gebhart/patrepeval huggingface dataset:
Nanometer-localized multiple single-molecule fluorescence microscopy (2004)

Fitting the image of a single molecule to the point spread function of an optical system greatly improves the precision with which single molecules can be located. Centroid localization with nanometer precision has been achieved when a sufficient number of photons are collected. However, if multiple single molecules reside within a diffraction-limited spot, this localization approach does not work. This paper demonstrates nanometer-localized multiple single-molecule (NALMS) fluorescence microscopy by using both centroid localization and photobleaching of the single fluorophores. Short duplex DNA strands are used as nanoscale “rulers” to validate the NALMS microscopy approach. Nanometer accuracy is demonstrated for two to five single molecules within a diffraction-limited area. NALMS microscopy will greatly facilitate single-molecule study of biological systems because it covers the gap between fluorescence resonance energy transfer-based (&lt;10 nm) and diffraction-limited microscopy (&gt;100 nm) measurements of the distance between two fluorophores. Application of NALMS microscopy to DNA mapping with &lt;10-nm (i.e., 30-base) resolution is demonstrated.
An automated design of minimum-area IC power/ground nets (1987)

Given tree topologies for routing power/ground (p/g) nets in integrated circuits, this paper formulates and solves the problem of determining the widths of the branches of the trees. Constraints are developed in order to maintain proper logic levels and switching speed, to prevent electromigration, and to satisfy certain design rule and regularity requirements. The area required by the p/g distribution system is minimized subject to these constraints. Some case studies are also presented.
Gene expression, polarising activity and skeletal patterning in reaggregated hind limb mesenchyme (1995)

The developing chick limb has two major signalling centres; the apical ectodermal ridge maintains expression of several important genes and outgrowth of the limb, and the polarising region specifies the pattern of skeletal elements along the anteroposterior axis. We have used reaggregated leg grafts (mesenchyme dissociated into single cells, placed in an ectodermal jacket and grafted to a host) to study patterning in a system where the developmental axes are severely disrupted. Reaggregates from different regions of leg mesenchyme developed correspondingly different digits, giving a system in which skeletal phenotype could be compared with the expression of genes thought to be important in patterning. We found that posterior third and whole leg reaggregates gave rise to different digits, yet expressed the same combination of HoxD, Bmp-2 and shh genes throughout their development. Anterior thirds initially only express the 3' end of the HoxD cluster but activate the more 5' members of the cluster sequentially over a period of 48 hours, a period during which Bmp-2 is activated but no shh or Fgf-4 expression could be detected. Our results suggest that there are two independent mechanisms for activating the HoxD complex, one polarising region-dependent and one independent, and that shh expression may not be necessary to maintain outgrowth and patterning once a ridge has been established.
The transcriptional response of normal and rheumatoid arthritis synovial fibroblasts to hypoxia (2010)

These data demonstrate that hypoxia induces significant changes in gene expression in HSFs and RASFs and identify differences between RASF and HSF profiles. The hypoxia-induced gene expression program in synovial fibroblasts identifies new factors and pathways relevant to understanding their contribution to the pathogenesis of chronic arthritis.
High-level synthesis of a heterologous milk protein in the mammary glands of transgenic swine. (1991)

The whey acidic protein (WAP) is a major milk protein in mice, rats, and rabbits but has not been found in milk of livestock including swine. To determine whether mammary gland regulatory elements from the WAP gene function across species boundaries and whether it is possible to qualitatively alter milk protein composition, we introduced the mouse WAP gene into the genome of swine. Three lines of transgenic swine were analyzed, and mouse WAP was detected in milk from all lactating females at concentrations of about 1 g/liter; these levels are similar to those found in mouse milk. Expression of the corresponding RNA was specific to the mammary gland. Our results suggest that the molecular basis of mammary-specific gene expression is conserved between swine and mouse. In addition the WAP gene must share, with other milk protein genes, elements that target gene expression to the mammary gland. Mouse WAP accounted for about 3% of the total milk proteins in transgenic pigs, thus demonstrating that it is possible to produce high levels of a foreign protein in milk of farm animals. that it is possible to produce high levels of a foreign protein in
Analogs of Pteroylglutamic Acid. I. N10-Alkylpteroic Acid and Derivatives (1948)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAnalogs of Pteroylglutamic Acid. I. N10-Alkylpteroic Acid and DerivativesDonna B. Cosulich and James M. Smith Jr.Cite this: J. Am. Chem. Soc. 1948, 70, 5, 1922–1926Publication Date (Print):May 1, 1948Publication History Published online1 May 2002Published inissue 1 May 1948https://pubs.acs.org/doi/10.1021/ja01185a081https://doi.org/10.1021/ja01185a081research-articleACS PublicationsRequest reuse permissionsArticle Views327Altmetric-Citations49LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
A potential role for CD69 in thymocyte emigration (2002)

