gebhart/patrepeval huggingface dataset:
Mammalian Nicotinic Acetylcholine Receptors: From Structure to Function (2009)

The classical studies of nicotine by Langley at the turn of the 20th century introduced the concept of a "receptive substance," from which the idea of a "receptor" came to light. Subsequent studies aided by the Torpedo electric organ, a rich source of muscle-type nicotinic receptors (nAChRs), and the discovery of alpha-bungarotoxin, a snake toxin that binds pseudo-irreversibly to the muscle nAChR, resulted in the muscle nAChR being the best characterized ligand-gated ion channel hitherto. With the advancement of functional and genetic studies in the late 1980s, the existence of nAChRs in the mammalian brain was confirmed and the realization that the numerous nAChR subtypes contribute to the psychoactive properties of nicotine and other drugs of abuse and to the neuropathology of various diseases, including Alzheimer's, Parkinson's, and schizophrenia, has since emerged. This review provides a comprehensive overview of these findings and the more recent revelations of the impact that the rich diversity in function and expression of this receptor family has on neuronal and nonneuronal cells throughout the body. Despite these numerous developments, our understanding of the contributions of specific neuronal nAChR subtypes to the many facets of physiology throughout the body remains in its infancy.
Micrococcal Nuclease Does Not Substantially Bias Nucleosome Mapping (2012)

We have mapped sequence-directed nucleosome positioning on genomic DNA molecules using high-throughput sequencing. Chromatins, prepared by reconstitution with either chicken or frog histones, were separately digested to mononucleosomes using either micrococcal nuclease (MNase) or caspase-activated DNase (CAD). Both enzymes preferentially cleave internucleosomal (linker) DNA, although they do so by markedly different mechanisms. MNase has hitherto been very widely used to map nucleosomes, although concerns have been raised over its potential to introduce bias. Having identified the locations and quantified the strength of both the chicken or frog histone octamer binding sites on each DNA, the results obtained with the two enzymes were compared using a variety of criteria. Both enzymes displayed sequence specificity in their preferred cleavage sites, although the nature of this selectivity was distinct for the two enzymes. In addition, nucleosomes produced by CAD nuclease are 8-10 bp longer than those produced with MNase, with the CAD cleavage sites tending to be 4-5 bp further out from the nucleosomal dyad than the corresponding MNase cleavage sites. Despite these notable differences in cleavage behaviour, the two nucleases identified essentially equivalent patterns of nucleosome positioning sites on each of the DNAs tested, an observation that was independent of the histone type. These results indicate that biases in nucleosome positioning data collected using MNase are, under our conditions, not significant.
Amphiphilic copolymers of ε-caprolactone and γ-substituted ε-caprolactone. Synthesis and functionalization of poly(D,L-lactide) nanoparticles (2003)

Fully biodegradable and surface-functionalized poly(D,L-lactide) (PLA) nanoparticles have been prepared by a co-precipitation technique. Novel amphiphilic random copolyesters P(CL-co-gammaXCL) were synthesized by controlled copolymerization of epsilon-caprolactone and epsilon-caprolactone substituted in the gamma-position by a hydrophilic X group, where X is either a cationic pyridinium (gammaPyCL) or a non-ionic hydroxyl (gammaOHCL). Nanoparticles were prepared by co-precipitation of PLA with the P(CL-co-gammaXCL) copolyester from a DMSO solution. Small amounts of cationic P(CL-co-gammaPyCL) copolymers are needed to quantitatively form stable nanoparticles (ca. 10 mg/ 100 mg PLA), although larger amounts of non-ionic P(CL-co-gammaOHCL) copolymers are needed (> or = 12.5 mg/ 100 mg PLA). Copolymers with a low degree of polymerization (ca. 40) are more efficient stabilizers, probably because of faster migration towards the nanoparticle-water interface. The nanoparticle diameter decreases with the polymer concentration in DMSO, e.g. from ca. 160 nm (16 mg/ml) to ca. 100 nm (2 mg/ml) for PLA/P(CL-co-gammaPyCL) nanoparticles. Migration of the P(CL-co-gammaXCL) copolyesters to the nanoparticle surface was confirmed by measurement of the zeta potential, i.e. ca. +65 mV for P(CL-co-gammaPCL) and -7 mV for P(CL-co-gammaOHCL). The polyamphiphilic copolyesters stabilize PLA nanoparticles by electrostatic or steric repulsions, depending on whether they are charged or not. They also impart functionality and reactivity to the surface, which opens up new opportunities for labelling and targeting purposes.
Pharmacokinetic studies on minocycline in man (1973)

