gebhart/patrepeval huggingface dataset:
Genetics of Alzheimer's disease (1998)

Mutations in any one of three genes can cause autosomal dominant, early-onset Alzheimer's disease: these genes are the amyloid precursor protein (APP) gene on chromosome 21, the presenilin-1 (PS-1) gene on chromosome 14 and the presenilin-2 (PS-2) gene on chromosome 1. Pathogenic mutations at all these loci cause mismetabolism of APP such that more of the peptide A beta 42 is produced. This peptide is deposited in the plaques in the brains of Alzheimer's patients. These facts have led to the dominant hypothesis for the disease process: the 'amyloid cascade hypothesis', which proposes that overproduction or failure to clear the peptide A beta 42 is always central to the disease. Genetic variability at the apoliprotein E locus is a major determinant of late onset Alzheimer's disease. The mechanism by which apoliprotein E is involved in the pathogenesis of Alzheimer's disease is not yet known. There are likely to be other genetic factors which impinge on Alzheimer's disease.
Origin of satellite cells in avian skeletal muscles. (1983)

The study of the embryonic origin of the striated satellite cells is based 1) on a comparison of the specific morphology of the nuclei in satellite cells and in myofibers, in late embryonic and postnatal chick and quail muscles; 2) on a species-identification of the satellite cell nuclei in hetero-specific muscle tissues where myofibers derive from implanted quail somite and connective tissue fibroblasts from the chick host somatopleura. Observations clearly demonstrate that myofibers and satellite cells are of the same somitic origin. It is concluded that satellite cells represent a portion of the myogenic cell lineage.
Hyperproliferative apoptosis-resistant endothelial cells in idiopathic pulmonary arterial hypertension (2007)

Idiopathic pulmonary arterial hypertension (IPAH) is characterized by plexiform vascular lesions, which are hypothesized to arise from deregulated growth of pulmonary artery endothelial cells (PAEC). Here, functional and molecular differences among PAEC derived from IPAH and control human lungs were evaluated. Compared with control cells, IPAH PAEC had greater cell numbers in response to growth factors in culture due to increased proliferation as determined by bromodeoxyuridine incorporation and Ki67 nuclear antigen expression and decreased apoptosis as determined by caspase-3 activation and TdT-mediated dUTP nick end labeling assay. IPAH cells had greater migration than control cells but less organized tube formation in in vitro angiogenesis assay. Persistent activation of signal transducer and activator of transcription 3 (STAT3), a regulator of cell survival and angiogenesis, and increased expression of its downstream prosurvival target, Mcl-1, were identified in IPAH PAEC. A Janus kinase (JAK) selective inhibitor reduced STAT3 activation and blocked proliferation of IPAH cells. Phosphorylated STAT3 was detected in endothelial cells of IPAH lesions in vivo, suggesting that STAT3 activation plays a role in the proliferative pulmonary vascular lesions in IPAH lungs.
Asymmetric Processing of Human Immunodeficiency Virus Type 1 cDNA In Vivo: Implications for Functional End Coupling during the Chemical Steps of DNA Transposition (2001)

Retroviral integration, like all forms of DNA transposition, proceeds through a series of DNA cutting and joining reactions. During transposition, the 3' ends of linear transposon or donor DNA are joined to the 5' phosphates of a double-stranded cut in target DNA. Single-end transposition must be avoided in vivo because such aberrant DNA products would be unstable and the transposon would therefore risk being lost from the cell. To avoid suicidal single-end integration, transposons link the activity of their transposase protein to the combined functionalities of both donor DNA ends. Although previous work suggested that this critical coupling between transposase activity and DNA ends occurred before the initial hydrolysis step of retroviral integration, work in the related Tn10 and V(D)J recombination systems had shown that end coupling regulated transposase activity after the initial hydrolysis step of DNA transposition. Here, we show that integrase efficiently hydrolyzed just the wild-type end of two different single-end mutants of human immunodeficiency virus type 1 in vivo, which, in contrast to previous results, proves that two functional DNA ends are not required to activate integrase's initial hydrolysis activity. Furthermore, despite containing bound protein at their processed DNA ends, these mutant viruses did not efficiently integrate their singly cleaved wild-type end into target DNA in vitro. By comparing our results to those of related DNA recombination systems, we propose the universal model that end coupling regulates transposase activity after the first chemical step of DNA transposition.
Chemoimmunotherapy may overcome the adverse prognostic significance of 11q deletion in previously untreated patients with chronic lymphocytic leukemia (2008)

