gebhart/patrepeval huggingface dataset:
Nanotubes in biosensing (2010)

Carbon nanotubes (CNTs) have extensively been used for electrochemical and optical biosensing due to the unique mechanical, chemical, and electrical properties. This review introduces two functionalization categories, noncovalent interaction along the CNTs sidewalls via physical adsorption or entrapment and covalent binding via carboxylate chemistry or nonselective attack of nanotube sidewalls by highly reactive species and gives an overview on the functionalized CNTs-based biosensing methodologies for DNA, antigen-antibody, cells, and other biological molecules. Furthermore, the in vivo near-IR fluorescence biosensing application of CNTs with high photostability and efficiency is discussed. Finally, field-effect transistors based on semiconductor CNTs are also summarized for ultrasensitive detection. Biosensors based on CNTs provide a significant avenue for the detection of biomolecules in vivo and in vitro applications.
Highly Efficient Solar Cell Polymers Developed via Fine-Tuning of Structural and Electronic Properties (2009)

This paper describes synthesis and photovoltaic studies of a series of new semiconducting polymers with alternating thieno[3,4-b]thiophene and benzodithiophene units. The physical properties of these polymers were finely tuned to optimize their photovoltaic effect. The substitution of alkoxy side chains to the less electron-donating alkyl chains or introduction of electron-withdrawing fluorine into the polymer backbone reduced the HOMO energy levels of polymers. The structural modifications optimized polymers' spectral coverage of absorption and their hole mobility, as well as miscibility with fulleride, and enhanced polymer solar cell performances. The open circuit voltage, V(oc), for polymer solar cells was increased by adjusting polymer energy levels. It was found that films with finely distributed polymer/fulleride interpenetrating network exhibited improved solar cell conversion efficiency. Efficiency over 6% has been achieved in simple solar cells based on fluorinated PTB4/PC(61)BM films prepared from mixed solvents. The results proved that polymer solar cells have a bright future.
Lesion Bypass by the Escherichia coli DNA Polymerase V Requires Assembly of a RecA Nucleoprotein Filament (2001)

Translesion replication is carried out in Escherichia coli by the SOS-inducible DNA polymerase V (UmuC), an error-prone polymerase, which is specialized for replicating through lesions in DNA, leading to the formation of mutations. Lesion bypass by pol V requires the SOS-regulated proteins UmuD' and RecA and the single-strand DNA-binding protein (SSB). Using an in vitro assay system for translesion replication based on a gapped plasmid carrying a site-specific synthetic abasic site, we show that the assembly of a RecA nucleoprotein filament is required for lesion bypass by pol V. This is based on the reaction requirements for stoichiometric amounts of RecA and for single-stranded gaps longer than 100 nucleotides and on direct visualization of RecA-DNA filaments by electron microscopy. SSB is likely to facilitate the assembly of the RecA nucleoprotein filament; however, it has at least one additional role in lesion bypass. ATPgammaS, which is known to strongly increase binding of RecA to DNA, caused a drastic inhibition of pol V activity. Lesion bypass does not require stoichiometric binding of UmuD' along RecA filaments. In summary, the RecA nucleoprotein filament, previously known to be required for SOS induction and homologous recombination, is also a critical intermediate in translesion replication.
<b>Serum HbA</b><sub>1c</sub><b> Levels and Exercise Capacity in Diabetic Patients</b> (2001)