Minocycline, a new member of the tetracycline series, has been reported to have a high level of activity against tetracycline‐sensitive organisms and significant activity against tetracycline‐resistant staphylococci. Results presented show that in man it has a biologic half‐life apprOXimately that of doxycycline but appreciably longer than that of other tetracyclines. It appears to be more rapidly absorbed than doxycycline, demethylchlortetracycline, and methacycline. Evidence indicates that with minocycline, like doxycycline, but unlike other tetracycline antibiotics, absorption following oral administration is essentially complete. Lower values for renal clearance are found for minocycline than for the other tetracyclines studied. Of the minocycline recovered, a higher percentage was excreted in the feces and biologic transformation was greater than with the other tetracyclines. Minocycline has greater lipophilic properties than other tetracyclines, which may account for the highly favorable ratios of tissue to serum concentrations.
VACUUM-ASSISTED CLOSURE (2004)

Stockton, CA AJNwelcomes letters to the editor regarding recently published articles, although critiques of original research may be submitted at any time. Submissions must be typed, contain fewer than 300 words, and list the correspondent’s name, address, and phone number or e-mail address; include no more than three references for any statistics or studies cited. Letters will be edited for length, clarity, and accuracy. Submission of a letter will constitute the author’s permission to publish it, although it doesn’t guarantee publication. Letters become the property of AJN and may be published in all media. Send letters to:AJN, Lippincott Williams & Wilkins 333 Seventh Avenue, 19th floor New York, NY 10001 [email protected]; (212) 886-1206 (fax)
The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum ) (2008)

This paper describes the genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum), which is the model acetogenic bacterium that has been widely used for elucidating the Wood-Ljungdahl pathway of CO and CO(2) fixation. This pathway, which is also known as the reductive acetyl-CoA pathway, allows acetogenic (often called homoacetogenic) bacteria to convert glucose stoichiometrically into 3 mol of acetate and to grow autotrophically using H(2) and CO as electron donors and CO(2) as an electron acceptor. Methanogenic archaea use this pathway in reverse to grow by converting acetate into methane and CO(2). Acetogenic bacteria also couple the Wood-Ljungdahl pathway to a variety of other pathways to allow the metabolism of a wide variety of carbon sources and electron donors (sugars, carboxylic acids, alcohols and aromatic compounds) and electron acceptors (CO(2), nitrate, nitrite, thiosulfate, dimethylsulfoxide and aromatic carboxyl groups). The genome consists of a single circular 2 628 784 bp chromosome encoding 2615 open reading frames (ORFs), which includes 2523 predicted protein-encoding genes. Of these, 1834 genes (70.13%) have been assigned tentative functions, 665 (25.43%) matched genes of unknown function, and the remaining 24 (0.92%) had no database match. A total of 2384 (91.17%) of the ORFs in the M. thermoacetica genome can be grouped in orthologue clusters. This first genome sequence of an acetogenic bacterium provides important information related to how acetogens engage their extreme metabolic diversity by switching among different carbon substrates and electron donors/acceptors and how they conserve energy by anaerobic respiration. Our genome analysis indicates that the key genetic trait for homoacetogenesis is the core acs gene cluster of the Wood-Ljungdahl pathway.
DNA Vaccination for HIV-1 and SIV (2000)

Control of the worldwide AIDS epidemic will only be achieved with a safe and effective prophylactic HIV-1 vaccine. DNA vaccination has recently emerged as a promising vaccine modality that can elicit both humoral and cellular immune responses. HIV-1- and SIV-specific immune responses have been elicited by DNA vaccines in both mice and nonhuman primates. However, these immune responses have not been capable of protecting nonhuman primates against pathogenic AIDS virus challenges. A number of approaches are therefore being investigated to augment DNA vaccine-elicited immune responses.
Thin film imaging technology on glass and plastic (2002)