CLL with an 11q22 deletion was associated with high rates of response, survival, and relapse-free survival when treated with chemoimmunotherapy.
<title>Three-dimensional microfabrication using two-photon-activated chemistry</title> (2000)

Photochemical reactions which can be activated by the simultaneous absorption of two photons provide a means for single-step fabrication of complex 3D microstructures. These types of structures are needed for a wide range of applications, including microfluidics, electrooptics, and micro-electromechanical systems. We have shown that chromophores can be engineered to have both large two-photon absorptivities as well as an efficient means for activating chemical processes, such as radical polymerization, subsequent to the photoexcitation. Chromophores designed following this strategy two-photon-activate the radical polymerization of acrylates at lower incident laser powers than conventional UV initiators. Efficient two-photon photopolymer resins based on these chromophores were used in the fabrication of complex microarchitectures, such as photonic bandgap structures and tapered waveguides. We have devised a strategy which allows this approach to be extended to other chemical systems.
Combined scanning optical coherence and two-photon-excited fluorescence microscopy (1999)

We demonstrate simultaneous imaging by optical coherence microscopy (OCM) and two-photon-excited (TPE) fluorescence microscopy. A mode-locked Ti:sapphire laser is focused and scanned in three dimensions through a fixed sample, generating both backscattered light and fluorescence light, which are independently detected. Both imaging modes provide rapid en-face imaging with submicrometer resolution. High-power delivery into the sample yields an OCM sensitivity in excess of 130 dB at 100-kHz pixel rates. Simultaneous imaging of cell nuclei with OCM and TPE is demonstrated in live drosophila embryos.
Determining Membrane Capacitance by Dynamic Control of Droplet Interface Bilayer Area (2011)

By making dynamic changes to the area of a droplet interface bilayer (DIB), we are able to measure the specific capacitance of lipid bilayers with improved accuracy and precision over existing methods. The dependence of membrane specific capacitance on the chain-length of the alkane oil present in the bilayer is similar to that observed in black lipid membranes. In contrast to conventional artificial bilayers, DIBs are not confined by an aperture, which enables us to determine that the dependence of whole bilayer capacitance on applied potential is predominantly a result of a spontaneous increase in bilayer area. This area change arises from the creation of new bilayer at the three phase interface and is driven by changes in surface tension with applied potential that can be described by the Young-Lippmann equation. By accounting for this area change, we are able to determine the proportion of the capacitance dependence that arises from a change in specific capacitance with applied potential. This method provides a new tool with which to investigate the vertical compression of the bilayer and understand the changes in bilayer thickness with applied potential. We find that, for 1,2-diphytanoyl-sn-glycero-3-phosphocholine membranes in hexadecane, specific bilayer capacitance varies by 0.6-1.5% over an applied potential of ±100 mV.
Cool-cache for hot multimedia (2001)

We claim that the unique characteristics of multimedia applications dictate media-sensitive architectural and compiler approaches to reduce the power consumption of the data cache. Our motivation is exploring energy savings for real-time multimedia workloads without sacrificing performance. In this paper, we present two complementary media-sensitive energy-saving techniques that leverage static information. While our first technique is applicable to existing architectures, in our second technique we adopt a more radical approach and propose a new caching architecture by re-evaluating the architecture-compiler interface. Our experiments show that substantial energy savings are possible in the data cache. Across a wide range of cache and architectural configurations we obtain up to 77% energy savings, while the performance varies from 14% improvement to 4% degradation depending on the application.
Attitudes of Mexican geneticists towards prenatal diagnosis and selective abortion (1998)

