gebhart/patrepeval huggingface dataset:
Analysis of the role of AML1-ETO in leukemogenesis, using an inducible transgenic mouse model (2000)

As reported previously, AML1-ETO knock-in mice were generated to investigate the role of AML1-ETO in leukemogenesis and to mimic the progression of t(8;21) leukemia. These knock-in mice died in midgestation because of hemorrhaging in the central nervous system and a block of definitive hematopoiesis during embryogenesis. Therefore, they are not a good model system for the development of acute myeloid leukemia. Therefore, mice were generated in which the expression of AML1-ETO is under the control of a tetracycline-inducible system. Multiple lines of transgenic mice have been produced with the AML1-ETO complementary DNA controlled by a tetracycline-responsive element. In the absence of the antibiotic tetracycline, AML1-ETO is strongly expressed in the bone marrow of AML1-ETO and tet-controlled transcriptional activator double-positive transgenic mice. Furthermore, the addition of tetracycline reduces AML1-ETO expression in double-positive mice to nondetectable levels. Throughout the normal murine lifespan of 24 months, mice expressing AML1-ETO have not developed leukemia. In spite of this, abnormal maturation and proliferation of progenitor cells have been observed from these animals. These results demonstrate that AML1-ETO has a very restricted capacity to transform cells. Either the introduction of additional genetic changes or the expression of AML1-ETO at a particular stage of hematopoietic cell differentiation will be necessary to develop a model for studying the pathogenesis of t(8;21).
Synthesis and Characterization of Amphiphilic Poly(urethaneurea)-comb-polyisobutylene Copolymers (2000)

In this paper we describe the synthesis and characterization of modified polyurethaneurea−polyether (PEUU) multiblock copolymers, designed to elicit lower permeability to water vapor and gases. The approach was to create polyisobutylene (PIB) segments, which were linked to the PEUU copolymer as combs. Macromonomers of PIB were synthesized, containing two hydroxyl sites on the initiating ends of the molecules for subsequent condensation polymerization. By using a polymerization scheme that offered no termination and no chain transfer, the PIB macromonomer would be assured of having two (and only two) hydroxyl groups. Characterization of the macromonomers and their precursors was performed by GPC, 1H NMR, and FTIR. Using these products, amphiphilic copolymers, with a polyurethaneurea−polyether multiblock backbone and polyisobutylene combs, were synthesized by a condensation reaction. PIB incorporation varied between about 2 and 30%, with comb lengths ranging from ∼3000 to 29 000 g/mol. Characterization of this new multiblock multicomb copolymer was performed by GPC, FTIR, solid state 13C NMR, and Soxhlet extraction techniques.
Current Challenges for the Early Detection of Alzheimer's Disease: Brain Imaging and CSF Studies (2009)

The development of prevention therapies for Alzheimer's disease (AD) would greatly benefit from biomarkers that are sensitive to the subtle brain changes that occur in the preclinical stage of the disease. Reductions in the cerebral metabolic rate of glucose (CMRglc), a measure of neuronal function, have proven to be a promising tool in the early diagnosis of AD. In vivo brain 2-[(18)F]fluoro-2-Deoxy-D-glucose-positron emission tomography (FDG-PET) imaging demonstrates consistent and progressive CMRglc reductions in AD patients, the extent and topography of which correlate with symptom severity. There is increasing evidence that hypometabolism appears during the preclinical stages of AD and can predict decline years before the onset of symptoms. This review will give an overview of FDG-PET results in individuals at risk for developing dementia, including: presymptomatic individuals carrying mutations responsible for early-onset familial AD; patients with Mild Cognitive Impairment (MCI), often a prodrome to late-onset sporadic AD; non-demented carriers of the Apolipoprotein E (ApoE) epsilon4 allele, a strong genetic risk factor for late-onset AD; cognitively normal subjects with a family history of AD; subjects with subjective memory complaints; and normal elderly followed longitudinally until they expressed the clinical symptoms and received post-mortem confirmation of AD. Finally, we will discuss the potential to combine different PET tracers and CSF markers of pathology to improve the early detection of AD.
Nonuniform Sampling and Reconstruction in Shift-Invariant Spaces (2001)