Hydrogenated amorphous silicon (a-Si:H) technology offers a viable technological alternative for improved imaging of optical signals and high energy radiation. This paper reviews X-ray imaging technology in terms of detector operating principles, including optoelectronic characteristics, and fabrication process issues related to pixel (Schottky diode detector plus thin film transistor) integration. Recent results which describe the extension of the current fabrication processes to low (/spl sim/120/spl deg/C) temperature are also presented. The low temperature processing enables fabrication of thin electronics on flexible (polymer) substrates.
Histidine affinity tags affect MSP142 structural stability and immunodominance in mice (2011)

Inclusion of affinity tags has greatly facilitated process development for protein antigens, primarily for their recovery from complex mixtures. Although generally viewed as supportive of product development, affinity tags may have unintended consequences on protein solubility, susceptibility to aggregation, and immunogenicity. Merozoite surface protein 1 (MSP1), an erythrocytic stage protein of Plasmodium falciparum and a candidate malaria vaccine, was used to evaluate the impact of a metal ion affinity-tag on both protein structure and the induction of immunity. To this end, codon harmonized gene sequences from the P. falciparum MSP1(42) of FVO and 3D7 parasites were cloned and purified with and without a histidine (His) tag. We report on the influence of His-affinity tags on protein expression levels, solubility, secondary structure, thermal denaturation, aggregation and the impact on humoral and cellular immune responses in mice. While the overall immunogenicity induced by His-tagged MSP1(42) proteins is greater, the fine specificity of the humoral and cellular immune responses is altered relative to anti-parasitic antibody activity and the breadth of T-cell responses. Thus, the usefulness of protein tags may be outweighed by their potential impact on structure and function, stressing the need for caution in their use. See accompanying commentary by Randolph DOI: 10.1002/biot.201100459.
Expression of Bluetongue Virus Group-specific Antigen VP3 in Insect Cells by a Baculovirus Vector: Its Use for the Detection of Bluetongue Virus Antibodies (1987)

DNA representing RNA segment 3 of bluetongue virus (BTV) serotype 17, corresponding to the gene that codes for a group-specific antigen VP3, has been inserted into a baculovirus transfer vector in lieu of the 5' coding region of the polyhedrin gene of Autographa californica nuclear polyhedrosis virus (AcNPV). After cotransfection of Spodoptera frugiperda cells with wild-type AcNPV DNA in the presence of the derived recombinant transfer vector DNA, polyhedrin-negative recombinant baculoviruses were recovered. When S. frugiperda cells were infected with one of these recombinant viruses, a protein that was similar in size and antigenic properties to the BTV VP3 protein was synthesized. Antibodies raised in mice or rabbits to the baculovirus-expressed VP3 protein immunoprecipitated the VP3 protein of BTV-17 as well as that of BTV-10. The expressed antigen reacted with antisera representing four U.S.A. BTV serotypes in an indirect ELISA test.
DETECTION OF THE FREE BETA SUBUNIT OF HUMAN CHORIONIC GONADOTROPIN (HCG) IN CULTURES OF NORMAL AND MALIGNANT TROPHOBLAST CELLS, PREGNANCY SERA, AND SERA OF PATIENTS WITH CHORIOCARCINOMA (1983)

Immunoaffinity adsorption techniques, utilizing specific antisera for hCG and its subunits bound to Sepharose 4B, have been employed to separate hCG alpha beta dimer and free subunits of hCG. As previously reported by this and a number of other laboratories, trophoblast cells (in vivo and in vitro) produce free alpha subunit in addition to hCG dimer. We have now shown that cultured JAr choriocarcinoma cells also secrete free beta subunit: 37% of the total beta subunit (combined and free) secreted by JAr cells is in the free form. Moreover, in pooled sera from choriocarcinoma patients 15% of total beta subunit is free, and in media from placental explant cultures and in pooled first trimester pregnancy sera 11% and 6.5%, respectively, of total beta subunit are in the free form. The free beta s are all of similar mol wt to the combined forms, and associate with urinary hCG alpha to form hCG. Free alpha s, which are larger than the combined forms, are unable to associate with urinary hCG beta to form hCG. We propose that the supply of combinable alpha subunit, rather than beta, limits dimer formation.
Stretching of Homopolymeric RNA Reveals Single-Stranded Helices and Base-Stacking (2007)

