of targeted therapy in human cancer. However, leukemic stem cells are insensitive to tyrosine kinase inhibitors (TKIs) and contribute to the persistence of disease by representing a reservoir of selfrenewing cells that replenish the disease after drug discontinuation. This finding has refocused the interest of scientists toward drug combinations, ie, treating with TKIs and simultaneously targeting alternative survival mechanisms. One candidate target mechanism is autophagy, a cellular recycling process that acts as a cytoprotective shield in CML cells in response to TKI-induced stress and in other cancer cells surviving in an inhospitable microenvironment. On that basis, inhibition of autophagy has now become an exciting option for combination treatment in cancer, and clinical trials have been initiated in solid and hemopoietic tumors such as CML, chronic lymphocytic leukemia, and multiple myeloma. This review describes the biology of CML and elucidates how the molecular driver BCR-ABL led to the development of TKIs. We then discuss the molecular regulation of autophagy and the potential for autophagy inhibition as the next step in our attempt to tackle the problem of CML persistence to offer a curative option.
Synthesis of a Pentasaccharide Corresponding to the Antithrombin III Binding Fragment of Heparin (1985)

Abstract The synthesis of a protected pentasaccharide 27b corresponding to the antithrombin III binding region of heparin is presented. This pentasaccharide was prepared from two disaccharides (12c and 23) and a monosaccharide (1). The glucuronic acid containing disaccharide 12c was prepared from easily available monomers 6 and 7. Oxidation to the uronic acid was performed in the disaccharide stage. L-Idose derivative 16, prepared via a new route, was coupled with 1,6-anhydro derivative 17, oxidized and transformed into disaccharide 23. Coupling of 12c and 23 to tetrasaccharide 24a has been investigated. Better yields were obtained without collidine, the reason for which is explained. Coupling of 24b and 1 afforded the pentasaccharide 27b, protected with acetyl at the positions to be sulphated, benzyl at the other hydroxyl functions and azide at the 2-position of the glucosamine residues. Conversion of 27b into the sulphated pentasaccharide Ib can be performed according to published procedures.
Persistence of four related human immunodeficiency virus subtypes during the course of zidovudine therapy: relationship between virion RNA and proviral DNA (1994)

Human immunodeficiency virus (HIV) virion RNA and proviral DNA sequences have been examined over a 1-year period in an HIV-seropositive patient, commencing with the start of zidovudine treatment. By characterizing the variable V3 and V4 env domains, four related but structurally discrete genotypes could be identified prior to the start of therapy and during the subsequent 60-week period of therapy. Each of the four subtypes showed a unique pattern in the preservation of glycosylation sites. A comparison of the V3 amino acid sequences in peripheral blood mononuclear cell proviral DNA and plasma virion RNA at 0, 24, 36, and 60 weeks demonstrated that proviral DNA did not serve as a predictor of the structure of virion RNA. HIV virion RNA subtype 3 was the most prevalent virion RNA subtype at three of the four periods studied, yet no corresponding proviral DNA was detected. Other virion subtypes have been observed, but only on a transient basis. The present data are consistent with a model of HIV infection in which related but different HIV substrains coexist and evolve independently within an individual. Characterization of virion RNA may be required to identify the unique properties of the virus involved in disease progression; characterization of proviral DNA will not yield this information.
Dental Plaque as a Microbial Biofilm (2004)

New technologies have provided novel insights into how dental plaque functions as a biofilm. Confocal microscopy has confirmed that plaque has an open architecture similar to other biofilms, with channels and voids. Gradients develop in areas of dense biomass over short distances in key parameters that influence microbial growth and distribution. Bacteria exhibit an altered pattern of gene expression either as a direct result of being on a surface or indirectly as a response to the local environmental heterogeneity within the biofilm. Bacteria communicate via small diffusible signalling molecules (e.g. competence-stimulating peptide, CSP; autoinducer 2); CSP induces both genetic competence and acid tolerance in recipient sessile cells. Thus, rates of gene transfer increase in biofilm communities, and this is one of several mechanisms (others include: diffusion-reaction, neutralization/inactivation, slow growth rates, novel phenotype) that contribute to the increased antimicrobial resistance exhibited by bacteria in biofilms. Oral bacteria in plaque do not exist as independent entities but function as a co-ordinated, spatially organized and fully metabolically integrated microbial community, the properties of which are greater than the sum of the component species. A greater understanding of the significance of dental plaque as a mixed culture biofilm will lead to novel control strategies.
Thin film Lamb wave resonators in frequency control and sensing applications: a review (2013)