This article discusses modern techniques for nonuniform sampling and reconstruction of functions in shift-invariant spaces. It is a survey as well as a research paper and provides a unified framework for uniform and nonuniform sampling and reconstruction in shift-invariant subspaces by bringing together wavelet theory, frame theory, reproducing kernel Hilbert spaces, approximation theory, amalgam spaces, and sampling. Inspired by applications taken from communication, astronomy, and medicine, the following aspects will be emphasized: (a) The sampling problem is well defined within the setting of shift-invariant spaces. (b) The general theory works in arbitrary dimension and for a broad class of generators. (c) The reconstruction of a function from any sufficiently dense nonuniform sampling set is obtained by efficient iterative algorithms. These algorithms converge geometrically and are robust in the presence of noise. (d) To model the natural decay conditions of real signals and images, the sampling theory is developed in weighted L p-spaces.
An organic user interface for searching citation links (1995)

This paper describes Butterfly, an Information Visualizer application for accessing DIALOG'S Science Citation databases across the Internet. Network information often involves slow access that conflicts with the use of highly-interactive information visualization. Butterfly addresses this problem, integrating search, browsing, and access management via four techniques: 1) visualization supports the assimilation of retrieved information and integrates search and browsing activity, 2) automatically-created "link-generating" queries assemble bibliographic records that contain reference information into citation graphs, 3) asynchronous query processes explore the resulting graphs for the user, and 4) process controllers allow the user to manage these processes. We use our positive experience with the Butterfly implementation to propose a general information access approach, called Organic User Inteifacesfor Infomiation Access, in which a virtual landscape grows under user control as information is accessed automatically.
Atomic force microscope lithography on carbonaceous films deposited by electron-beam irradiation (1998)

A nanometer-scale mask that can be used for selective growth or selective etching was obtained by two-stage patterning. In the first step, a microscopic patterning was performed using a scanning electron microscope (SEM). In the SEM the mask was deposited by decomposition of residual oil molecules in the vicinity of the semiconductor surface. In the second stage, patterning of the carbonaceous film was made using an atomic force microscope (AFM). Use of the AFM assures not only a precise alignment with the previous marks but also a better resolution. Applying an electric bias between the conductive tip and the substrate surface previously covered with the carbonaceous film gave the local modification of the film composition. Further etching resulted in the pattern formation on the semiconductor surface with a minimum linewidth of ∼22 nm.
TRANSFAC(R): transcriptional regulation, from patterns to profiles (2003)

The TRANSFAC database on eukaryotic transcriptional regulation, comprising data on transcription factors, their target genes and regulatory binding sites, has been extended and further developed, both in number of entries and in the scope and structure of the collected data. Structured fields for expression patterns have been introduced for transcription factors from human and mouse, using the CYTOMER database on anatomical structures and developmental stages. The functionality of Match, a tool for matrix-based search of transcription factor binding sites, has been enhanced. For instance, the program now comes along with a number of tissue-(or state-)specific profiles and new profiles can be created and modified with Match Profiler. The GENE table was extended and gained in importance, containing amongst others links to LocusLink, RefSeq and OMIM now. Further, (direct) links between factor and target gene on one hand and between gene and encoded factor on the other hand were introduced. The TRANSFAC public release is available at http://www.gene-regulation.com. For yeast an additional release including the latest data was made available separately as TRANSFAC Saccharomyces Module (TSM) at http://transfac.gbf.de. For CYTOMER free download versions are available at http://www.biobase.de:8080/index.html.
Phorbol esters, phospholipase C, and growth factors rapidly stimulate the phosphorylation of a Mr 80,000 protein in intact quiescent 3T3 cells. (1983)