The early activation marker, CD69, is transiently expressed on activated mature T cells and on thymocytes that are undergoing positive or negative selection in the thymus. CD69 is a member of the NK gene complex family of C-type lectin-like signaling receptors; however, its function is unknown. In this report, we describe the characterization of mice that constitutively express high levels of surface CD69 on immature and mature T cells throughout development. Constitutive surface expression of CD69 did not affect T cell maturation, signaling through the TCR or thymocyte selection. However, phenotypically and functionally mature thymocytes accumulated in the medulla of CD69 transgenic mice and failed to be exported from the thymus. The retention of mature thymocytes correlated with transgene dose and CD69 surface levels. These results identify a potential role for CD69 in controlling thymocyte export, and suggest that the transient expression of CD69 on thymocytes and T cells may function to regulate thymocyte and T cell trafficking.
Pulmonary Necrosis Resulting from DNA Vaccination against Tuberculosis (2003)

The use of DNA constructs encoding mycobacterial proteins is a promising new approach to vaccination against tuberculosis. A DNA vaccine encoding the hsp60 molecule of Mycobacterium leprae has previously been shown to protect against intravenous infection of mice with Mycobacterium tuberculosis in both the prophylactic and immunotherapeutic modes. It is shown here, however, that this vaccine was not effective in a more realistic aerosol infection model or in a model of latent tuberculosis in the lungs. Moreover, when given in an immunotherapeutic model the immunized mice developed classical Koch reactions characterized by multifocal discrete regions of cellular necrosis throughout the lung granulomas. Similar and equally severe reactions were seen in mice given a vaccine with DNA coding for the Ag85 antigen of M. tuberculosis. This previously unanticipated safety problem indicates that DNA vaccines should be used with caution in individuals who may have already been exposed to tuberculosis.
A novel on-demand cognitive pilot channel enabling dynamic spectrum allocation (2007)

This paper addresses the implementation of the cognitive pilot channel (CPC), which has been recently proposed as a solution to assist the mobile reconfigurable and cognitive terminals in heterogeneous wireless scenarios with different access networks available and varying spectrum allocations. The paper describes the operation of the CPC and the different approaches existing in the literature depending on how it is mapped onto specific radio resources. Then, it focuses on the implementation of the CPC information delivery and proposes the use of an on-demand CPC, which requires a significantly lower bit rate than the broadcast approach to achieve similar performance.
Expression of factor I‐resistant mutants of the human complement component C3 in heterologous systems (1998)

Complement plays a major role in hyperacute rejection of xenografts. In order to overcome this, we are developing, by minimal mutagenesis, a modified C3 molecule that, like cobra venom factor (CVF), escapes normal complement regulatory processes and inhibits complement-mediated responses by systemic depletion of C3. Unlike CVF, this protein should have little or no immunogenicity and be suitable for repeat administrations. As an initial step in this process, we have modified human C3 to make it resistant to inactivation by factor I. The factor I resistant C3 is capable of forming an active C3 convertase. Preincubation with normal human serum abrogated subsequent complement-mediated cytolysis by both the classical and alternative pathways, while wild-type (wt) C3 was inactive. The modified human C3 also blocked complement activity of guinea-pig serum. For economical and rapid production, we have developed expression of recombinant C3 wt and mutant proteins in the Baculovirus system. Large quantities are also being produced from stably transfected CHO cell lines. In addition, we have developed a fast C3 purification method by engineering a 6XHIS tag into the C3a portion of the molecule, thereby avoiding the need for subsequent separation of the tag from active C3b molecules.
Severe acute respiratory syndrome coronavirus spike protein expressed by attenuated vaccinia virus protectively immunizes mice (2004)

The spike protein (S), a membrane component of severe acute respiratory syndrome coronavirus (SARS-CoV) is anticipated to be an important component of candidate vaccines. We constructed recombinant forms of the highly attenuated modified vaccinia virus Ankara (MVA) containing the gene encoding full-length SARS-CoV S with and without a C-terminal epitope tag called MVA/S-HA and MVA/S, respectively. Cells infected with MVA/Sor MVA/S-HA synthesized a 200-kDa protein, which was recognized by antibody raised against a synthetic peptide of SARS-CoV S or the epitope tag in Western blot analyses. Further studies indicated that S was N-glycosylated and migrated in SDS polyacrylamide gels with an apparent mass of approximately 160 kDa after treatment with peptide N-glycosidase F. The acquisition of resistance to endoglycosidase H indicated trafficking of S to the medial Golgi compartment, and confocal microscopy showed that S was transported to the cell surface. Intranasal or intramuscular inoculations of BALB/c mice with MVA/S produced serum antibodies that recognized the SARS S in ELISA and neutralized SARS-CoV in vitro. Moreover, MVA/S administered by either route elicited protective immunity, as shown by reduced titers of SARS-CoV in the upper and lower respiratory tracts of mice after challenge. Passive transfer of serum from mice immunized with MVA/S to naïve mice also reduced the replication of SARS-CoV in the respiratory tract after challenge, demonstrating a role for antibody to S in protection. The attenuated nature of MVA and the ability of MVA/S to induce neutralizing antibody that protects mice support further development of this candidate vaccine.
Dietary correlates of plasma insulin-like growth factor I and insulin-like growth factor binding protein 3 concentrations. (2002)