This work makes an overview of the progress made during the last decade with regard to a novel class of piezoelectric microwave devices employing acoustic Lamb waves in micromachined thin film membranes. This class of devices is referred to as either thin film Lamb wave resonators or piezoelectric contour-mode resonators both employing thin film aluminum nitride membranes. These devices are of interest for applications in both frequency control and sensing. High quality factor Lamb wave resonators exhibiting low noise, low loss and thermally stable performance are demonstrated and their application in high resolution gravimetric and pressure sensors further discussed. A specific emphasis is put on the ability of these devices to operate in contact with liquids. Future research directions are further outlined.
Assessing real-world survival outcomes of patients (pts) with metastatic pancreatic ductal adenocarcinoma (mPDAC) treated with first-line FOLFIRINOX compared to patients from a phase 1/2 trial treated with NALIRIFOX. (2021)

e16252 Background: Treatment options remain limited for pts newly diagnosed with mPDAC. NCCN and ASCO guidelines both recommend treatment with FOLFIRINOX or gemcitabine plus nab-paclitaxel in the first line (1L) setting for pts with mPDAC and good performance status. Over 80% of randomized clinical trials (RCTs) studying treatments for mPDAC have failed to meet their primary endpoints. Recently published analyses have utilized real-world (RW) data to compare outcomes between pts enrolled in clinical trials and RW pts. This study sought to identify the eligible population of pts with mPDAC treated with FOLFIRINOX in the 1L setting who would meet RCT eligibility criteria for the phase 1/2 study (NCT02551991) evaluating NALIRIFOX for pts with previously untreated locally advanced or mPDAC, and to assess their survival outcomes. Methods: This retrospective observational study utilized the Flatiron Health EHR database. Data were analyzed for adult pts diagnosed with mPDAC between January 2016 and February 2020 who initiated treatment with FOLFIRNOX in 1L within 90 days of their diagnosis for metastatic disease. Eligibility criteria from the phase 1/2 trial were applied to select a population of RW pts who may have been eligible to enter the RCT. Pts meeting the following criteria were included: good performance scores (ECOG 0-1), adequate hematological, hepatic, and renal function, were recovered from the effects of surgery, were untreated in the year prior to initiating 1L, and had no evidence of a different cancer in the last three years. Kaplan-Meier analyses were used to assess the median overall survival (mOS) from the start of 1L FOLFIRNOX treatment. Results: Of the 1,210 pts treated with 1L FOLFIRINOX, 652 pts (53.8%) met less stringent versions of the RCT eligibility criteria in which missing values were deemed to indicate normal function/performance; 244 pts (20.2%) met the more stringent criteria and had complete data. The most restrictive selection criteria were the requirements for adequate hematological, hepatic, and renal function and having received prior therapy. The median age at treatment initiation among the 244 pts was 64 years (IQR: 58 – 70). 153 pts were male (62.7%), 158 were White (64.8%), and ECOG scores of 0 and 1 were split among the cohort 50%/50%. The mOS observed for the 244 pts was 10.1 months (95% CI: 9.1 – 11.3). The reported mOS from the phase 1/2 trial of NALIRIFOX was 12.6 months (8.7 – 18.7). Conclusions: This study demonstrates that RW data may be used to select a comparator cohort for a clinical trial. Initial estimates suggest NALIRIFOX pts from the RCT experienced longer survival than those receiving 1L FOLFIRINOX in the RW setting. Further analysis is necessary to minimize the effects of confounding and the differences in data collection between the RW and the RCT settings.
Differential expression of platelet-derived growth factor receptors in human malignant glioma cell lines. (1991)