Addition of biologically active phorbol esters to intact quiescent 3T3 mouse cells stimulates an extremely rapid (detectable within seconds) phosphorylation of a Mr 80,000 cellular protein (termed "80k"). Phorbol 12,13-dibutyrate enhances 80k phosphorylation in a dose-dependent manner; half-maximal effect is obtained at 32 nM. The possibility that this phosphorylation is related to the activation of Ca2+-activated phospholipid-dependent protein kinase is suggested by the fact that phospholipid breakdown induced by exogenous treatment of the cells with phospholipase C from Clostridium perfringens or with platelet-derived growth factor, which is a potent activator of endogenous phospholipase C activity, also causes a rapid enhancement of 80k phosphorylation. Moreover, prolonged pretreatment of the cells with phorbol 12,13-dibutyrate, which leads to a marked decrease in the number of specific phorbol ester binding sites, prevents the phosphorylation of 80k stimulated by phorbol esters, phospholipase C, and platelet-derived growth factor. These findings provide evidence obtained with intact cells that implicate the stimulation of Ca2+-activated phospholipid-dependent protein kinase in the action of phorbol esters and other growth factors.
Modulation of Escherichia coli RecBCD activity by the bacteriophage lambda Gam and P22 Abc functions (1988)

Plasmids that express the bacteriophage lambda gam gene or the P22 abc2 gene (with and without abc1) at controllable levels were placed in Escherichia coli and tested for effects on the activity of RecBCD. Like Gam, Abc2 inhibited the ATP-dependent exonuclease activity of RecBCD, apparently not by binding to DNA. However, Abc2-mediated inhibition was partial, while Gam-mediated inhibition was complete. Both Abc2 and Gam inhibited host system-mediated homologous recombination in a Chi-containing interval in the chromosome of a hybrid lambda phage; Abc2 inhibited it more strongly than Gam. Gam but not Abc2 spared a phage T4 gene 2 mutant from restriction by RecBCD; Abc2 exhibited weak sparing activity in combination with Abc1 and substantial activity in combination with both Abc1 and P22 homologous recombination function Erf. Either Gam or the combination of the lambda recombination functions Exo and Bet was sufficient to induce a mode of plasmid replication that produced linear multimers. The combination of Abc2, Abc1, and Erf also exhibited this activity. However, Erf was inactive, both by itself and in combination with Abc1; Abc2 had weak activity. These results indicate that Gam and Abc2 modulate the activity of RecBCD in significantly different ways. In comparison with lambda Gam, P22 Abc2 has a weak effect on RecBCD nuclease activity but a strong effect on its recombination-promoting activity.
Highly conformal deposition of pure Co films by MOCVD using Co2(CO)8 as a precursor (2006)

We have investigated the effect of the experimental variables such as temperature and pressure on conformality of Co films deposited over high aspect ratio trenches using <TEX>$Co_2(CO)_8$</TEX> as a precursor. The results show that the conformality of Co films is a strong function of temperature and process pressure. Lowering the pressure and temperature significantly improves the conformality. As the pressure decreases from 0.6 Torr to 0.2 Torr at <TEX>$50^{\circ}C$</TEX>, the bottom coverage of Co films over <TEX>$0.2{\mu}m$</TEX> width trenches with an aspect ratio of 13 to 1 significantly increases to 85%. However, further increasing the temperature from 50 to <TEX>$60^{\circ}C$</TEX> at the pressure of 0.2 Torr degrades the bottom coverage to 14%. In contrast, the extremely low pressure of 0.03 Torr allows the excellent conformal deposition of Co films up to <TEX>$70^{\circ}C$</TEX>. This can be attributed to the suppression of homogeneous reaction in the gas phase, which can create the intermediate products with high sticking coefficient. In addition, the Co films deposited at <TEX>$50^{\circ}C$</TEX> show the low resistivity with negligible contamination. As a result, the newly developed Co process using MOCVD can be implemented into the next generation devices with complex shapes.
FT8-3 Advanced Low Emissions Combustor Design (2011)