We have found strong supporting evidence for the helical structures of single-stranded nucleic acids by stretching individual molecules of polyadenylic acid [poly(A)] and polycytidylic acid [poly(C)]. Analyzing the force versus extension data using a two-state elastic model in which random-coil domains alternate with rigid helical domains allows one to extract the thermodynamic and structural properties. In addition, it also yields moderate to low cooperativity of the helix-coil transition for poly(A) and poly(C), respectively.
Tyrosine Cross-Linking Reveals Interfacial Dynamics in Adeno-Associated Viral Capsids during Infection (2012)

Viral capsid dynamics are often observed during infectious events such as cell surface attachment, entry and genome release. Structural analysis of adeno-associated virus (AAV), a helper-dependent parvovirus, revealed a cluster of surface-exposed tyrosine residues at the icosahedral two-fold symmetry axis. We exploited the latter observation to carry out selective oxidation of Tyr residues, which yielded cross-linked viral protein (VP) subunit dimers, effectively "stitching" together the AAV capsid two-fold interface. Characterization of different Tyr-to-Phe mutants confirmed that the formation of cross-linked VP dimers is mediated by dityrosine adducts and requires the Tyr704 residue, which crosses over from one neighboring VP subunit to the other. When compared to unmodified capsids, Tyr-cross-linked AAV displayed decreased transduction efficiency in cell culture. Surprisingly, further biochemical and quantitative microscopy studies revealed that restraining the two-fold interface hinders externalization of buried VP N-termini, which contain a phospholipase A2 domain and nuclear localization sequences critical for infection. These adverse effects caused by tyrosine oxidation support the notion that interfacial dynamics at the AAV capsid two-fold symmetry axis play a role in externalization of VP N-termini during infection.
New Application of Evanescent Mode Wave-Guide to Filter Design (1977)

Evanescent waveguide (rectangular or round) sections are used in conjunction with an admittance inverter synthesis technique incorporating frequency variable turns ratios to realize wide-band microwave (up to 1 octave) and low-frequency (60-MHz) low-loss bandpass filters. This work extends and corrects previous published information.
Inferring Internet Denial-of-Service Activity (2001)

In this paper, we seek to answer a simple question: How prevalent are denial-of-service attacks in the Internet today?. Our motivation is to understand quantitatively the nature of the current threat as well as to enable longer-term analyses of trends and recurring patterns of attacks. We present a new technique, called backscatter analysis, that provides an estimate of worldwide denial-of-service activity. We use this approach on three week-long datasets to assess the number, duration and focus of attacks, and to characterize their behavior. During this period, we observe more than 12,000 attacks against more than 5,000 distinct targets, ranging from well known e-commerce companies such as Amazon and Hotmail to small foreign ISPs and dial-up connections. We believe that our work is the only publically available data quantifying denial-of-service activity in the Internet.
DeepCut: Object Segmentation From Bounding Box Annotations Using Convolutional Neural Networks (2016)

In this paper, we propose DeepCut, a method to obtain pixelwise object segmentations given an image dataset labelled weak annotations, in our case bounding boxes. It extends the approach of the well-known GrabCut [1] method to include machine learning by training a neural network classifier from bounding box annotations. We formulate the problem as an energy minimisation problem over a densely-connected conditional random field and iteratively update the training targets to obtain pixelwise object segmentations. Additionally, we propose variants of the DeepCut method and compare those to a naïve approach to CNN training under weak supervision. We test its applicability to solve brain and lung segmentation problems on a challenging fetal magnetic resonance dataset and obtain encouraging results in terms of accuracy.
Protective efficacy of antibodies to the Staphylococcus aureus type 5 capsular polysaccharide in a modified model of endocarditis in rats (1997)