Glioma cells in culture express platelet-derived growth factor (PDGF) A- and B-chains and secrete PDGF-like activity that is mainly PDGF-AA. In this work, we show that the PDGF alpha- and beta-receptors are independently expressed in human malignant glioma cells. We also define three different receptor phenotypes that are related to the morphology of glioma cells: cells with only alpha-receptors, only beta-receptors, or with both types of receptors. By the help of Northern blot analyses, 125I-PDGF-binding experiments, and immunoprecipitations the receptors are shown to be structurally normal PDGF receptors, except for minor variations in size that probably are due to differences in glycosylation. PDGF-BB induces DNA synthesis in cells of all three receptor phenotypes, whereas PDGF-AA or PDGF-AB has this effect only on cells with alpha- or with alpha- and beta-receptors. 125I-PDGF-AB binds with high affinity and down-regulates beta-receptors only in cells where alpha-receptors are present in addition to beta-receptors. Thus, the different functional capacities of PDGF isoforms on glioma cells fit with their known receptor-binding specificities and are compatible with the hypothesis that the isoforms act by inducing dimeric receptor complexes. When data on PDGF A- and B-chains, as well as alpha- and beta-receptor expression are compiled and the pattern of receptor binding specificity is taken into account, the majority of glioma cell lines are found to have a phenotype that makes autocrine stimulation possible.
Temperature dependence of ultrasonic propagation speed and attenuation in excised canine liver tissue measured using transmitted and reflected pulses (2004)

Previous reported data from our laboratory demonstrated the temperature dependence of propagation speed and attenuation of canine tissue in vitro at discrete temperatures ranging from 25 to 95 degrees C. However, concerns were raised regarding heating the same tissue specimen over the entire temperature range, a process that may introduce irreversible and, presumably, cumulative tissue degradation. In this paper propagation speed and attenuation vs temperature are measured using multiple groups of samples, each group heated to a different temperature. Sample thicknesses are measured directly using a technique that uses both transmitted and reflected ultrasound pulses. Results obtained using 3 and 5 MHz center frequencies demonstrate a propagation speed elevation of around 20 m/s in the 22-60 degrees C range, and a decrease of 15 m/s in the 60-90 degrees C range, in agreement with previous results where the same specimens were subjected to the entire temperature range. However, sound speed results reported here are slightly higher than those reported previously, probably due to more accurate measurements of sample thickness in the present experiments. Results also demonstrate that while the propagation speed varies with temperature, it is not a function of tissue coagulation. In contrast, the attenuation coefficient depends on both tissue coagulation effects and temperature elevation.
New thermosensitive plasmid for gram-positive bacteria (1992)

We isolated a replication-thermosensitive mutant of the broad-host-range replicon pWV01. The mutant pVE6002 is fully thermosensitive above 35 degrees C in both gram-negative and gram-positive bacteria. Four clustered mutations were identified in the gene encoding the replication protein of pVE6002. The thermosensitive derivative of the related plasmid pE194 carries a mutation in the analogous region but not in the same position. Derivatives of the thermosensitive plasmid convenient for cloning purposes have been constructed. The low shut-off temperature of pVE6002 makes it a useful suicide vector for bacteria which are limited in their own temperature growth range. Using pVE6002 as the delivery vector for a transposon Tn10 derivative in Bacillus subtilis, we observed transposition frequencies of about 1%.
Frequency-Dependent Activation of a Constitutive Nitric Oxide Synthase and Regulation of Contractile Function in Adult Rat Ventricular Myocytes (1996)

Cardiac myocytes have recently been shown to express a constitutive Ca(2+)-sensitive isoform of NO synthase (NOS3), although the mechanism(s) responsible for activation of NOS3 and its physiological function remain to be determined. Since the activity of NOS3 is known to be regulated in part by the intracellular Ca2+ activity ([Ca2+]i) in endothelial cells, we determined whether increasing myocyte [Ca2+]i by uniform electric field pacing was accompanied by an increase in NOS3 activity, detected as nitrite accumulation in the medium. A higher [Ca2+]i with increasing pacing frequencies was shown to be accompanied by a time-dependent accumulation of nitrite in medium that bathed adult rat ventricular myocytes stimulated at 3 Hz. Nitrite release by paced cells was significantly attenuated by treatment with either the NO synthase inhibitor nitro-L-arginine (L-NA, 1 mmol/L) or the intracellular Ca2+ chelator BAPTA-AM (20 mumol/L). Paced myocytes also exhibited a frequency- and time-dependent increase in intracellular cGMP content that could be inhibited significantly by either L-NA or the soluble guanylate cyclase inhibitor LY83583 (5 mumol/L). To determine whether the increase in NOS3 activity with pacing affected contractile function, myocytes were sequentially paced at frequencies from 0.5 to 3 Hz. Methylene blue, L-NA, and LY83583 all increased the amplitude of shortening of myocytes paced at 3 Hz. Furthermore, a significantly greater positive inotropic response to high extracellular Ca2+ (3 mmol/L) was demonstrated by myocytes pretreated with L-NA compared with control cells. These data indicate that myocyte NOS3 activity is regulated in part by [Ca2+]i, whether induced by changes in pacing frequency or [Ca2+]o, and depresses myocyte contractile responsiveness to higher stimulation frequencies.
0.2 mu m or less i-line lithography by phase-shifting-mask technology (2002)