Prenatal diagnosis (PD) provides the physician information on whether the unborn fetus has a genetic or chromosomal disorder, and offers patients a new option: selective abortion. In the present study, we analyzed the answers Mexican geneticists provided to a few selected questions from a multinational survey designed by Wertz and Fletcher [1988: Am J Hum Genet 42:592-600]. The selected questions were related to the use of PD, the acceptance of selective abortion, and the self-reported directiveness of counselling following the diagnosis of a fetal anomaly. Our results show that the great majority of Mexican geneticists participating in the study agree with PD when medically indicated, but not on free demand. Specific cases stimulated the group on thinking more than the general statements provided in the survey. Although the majority agreed that PD should be available to all women, when faced with cases of nonmorbid maternal anxiety, paternity testing, and sex selection, the proportion of geneticists willing to perform the test decreased substantially. When counselling patients on a fetal anomaly, the minority would be as unbiased as possible, and this seems to be the tendency in developing countries where counselling, as stated in the respondents' comments, reflects the belief that the goal of genetics is the prevention of or opposition to abortion. Counselling was influenced by the severity of the disorder. The geneticists' personal attitude toward abortion in the same situations was stronger than when counselling others. Analysis of directiveness in counselling for fetal anomaly showed that older geneticists, with more years of experience in medical genetics, were more likely to be neutral. When counselling directively, the group showed an overall direction toward continuing affected pregnancies. However, older geneticists and those with more than 10 years of practice were more likely than their younger counterparts to counsel towards terminating affected pregnancies. In personal situations of fetal disorder, the general tendency was to abort; however, geneticists seeing more than 5 patients per week, and those who believe that religion is important, were more likely to reject abortion. The sample is representative of Mexican geneticists, and the main limitation of this study is that the geneticists have very little experience in PD, and that their responses were mostly based on theory. However, their opinions may influence the demand and the availability of PD and abortion, as well as the possibility of legalization of abortion on the basis of a fetal defect.
Prime-Boost Immunization with DNA Vaccine: Mucosal Route of Administration Changes the Rules (2001)

In this study we assessed prime-boost immunization strategies with a DNA vaccine (gB DNA) and attenuated recombinant vaccinia virus vector (rvacgB), both encoding the gB protein of HSV, for their effectiveness at inducing mucosal as well as systemic immunity to HSV. Confirming the reports of others, systemic priming with gB DNA and systemic boosting with rvacgB were the most effective means of inducing serum Ab and splenic T cell responses. Nevertheless, the systemic prime-boost approach failed to induce detectable humoral or T cell responses at mucosal sites. However, such responses, at both proximal and distal locations, were induced if immunizations, especially the priming dose, were administered mucosally. Curiously, whereas optimal immunity with systemic priming and boosting occurred when gB DNA was used to prime and rvacgB was used as a boost, mucosal responses were optimal when animals were mucosally primed with rvacgB and boosted with gB DNA given mucosally. Furthermore, notable mucosal responses also occurred in animals mucosally primed with rvacgB and subsequently boosted systemically with gB DNA. Because the mucosal prime-boost immunization protocol also induced excellent systemic immune responses, the approach should be useful to vaccinate against agents for which both mucosal and systemic immunity are important for protection.
Influence of composition of gasoline - ethanol blends on parameters of internal combustion engines (2003)

The purpose of this study is to investigate experimentally and compare the engine performance and pollutant emission of a SI engine using ethanol–gasoline blended fuel and pure gasoline. The results showed that when ethanol is added, the heating value of the blended fuel decreases, while the octane number of the blended fuel increases. The results of the engine test indicated that when ethanol–gasoline blended fuel is used, the engine power and specific fuel consumption of the engine slightly increase; CO emission decreases dramatically as a result of the leaning effect caused by the ethanol addition; HC emission decreases in some engine working conditions; and CO2 emission increases because of the improved combustion.
IL-2 Regulates CD103 Expression on CD4+ T Cells in Scurfy Mice that Display Both CD103-Dependent and Independent Inflammation (2009)