It is well known that cardiovascular morbidity and mortality are high in diabetic patients. Cardiac involvement is silent and early and these diabetic patients generally complain of chronic fatigue. This study was designed to evaluate the relation between glycemic control and exercise capacity in 330 diabetic patients who have no cardiac symptoms by sustaining dynamic exercise. After a cardiac examination, patients with coronary heart disease, ECG abnormalities, cardiac failure, valvular disease, cerebrovascular disease, peripheral artery disease, anaemia and peripheral neuropathy were excluded. Plasma HbA1c and lipid levels were obtained and a symptom limited exercise test based on "Bruce Protocol" was performed on all patients. Plasma HbA1c levels were significantly increased in smokers and in hypercholesterolemic patients (p<0.001, p=0.006). A moderate correlation between exercise capacity and HbA1c levels, and a weak correlation between duration of diabetes, age, sex, hypertension and plasma lipids were obtained. Multivariant regression analys is revealed that only HbA1c and hypercholesterolemia affected exercise capacity independently (r=-0.54 r=-0.30). In conclusion, poor glycemic control in diabetic patients causes earlier cellular involvement. Because of the high affinity of HbA1c to oxygen, the energy metabolism of the cell is affected, with a clinical correlation between chronic fatigue and worsening exercise capacity.
Similarities and Differences between Two Modes of Antagonism of the Thyroid Hormone Receptor (2011)

Thyroid hormone (T3) mediates diverse physiological functions including growth, differentiation, and energy homeostasis through the thyroid hormone receptors (TR). The TR binds DNA at specific recognition sequences in the promoter regions of their target genes known as the thyroid hormone response elements (TREs). Gene expression at TREs regulated by TRs is mediated by coregulator recruitment to the DNA bound receptor. This TR-coregulator interaction controls transcription of target genes by multiple mechanisms including covalent histone modifications and chromatin remodeling. Our previous studies identified a β-aminoketone as a potent inhibitor of the TR-coactivator interaction. We describe here the activity of one of these inhibitors in modulating effects of T3 signaling in comparison to an established ligand-competitive inhibitor of TR, NH-3. The β-aminoketone was found to reverse thyroid hormone induced gene expression by inhibiting coactivator recruitment at target gene promoters, thereby regulating downstream effects of thyroid hormone. While mimicking the downstream effects of NH-3 at the molecular level, the β-aminoketone affects only a subset of the thyroid responsive signaling network. Thus antagonists directed to the coregulator binding site have distinct pharmacological properties relative to ligand-based antagonists and may provide complementary activity in vivo.
Generation of an LFA-1 Antagonist by the Transfer of the ICAM-1 Immunoregulatory Epitope to a Small Molecule (2002)

The protein-protein interaction between leukocyte functional antigen-1 (LFA-1) and intercellular adhesion molecule-1 (ICAM-1) is critical to lymphocyte and immune system function. Here, we report on the transfer of the contiguous, nonlinear epitope of ICAM-1, responsible for its association with LFA-1, to a small-molecule framework. These LFA-1 antagonists bound LFA-1, blocked binding of ICAM-1, and inhibited a mixed lymphocyte reaction (MLR) with potency significantly greater than that of cyclosporine A. Furthermore, in comparison to an antibody to LFA-1, they exhibited significant anti-inflammatory effects in vivo. These results demonstrate the utility of small-molecule mimics of nonlinear protein epitopes and the protein epitopes themselves as leads in the identification of novel pharmaceutical agents.
A Clinically Relevant Androgen Receptor Mutation Confers Resistance to Second-Generation Antiandrogens Enzalutamide and ARN-509 (2013)

A missense mutation in the ligand-binding domain of the androgen receptor F876L confers resistance to the second-generation antiandrogens enzalutamide and ARN-509 in preclinical models of AR function and prostate cancer and is detected in plasma DNA from ARN-509-treated patients with progressive disease. These results chart a new path for the discovery and development of next-generation antiandrogens that could be coupled with a blood-based companion diagnostic to guide treatment decisions.
High resolution ambulatory electrocardiographic monitoring using wrist-mounted electric potential sensors (2003)

In this paper we describe the application of an electric potential sensor to the ambulatory monitoring of the human electrocardiogram (ECG). We show that a high resolution ECG can be acquired using two of these sensors mounted wristwatch style, one on each wrist. These sensors, which do not require a real current conducting path in order to operate, are used non-invasively without making electrical contact to the subject. Furthermore, their sensitivity and low noise floor have made it possible to detect a peak which corresponds, in timing, to the His bundle depolarization—a feature not normally seen in conventional surface ECGs. We predict that these new devices will rapidly find application in the areas of clinical medicine and ambulatory monitoring.
Astrocyte Senescence as a Component of Alzheimer’s Disease (2012)