A novel phase-shifting technology has been developed for improving resolution of isolated patterns. A phase-shifter edge line (PEL) is used as an opaque mask instead of a chrome pattern. The intensity distribution of the PEL is sharper than those of chrome patterns under the same illumination conditions. 0.15 mu m wide space patterns in LMR-UV (negative resist) are delineated in the focus range of more than 1.5 mu m by using a PEL-mask and an i-line stepper. In the same manner, 0.15 mu m wide line patterns are clearly formed by use of PFR-TT15 (positive resist). In addition, a new modification adapted to hole or pillar patterns has been developed by applying double exposure with a pair of PEL-masks. By this method 0.2 mu m hole patterns in LMR-UV are successfully delineated in a wide focus latitude of 1.5 mu m.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Joint Multimodal Learning with Deep Generative Models (2016)

We investigate deep generative models that can exchange multiple modalities bi-directionally, e.g., generating images from corresponding texts and vice versa. Recently, some studies handle multiple modalities on deep generative models, such as variational autoencoders (VAEs). However, these models typically assume that modalities are forced to have a conditioned relation, i.e., we can only generate modalities in one direction. To achieve our objective, we should extract a joint representation that captures high-level concepts among all modalities and through which we can exchange them bi-directionally. As described herein, we propose a joint multimodal variational autoencoder (JMVAE), in which all modalities are independently conditioned on joint representation. In other words, it models a joint distribution of modalities. Furthermore, to be able to generate missing modalities from the remaining modalities properly, we develop an additional method, JMVAE-kl, that is trained by reducing the divergence between JMVAE's encoder and prepared networks of respective modalities. Our experiments show that our proposed method can obtain appropriate joint representation from multiple modalities and that it can generate and reconstruct them more properly than conventional VAEs. We further demonstrate that JMVAE can generate multiple modalities bi-directionally.
Ataxin-2 repeat-length variation and neurodegeneration (2011)

Expanded glutamine repeats of the ataxin-2 (ATXN2) protein cause spinocerebellar ataxia type 2 (SCA2), a rare neurodegenerative disorder. More recent studies have suggested that expanded ATXN2 repeats are a genetic risk factor for amyotrophic lateral sclerosis (ALS) via an RNA-dependent interaction with TDP-43. Given the phenotypic diversity observed in SCA2 patients, we set out to determine the polymorphic nature of the ATXN2 repeat length across a spectrum of neurodegenerative disorders. In this study, we genotyped the ATXN2 repeat in 3919 neurodegenerative disease patients and 4877 healthy controls and performed logistic regression analysis to determine the association of repeat length with the risk of disease. We confirmed the presence of a significantly higher number of expanded ATXN2 repeat carriers in ALS patients compared with healthy controls (OR = 5.57; P= 0.001; repeat length >30 units). Furthermore, we observed significant association of expanded ATXN2 repeats with the development of progressive supranuclear palsy (OR = 5.83; P= 0.004; repeat length >30 units). Although expanded repeat carriers were also identified in frontotemporal lobar degeneration, Alzheimer's and Parkinson's disease patients, these were not significantly more frequent than in controls. Of note, our study identified a number of healthy control individuals who harbor expanded repeat alleles (31-33 units), which suggests caution should be taken when attributing specific disease phenotypes to these repeat lengths. In conclusion, our findings confirm the role of ATXN2 as an important risk factor for ALS and support the hypothesis that expanded ATXN2 repeats may predispose to other neurodegenerative diseases, including progressive supranuclear palsy.