The protective efficacy of antibodies to the Staphylococcus aureus type 5 capsular polysaccharide (CP5) was examined in a modified model of catheter-induced endocarditis. Rats were catheterized by surgically passing a polyethylene catheter through the right carotid artery and aortic valve into the left ventricle. The following day, the rats were injected by the intraperitoneal (i.p.) route with immunoglobulin G (IgG) purified from nonimmunized rabbits or from rabbits immunized with a conjugate vaccine composed of CP5 and CP8 linked covalently to recombinant Pseudomonas aeruginosa exotoxoid A. One day after passive immunization, the animals were challenged i.p. with one of three serotype 5 S. aureus isolates (strain Reynolds, Lowenstein, or VP) or nontypeable strain 521. Protection was evaluated by comparing quantitative cultures of blood, endocardial vegetations, and kidneys from control and immune animals. For experiments performed with S. aureus Reynolds and Lowenstein, rats given capsular antibodies (645 microg of CP5-specific IgG) showed a significantly (P < 0.05) lower prevalence of endocarditis than rats injected with nonimmune IgG. Similarly, quantitative cultures of the blood, kidneys, and aortic valve vegetations revealed that fewer S. aureus cells were recovered from rats given capsule-specific IgG than from rats administered nonimmune IgG. Rats challenged with strain VP were protected with 1.145 mg of CP5-specific IgG. Capsular antibodies did not protect against infection elicited by a nontypeable strain. These results demonstrate that capsular antibodies elicited by immunization with a polysaccharide-protein conjugate vaccine protect experimental animals against serotype 5 S. aureus infection in a modified model of endocarditis.
Characterization of Circulating Endothelial Cells in Acute Myocardial Infarction (2012)

Acute myocardial infarction (MI), which involves the rupture of existing atheromatous plaque, remains highly unpredictable despite recent advances in the diagnosis and treatment of coronary artery disease. Accordingly, a clinical measurement that can predict an impending MI is desperately needed. Here, we characterize circulating endothelial cells (CECs) using an automated and clinically feasible CEC three-channel fluorescence microscopy assay in 50 consecutive patients with ST-segment elevation MI and 44 consecutive healthy controls. CEC counts were significantly elevated in MI cases versus controls, with median numbers of 19 and 4 cells/ml, respectively (P = 1.1 × 10(-10)). A receiver-operating characteristic (ROC) curve analysis demonstrated an area under the ROC curve of 0.95, suggesting near-dichotomization of MI cases versus controls. We observed no correlation between CECs and typical markers of myocardial necrosis (ρ = 0.02, creatine kinase-myocardial band; ρ = -0.03, troponin). Morphological analysis of the microscopy images of CECs revealed a 2.5-fold increase (P < 0.0001) in cellular area and a twofold increase (P < 0.0001) in nuclear area of MI CECs versus healthy controls, age-matched CECs, as well as CECs obtained from patients with preexisting peripheral vascular disease. The distribution of CEC images that contained from 2 to 10 nuclei demonstrates that MI patients were the only subject group to contain more than 3 nuclei per image, indicating that multicellular and multinuclear clusters are specific for acute MI. These data indicate that CEC counts may serve as a promising clinical measure for the prediction of atherosclerotic plaque rupture events.
A new multicasting-based architecture for Internet host mobility (1997)

Article A new multicasting-based architecture for Internet host mobility Share on Authors: Jayanth Mysore Coordinated Sciences Laboratory, University of Illinois at Urbana-Champaign Coordinated Sciences Laboratory, University of Illinois at Urbana-ChampaignView Profile , Vaduvur Bharghavan Coordinated Sciences Laboratory, University of Illinois at Urbana-Champaign Coordinated Sciences Laboratory, University of Illinois at Urbana-ChampaignView Profile Authors Info & Claims MobiCom '97: Proceedings of the 3rd annual ACM/IEEE international conference on Mobile computing and networkingSeptember 1997 Pages 161–172https://doi.org/10.1145/262116.262144Online:26 September 1997Publication History 71citation872DownloadsMetricsTotal Citations71Total Downloads872Last 12 Months3Last 6 weeks0 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