Pratt and Whitney developed a novel water-injected industrial gas turbine combustor liner design that has demonstrated significant reduction in CO emissions when compared with typical film-cooled combustor designs. The CO reduction demonstrated in a prototype test shows that the CO quenching due to cooler film temperatures near the liner wall is a significant source of CO emissions in a conventional water-injected combustor operating on natural gas fuel. This finding paved the way for a combustor design that reduces CO emissions while still maintaining low levels of NOx emissions. This design also has potential for lower NOx since the low CO emissions characteristic enables increased water injection. This paper presents the emissions characteristic measured on prototype hardware and the design of the engine hardware for future validation. Significant reduction in gaseous emissions was demonstrated with the testing of a prototype at the United Technologies Research Center in East Hartford, CT. This reduction in emissions compared with the baseline film-cooled design for a given operating condition has many benefits to the customer, including the reduced need for exhaust catalyst cleanup and extended operating times while still meeting site permits specified in CO tons per year. Other benefits may include the ability to guarantee lower NOx emissions through increased water injection for the current CO emissions output.
Use of Sterol Mutants as Probes for Sterol Functions in the Yeast,Saccharomyces cerevisiae (1999)

(1999). Use of Sterol Mutants as Probes for Sterol Functions in the Yeast, Saccharomyces cerevisiae. Critical Reviews in Biochemistry and Molecular Biology: Vol. 34, No. 6, pp. 399-404.
Recombinant proteins from plants : production and isolation of clinically useful compounds (1998)

In Recombinant Proteins from Plants, leading researchers from around the world present the latest molecular and classical approaches to the separation, analysis, and characterization of recombinant plant proteins. Focusing on the large-scale, cost-effective production of such proteins for use as specialist industrial or therapeutic biomolecules, these authoritative scientists also include promising experimental techniques that will become increasingly important in the future-such techniques as those for the efficient transformation of monocots with Agrobacterium tumefaciens, for optimizing the stability of recombinant proteins, and for exploiting the immunotherapeutic potential of plant-expressed proteins. Recombinant Proteins from Plants provides a comprehensive and detailed handbook of essential techniques that will benefit both scientists new to the field and established laboratories. It will become the standard reference for even highly skilled researchers working in this most exciting and fast developing field of biology
Filter banks in digital communications (2001)

Digital signal processing has played a key role in the development of telecommunication systems over the last two decades. In recent years digital filter banks have been occupying an increasingly important role in both wireless and wireline communication systems. In this paper we review some of these applications of filter banks with special emphasis on discrete multitone modulation which has had an impact on high speed data communication over the twisted pair telephone line. We also review filter bank precoders which have been shown to be important for channel equalization applications.
Model of functional cardiac aging: young adult mice with mild overexpression of serum response factor (2003)

Serum response factor (SRF) is an important transcription factor that may have a role in the maintenance of cardiac structure and function. The level of SRF mRNA expression increases approximately 16% in the hearts of mice during adult aging. To model the effect of mild SRF elevation in the aging heart, transgenic mice with low levels of SRF overexpression were generated. By 6 mo of age, the transgenic mice had a 19% increase of heart-to-body weight ratio compared with nontransgenic mice. In addition, they had a 12% increase in myocyte size, a 6.7% increase in collagen deposition, and altered gene expression of a number of muscle-specific and cardiac genes. Doppler echocardiography revealed that these transgenic mice had increased left ventricular wall thickness and decreased left ventricular (LV) volumes, increased LV stiffness with 20% reduction in early diastolic LV filling (peak E), and 35% decline in peak E-to-peak A (late diastolic filling) ratio. The observed changes, especially those in the E/A ratio, are similar to those seen clinically in late life as a part of human adult myocardial aging.
Chromosome 13 abnormalities identified by FISH analysis and serum β2-microglobulin produce a powerful myeloma staging system for patients receiving high-dose therapy (2001)