Aging is the main risk factor for Alzheimer's disease (AD); however, the aspects of the aging process that predispose the brain to the development of AD are largely unknown. Astrocytes perform a myriad of functions in the central nervous system to maintain homeostasis and support neuronal function. In vitro, human astrocytes are highly sensitive to oxidative stress and trigger a senescence program when faced with multiple types of stress. In order to determine whether senescent astrocytes appear in vivo, brain tissue from aged individuals and patients with AD was examined for the presence of senescent astrocytes using p16(INK4a) and matrix metalloproteinase-1 (MMP-1) expression as markers of senescence. Compared with fetal tissue samples (n = 4), a significant increase in p16(INK4a)-positive astrocytes was observed in subjects aged 35 to 50 years (n = 6; P = 0.02) and 78 to 90 years (n = 11; P<10(-6)). In addition, the frontal cortex of AD patients (n = 15) harbored a significantly greater burden of p16(INK4a)-positive astrocytes compared with non-AD adult control subjects of similar ages (n = 25; P = 0.02) and fetal controls (n = 4; P<10(-7)). Consistent with the senescent nature of the p16(INK4a)-positive astrocytes, increased metalloproteinase MMP-1 correlated with p16(INK4a). In vitro, beta-amyloid 1-42 (Aβ(1-42)) triggered senescence, driving the expression of p16(INK4a) and senescence-associated beta-galactosidase. In addition, we found that senescent astrocytes produce a number of inflammatory cytokines including interleukin-6 (IL-6), which seems to be regulated by p38MAPK. We propose that an accumulation of p16(INK4a)-positive senescent astrocytes may link increased age and increased risk for sporadic AD.
Instituciones Extractivas e Improductivas: el caso de Puerto Rico (2019)

El siguiente trabajo examina el papel de las instituciones en la isla de Puerto Rico; colonia y región económica estadounidense. En él, se explora las principales fuentes que definen a las instituciones como inclusivas o extractivas, determinantes para el desarrollo económico. Los datos analizados sugieren que Puerto Rico padece de unas instituciones extractivas, condición que sumerge al estancamiento económico y social que a su vez lo ha llevado a su peor crisis. Su destrucción, no es la de una destrucción creativa, sino de una destrucción improductiva, destrucción que invita a la suspensión de la innovación, que conlleva al descenso poblacional de la isla. El desarrollo industrial que se promovió fue la de un enclave económico que ha llevado a los puertorriqueños en una especie de encapsulamiento ceremonial. Teniendo esto en cuenta, se reflexiona y se sugiere cuáles son las riendas que debería optar el autogobierno, pero sobre todo como los isleños pueden superar estas instituciones.
Discrete Spherical Harmonic Oscillator Transforms on the Cartesian Grids Using Transformation Coefficients (2012)

The analog harmonic oscillators are well-studied in quantum physics, including their energy states, wavefunctions, orthogonal properties, and eigenfunctions of the Fourier transform. In addition, the continuous solutions in different dimension and coordinate systems are known. Some discrete equivalents of the 1D wavefunctions were also studied. However, in the 3D spherical coordinate system, the discrete equivalents of the 3D wavefunctions are not established. In this paper, we focus on the spherical harmonic oscillator wavefunctions (SHOWs) the spherical harmonic oscillator transforms (SHOTs), and their discrete implementation. The SHOWs can be synthesized by linear combinations of the Hermite Gaussian functions with proper transformation coefficients. We find that computing the coefficients can be speeded up using the fast Fourier transforms or some recursive relations. These coefficients relate the Hermite transforms with the SHOTs. Some applications of the discrete SHOWs and the discrete SHOTs are introduced. First, the SHOWs are exactly the eigenfunctions of the 3D DFT. Also, the SHOTs can be used to derive the spherical harmonic oscillator descriptor (SHOD), which is a rotational invariant descriptor. We find that the SHOD is not only compatible with the existing rotational descriptors for the spherically sampled data but also outperforms the existing rotational descriptors for 3D Cartesian sampled, bandlimited input data. Besides, the SHOTs can be used to decompose 3D signals into spherical components. Hence, 3D signal reconstruction is done using partially chosen spherical component, and 3D data compression for MRI data is demonstrated using SHOTs for medical applications.
Measuring privacy leaks in Online Social Networks (2013)