Scurfy (Sf) mice lack CD4(+)Foxp3(+) regulatory T cells and develop fatal multiorgan inflammation (MOI) mediated by CD4(+) T cells. Introducing Il2(-/-) gene into Sf mice (Sf.Il2(-/-)) inhibited inflammation in skin and lung. As a major integrin receptor for the organs, we compared CD103 expression on the CD4(+) T cells of B6, Il2(-/-), Sf, and Sf.Il2(-/-) mice. CD103(+)CD4(+) T cells, but not CD8(+) T cells or CD11c(+) dendritic cells, were significantly up-regulated only in Sf mice, indicating Il2(-/-) dominantly and specifically inhibited CD103 up-regulation in Sf CD4(+) T cells. In addition, CD4(+)Foxp3(+) regulatory T cell CD103 expression was not reduced in Il2(-/-) mice. Introducing CD103(-/-) into Sf mice inhibited inflammation in skin and lung as compared with age-matched Sf mice, but they died at approximately 7 wk old with inflammation developed in skin, lungs, and colon, demonstrating fatal MOI induced by CD103-independent mechanism. Transfer of Sf CD4(+) T cells induced MOI more rapidly than CD103(-)CD4(+) T cells, indicating the presence of CD103-dependent mechanism for inflammation. In vitro stimulation with anti-CD3 plus anti-CD28 beads confirmed that CD103 induction in the CD4(+)Foxp3(-) T cells in Il2(-/-) and Sf.Il2(-/-) is defective and cannot be restored by rIL-2 or rIL-15. The data indicate that IL-2 is required for optimal CD103 induction on CD4(+) T cells in Sf mice and this effect contributes to inflammation in an organ-specific manner. IL-2 also has additional roles because the protection of skin and lung inflammation in Sf.Il2(-/-), but not Sf.CD103(-/-) mice is lifelong and Sf.Il2(-/-) mice have longer lifespan than Sf.CD103(-/-) mice.
The Insulin-Like Growth Factors (1993)

The recent availability of reagents to study the IGFs, their receptors, and binding proteins has led to an explosive growth in the study of IGF physiology. However, most studies to date have been descriptive, and studies delineating mechanisms of action are limited. It is apparent that most organ systems synthesize several components of the IGF system necessary for IGF to function in an autocrine or paracrine fashion and that regulation of this system occurs at the local level. However, the relative importance of locally produced IGF vs circulating IGF remains unclear. The mechanisms by which the IGFBPs modulate IGF activity are crucial to understanding this system, and identification of specific roles for each of these proteins will be required. Of critical importance is the identity of the intracellular signal transduction system by which the IGF receptor mediates the effects of the IGFs, and the delineation of mechanisms by which the IGFBPs interact with the receptor at the cellular level. It is also of interest to determine what role, if any, the IGF-II receptor plays in mediating the growth-promoting effects of the IGFs. The ubiquitous distribution of the IGFs, IGFBPs, and IGF receptors indicates that they may play a role in the regulation of coordinate growth among several tissues and cell types. Understanding the mechanisms by which these components interact to coordinate growth responses between different cell types should greatly enhance our understanding of normal growth and development.
Identification of many microRNAs that copurify with polyribosomes in mammalian neurons (2003)

Localized translation in mammalian dendrites may play a role in synaptic plasticity and contribute to the molecular basis for learning and memory. The regulatory mechanisms that control localized translation in neurons are not well understood. We propose a role for microRNAs (miRNAs), a class of noncoding RNAs, as mediators of neuronal translational regulation. We have identified 86 miRNAs expressed in mammalian neurons, of which 40 have not previously been reported. A subset of these miRNAs exhibits temporally regulated expression in cortical cultures. Moreover, all of the miRNAs that were tested cofractionate with polyribosomes, the sites of active translation. These findings indicate that a large, diverse population of miRNAs may function to regulate translation in mammalian neurons.
Stitched α-Helical Peptides via Bis Ring-Closing Metathesis (2014)