A careful prognostic evaluation of patients referred for high-dose therapy (HDT) is warranted to identify those who maximally benefit from HDT as well as those who clearly fail current HDT and are candidates for more innovative treatments. In a series of 110 patients with myeloma who received HDT as first-line therapy, times to event (disease progression and death) were studied through proportional hazard models, in relation to different prognostic factors, including a chromosome 13 fluorescence in situ hybridization (FISH) analysis using a D13S319 probe. Delta13 was detected in 42 patients (38%). Follow-up time among surviving patients and survival time were 48 +/- 3 and 51 +/- 7 months, respectively (median +/- SE). In the univariate analysis, Delta13 was the most powerful adverse prognostic factor for all times to event, especially for the survival time (P <.0001) and was followed by beta2-microglobulin (beta2m) levels 2.5 mg/L or higher (P =.0001). The comparison of survival prognostic models including beta2m 2.5 mg/L or greater and another factor favored the Delta13/beta2m combination. In 22 patients (20%) with no unfavorable factor, the median survival time was not reached at 111 months. In contrast, among 55 patients (50%) with one unfavorable factor and 33 patients (30%) with 2 unfavorable factors, median survival times were 47.3 +/- 4.6 months and 25.3 +/- 3.2 months, respectively (P <.0001). We conclude that delta13, adequately detected by FISH analysis, is a very strong factor related to poor survival, especially when associated with a beta2m level of 2.5 mg/L or higher. Routine FISH Delta13 assessment is strongly recommended for patients considered for HDT.
Biochemical Mechanisms of Resistance to Small-Molecule Protein Kinase Inhibitors (2010)

Protein kinases have emerged as one of the most frequently targeted families of proteins in drug discovery. While the development of small-molecule inhibitors that have the potency and selectivity necessary to be effective cancer drugs is still a formidable challenge, there have been several notable successes in this area over the past decade. However, in the course of the clinical use of these inhibitors, it has become apparent that drug resistance is a recurring problem. Because kinase inhibitors act by targeting a specific kinase or set of kinases, there is a strong selective pressure for the development of mutations that hinder drug binding but preserve the catalytic activity of these enzymes. To date, resistance mutations to clinically approved kinase inhibitors have been identified in a number of kinases. This review will highlight recent work that has been performed to understand how mutations in the kinase catalytic domain confer drug resistance. In addition, recent experimental efforts to predict potential sites of clinical drug resistance will be discussed.
Preeclampsia: Animal models for a human cure (2011)

Preeclampsia (PE) affects ∼5% of human pregnancies and is a leading cause of perinatal mortality, preterm birth, and maternal morbidity (1). Through positive effects on vascular tone and glomerular capillary health, vascular endothelial growth factor (VEGF) and placental growth factor (PGF) are necessary for normal pregnancy (2–4). In PE, these proteins are antagonized by excessive placental production of soluble fms-like tyrosine kinase-1 (sFLT1), a splice variant of the VEGF receptor (2, 3), and in later pregnancy, by soluble endoglin (sENG), a soluble form of a transforming growth factor beta (TGFB1) receptor that prevents binding of TGFB1 to membrane-bound endoglin (5). The report by Kumasawa et al. (6) in PNAS describes the use of a mouse model in which placenta-specific expression of human sFLT1 is present from the time of implantation. The model faithfully reproduces many of the human findings of late-onset PE. The investigators also show that the lipid-lowering drug, pravastatin, ameliorates sFLT1-induced PE in these sFLT mice (6).
SARS-CoV-2-induced humoral immunity through B cell epitope analysis and neutralizing activity in COVID-19 infected individuals in Japan (2020)

Abstract The aim of this study is to understand adaptive immunity to SARS-CoV-2 through the analysis of B cell epitope and neutralizing activity in coronavirus disease 2019 (COVID-19) patients. We obtained serum from thirteen COVID-19 patients. Most individuals revealed neutralizing activity against SARS-CoV-2 assessed by a pseudotype virus-neutralizing assay. The antibody production against the spike glycoprotein (S protein) or receptor-binding domain (RBD) of SARS-CoV-2 was elevated, with large individual differences, as assessed by ELISA. In the analysis of the predicted the linear B cell epitopes, two regions (671-690 aa. and 1146-1164 aa.), which were located in S1 and S2 but not in the RBD, were highly reactive with the sera from patients. In the further analysis of the B cell epitope within the S protein by utilizing a B cell epitope array, a hot spot in the N-terminal domain of the S protein but not the RBD was observed in individuals with neutralizing activity. Overall, the analysis of antibody production and B cell epitopes of the S protein from patient serum may provide a novel target for the vaccine development against SARS-CoV-2.