Online Social Networking has gained huge popularity amongst the masses. It is common for the users of Online Social Networks (OSNs) to share information with digital friends but in the bargain they loose privacy. Users are unaware of the privacy risks involved when they share their sensitive information in the network. The users should be aware of their privacy quotient and should know where they stand in the privacy measuring scale. In this paper we have described and calculated the Privacy Quotient i.e a privacy metric to measure the privacy of the user's profile using the naive approach. In the starting of the paper we have given the detailed analysis of the survey that we have carried out to know how well do people understand privacy in online social networks. At last we have proposed a model that will ensure privacy in the unstructured data. It will make use of the Item Response Theory model to measure the privacy leaks in the messages and text that is being posted by the users of the online social networking sites.
Sequence-specific recognition of the major groove of DNA by oligodeoxynucleotides via triple helix formation. Footprinting studies (1988)

Homopyrimidine oligodeoxynucleotides recognize the major groove of the DNA double helix at homopurine.homopyrimidine sequences by forming local triple helices. The oligonucleotide is bound parallel to the homopurine strand of the duplex. This binding can be revealed by a footprinting technique using copper-phenanthroline as a cleaving reagent. Oligonucleotide binding in the major groove prevents cleavage by copper-phenanthroline. The cleavage patterns on opposite strands of the duplex at the boundaries of the triple helix are asymmetric. They are shifted to the 3'-side, indicating that the copper-phenanthroline chelate binds in the minor groove of the duplex structure. Binding of the chelate at the junction between the triple and the double helix is not perturbed on the 5'-side of the bound homopyrimidine oligonucleotide. In contrast, a strong enhancement of cleavage is observed on the purine-containing strand at the triplex-duplex junction on the 3'-side of the homopyrimidine oligonucleotide.
Hierarchical Z-buffer visibility (1993)

Article Hierarchical Z-buffer visibility Share on Authors: Ned Greene View Profile , Michael Kass View Profile , Gavin Miller View Profile Authors Info & Claims SIGGRAPH '93: Proceedings of the 20th annual conference on Computer graphics and interactive techniquesSeptember 1993 Pages 231–238https://doi.org/10.1145/166117.166147Online:01 September 1993Publication History 267citation2,634DownloadsMetricsTotal Citations267Total Downloads2,634Last 12 Months91Last 6 weeks9 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Interaction between streptococcal IgG Fc receptors and human and rabbit IgG domains. (1986)

Groups A, C and G streptococci were tested for their ability to bind 125I-labelled fragments of human and rabbit IgG in order to localize their sites of interaction with IgG domains. Among the Group A streptococci, strains with IgG Fc receptors bound 85% of the added IgG Fc fragments in the test systems, whereas these strains showed practically no reactivity with F(ab')2, Facb (F(ab')2 + C gamma 2 domains) or pFc' (C gamma 3 domains). The Group C and Group G strains bound 48-100% of IgG Fc, but could also bind up to 36% of the added F(ab')2 in accordance with a previously described 'alternative' Fab reactivity. However, unlabelled IgG F(ab')2 or Facb showed no, or only slight, inhibitory capacity for the binding of 125I-labelled IgG Fc to the C and G strains. Collectively, these results indicate that Groups A, C and G streptococci require both the C gamma 2 and C gamma 3 domains for interaction with IgG, and most probably also bind in the interface region between the C gamma 2 and C gamma 3 domains as has been shown for staphylococcal protein A.
Toward a protein–protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins (2000)