Conformationally stabilized α-helical peptides are capable of inhibiting disease-relevant intracellular or extracellular protein-protein interactions in vivo. We have previously reported that the employment of ring-closing metathesis to introduce a single all-hydrocarbon staple along one face of an α-helical peptide greatly increases α-helical content, binding affinity to a target protein, cell penetration through active transport, and resistance to proteolytic degradation. In an effort to improve upon this technology for stabilizing a peptide in a bioactive α-helical conformation, we report the discovery of an efficient and selective bis ring-closing metathesis reaction leading to peptides bearing multiple contiguous staples connected by a central spiro ring junction. Circular dichroism spectroscopy, NMR, and computational analyses have been used to investigate the conformation of these "stitched" peptides, which are shown to exhibit remarkable thermal stabilities. Likewise, trypsin proteolysis assays confirm the achievement of a structural rigidity unmatched by peptides bearing a single staple. Furthermore, fluorescence-activated cell sorting (FACS) and confocal microscopy assays demonstrate that stitched peptides display superior cell penetrating ability compared to their stapled counterparts, suggesting that this technology may be useful not only in the context of enhancing the drug-like properties of α-helical peptides but also in producing potent agents for the intracellular delivery of proteins and oligonucleotides.
Biocompatible Copper(I) Catalysts for in Vivo Imaging of Glycans (2010)

The Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) is the standard method for bioorthogonal conjugation. However, current Cu(I) catalyst formulations are toxic, hindering their use in living systems. Here we report that BTTES, a tris(triazolylmethyl)amine-based ligand for Cu(I), promotes the cycloaddition reaction rapidly in living systems without apparent toxicity. This catalyst allows, for the first time, noninvasive imaging of fucosylated glycans during zebrafish early embryogenesis. We microinjected embryos with alkyne-bearing GDP-fucose at the one-cell stage and detected the metabolically incorporated unnatural sugars using the biocompatible click chemistry. Labeled glycans could be imaged in the enveloping layer of zebrafish embryos between blastula and early larval stages. This new method paves the way for rapid, noninvasive imaging of biomolecules in living organisms.
GAN（Generative Adversarial Nets） (2017)

We propose a new framework for estimating generative models via an adversarial process, in which we simultaneously train two models: a generative model G that captures the data distribution, and a discriminative model D that estimates the probability that a sample came from the training data rather than G. The training procedure for G is to maximize the probability of D making a mistake. This framework corresponds to a minimax two-player game. In the space of arbitrary functions G and D, a unique solution exists, with G recovering the training data distribution and D equal to ½ everywhere. In the case where G and D are defined by multilayer perceptrons, the entire system can be trained with backpropagation. There is no need for any Markov chains or unrolled approximate inference networks during either training or generation of samples. Experiments demonstrate the potential of the framework through qualitative and quantitative evaluation of the generated samples.
Perfusion of the cerebral ventricular system in unanesthetized goats (1962)

Techniques have been devised for repeated perfusion of the ventriculocisternal system in chronically prepared, unanesthetized goats. The methods are designed for investigations of a) functional effects of prolonged changes of cerebrospinal fluid (CSF) composition and b) quantitative aspects of CSF formation and exchange of materials between CSF and blood. The present paper provides a technical background for subsequent papers dealing with specific problems. Goats tolerate perfusion rates of 1–3 ml/min at pressures adjustable between –10 and +30 cm H 2 O. Measurements are made of inflow rates, outflow rates, and concentrations of test materials entering and leaving the system. Composition of normal CSF has been determined and directions are given for preparation of sterile synthetic CSF. Brain weight is about 100 g and choroid plexuses 500 mg. CSF volume is 20–25 ml of which 8–12 ml is in the ventricles. Pressure-volume characteristics are described. Steady-state difference between inflow and outflow rates is a linear function of hydrostatic pressure; the slope is related to hydrodynamic resistance to bulk absorption. Preliminary observations are given to show effects of reduced Ca ++ on nervous control of the cardiovascular system.