Protein-protein interactions play pivotal roles in various aspects of the structural and functional organization of the cell, and their complete description is indispensable to thorough understanding of the cell. As an approach toward this goal, here we report a comprehensive system to examine two-hybrid interactions in all of the possible combinations between proteins of Saccharomyces cerevisiae. We cloned all of the yeast ORFs individually as a DNA-binding domain fusion ("bait") in a MATa strain and as an activation domain fusion ("prey") in a MATalpha strain, and subsequently divided them into pools, each containing 96 clones. These bait and prey clone pools were systematically mated with each other, and the transformants were subjected to strict selection for the activation of three reporter genes followed by sequence tagging. Our initial examination of approximately 4 x 10(6) different combinations, constituting approximately 10% of the total to be tested, has revealed 183 independent two-hybrid interactions, more than half of which are entirely novel. Notably, the obtained binary data allow us to extract more complex interaction networks, including the one that may explain a currently unsolved mechanism for the connection between distinct steps of vesicular transport. The approach described here thus will provide many leads for integration of various cellular functions and serve as a major driving force in the completion of the protein-protein interaction map.
Quantification of urinary TIMP-2 and IGFBP-7: an adequate diagnostic test to predict acute kidney injury after cardiac surgery? (2015)

German Clinical Trials Register (DRKS) DRKS00005457. Registered 26 November 2013.
Molecular endocrinology : basic concepts and clinical correlations (1995)

Integrates the basic and clinical aspects of molecular endocrinology. The three sections cover: basic concepts and techniques in molecular biology; the elucidation of various genes encoding hormones and their receptors; and the mechanisms of action of steroid and thyroid hormone receptors.
Notch Signaling in Cardiovascular Disease and Calcification (2008)

Recent increase in human lifespan has shifted the spectrum of aging-related disorders to an unprecedented upsurge in cardiovascular diseases, especially calcific aortic valve stenosis, which has an 80% risk of progression to heart failure and death. A current therapeutic option for calcified valves is surgical replacement, which provides only temporary relief. Recent progress in cardiovascular research has suggested that arterial and valve calcification are the result of an active process of osteogenic differentiation, induced by a pro-atherogenic inflammatory response. At molecular level, the calcification process is regulated by a network of signaling pathways, including Notch, Wnt and TGFbeta/BMP pathways, which control the master regulator of osteogenesis Cbfa1/Runx2. Genetic and in vitro studies have implicated Notch signaling in the regulation of macrophage activation and cardiovascular calcification. Individuals with inactivating Notch1 mutations have a high rate of cardiovascular disorders, including valve stenosis and calcification. This article reviews recent progress in the mechanism of cardiovascular calcification and discusses potential molecular mechanisms involved, focusing on Notch receptors. We propose a calcification model where extreme increases in vascular wall cell density due to inflammation-induced cell proliferation can trigger an osteogenic differentiation program mediated by Notch receptors.
Germline regulatory element of Oct-4 specific for the totipotent cycle of embryonal cells (1996)

The totipotent stem cells of the pregastrulation mouse embryo which give rise to all embryonic somatic tissues and germ cells express Oct-4. The expression is downregulated during gastrulation and is thereafter only maintained in the germline lineage. Oct-4/lacZ transgenes were used to determine how this pattern of expression was achieved, and resulted in the identification of two separate regulatory elements. The distal element drives Oct-4 expression in preimplantation embryos, in migratory and postmigratory primordial germ cells but is inactive in cells of the epiblast. In cell lines this element is specifically active in embryonic stem and embryonic germ cells. The proximal element directs the epiblast-specific expression pattern, including downregulation during gastrulation; in cell lines its activity is restricted to epiblast-derived cells. Thus, Oct-4 expression in the germline is regulated separately from epiblast expression. This provides the first marker for the identification of totipotent cells in the embryo, and suggests that expression of Oct-4 in the totipotent cycle is dependent on a set of factors unique to the germline.