Plasma levels of insulin-like growth factor I (IGF-I) have been associated with risk of several cancers. Although protein-calorie malnutrition is known to decrease IGF-I levels, few published studies have related diet to IGF-I levels in well-nourished humans. We examined the cross-sectional association of plasma IGF-I and IGF-binding protein 3 (IGFBP-3) levels with intakes of alcohol, energy, macronutrients, micronutrients, and specific foods in 1037 healthy women. Adjusted mean hormone levels across categories of dietary variables were calculated by linear regression. Results were adjusted for non-dietary factors found to be associated with IGF levels. Total energy intake was positively associated with IGF-I levels when adjusted for covariates. Adjusted mean levels of IGF-I (ng/ml) across increasing quintiles of energy intake were 181, 185, 191, 199, and 195 (P for the linear trend = 0.006). In other multivariate analyses, energy-adjusted fat and carbohydrate intake had no association with IGF-I levels. The most consistent finding was a positive association between protein intake with circulating IGF-I concentration (174, 188, 201, 192, and 196 ng/ml across quintiles of protein intake; P = 0.002), which was largely attributable to milk intake. Adjusted mean levels of IGF-I (ng/ml) across increasing quartiles of milk intake were 183, 189, 188, and 200 (P = 0.01). Higher fat intake, in particular saturated fat, was associated with lower levels of IGFBP-3. We conclude that higher energy, protein, and milk intakes were associated with higher levels of IGF-I. These associations raise the possibility that diet could affect cancer risk through influencing IGF-I level.
Appropriateness of Lyme Disease Serologic Testing (2004)

Many LDSTs are ordered inappropriately, often influenced by patient demand. Education of clinicians and patients about testing indications and contraindications is needed to reduce the number of inappropriate LDSTs.
Morphology of anisotropic polymer-dispersed liquid crystals and the effect of monomer functionality (1997)

The morphology of transmission gratings with varying Bragg spacings formed using polymer-dispersed liquid crystals were examined using high-resolution scanning electron microscopy and image analysis techniques. The effect on the morphology of small changes in the overall functionality of the prepolymer syrup was observed. An increase in the amount of monofunctional compound resulted in small, nearly spherical domains (<100 nm in diameter) confined in well-defined lamellae for samples with a 0.49 μm Bragg spacing. A decrease in concentration (an effective increase in monomer functionality) at this Bragg spacing resulted in larger domains (100–200 nm) with much greater distribution of sizes and shapes. The local volume fractions of discrete liquid crystalline (LC) domains was considerably larger in the latter case. An increase in the Bragg spacing to 1.35 μm also resulted in well-defined lamellae of LC domains, although much more coalescence into irregularly shaped individual domains was observed. Surprisingly, the local volume fraction of LC increased in the larger Bragg spacing samples. The morphology results are discussed qualitatively in terms of liquid–gel demixing where the inherent crosslink density and elasticity of the polymeric host must be considered in phase separation processes on the nanoscale. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 35: 2825–2833, 1997
A phase I study of paclitaxel (taxol®) (T) in combination with SDZ PSC 833, a potent modulator of multidrug resistance (MDR) (1994)

Fisher, G A; Halsey, J; Hausdorff, J; Lum, B L; Brophy, N A; Collins, H; Nix, D; Sikic, B I Author Information
Simplified Polymer Mimics of Cross-Linking Adhesive Proteins (2007)

Marine mussels and barnacles attach themselves to surfaces by depositing mixtures of proteins and then cross-linking these polymers for curing of their adhesive. Obtaining large quantities of these biological materials for applications development has proven to be problematic. Here we present the synthesis, reactivity, and adhesive characteristics of simplified polymer mimics of bioadhesives. A polystyrene backbone is used to take the place of the protein polyamide chain. Cross-linkable catechol groups are appended to the polystyrene in order to mimic 3,4-dihydroxystyrene (DOPA), the key cross-linking group in mussel adhesive proteins. We show that poly[(3,4-dimethoxystyrene)-co-styrene] polymers exhibit curing analogous to that of the proteins after which they were modeled. The styrene−catechol copolymers also display enhanced adhesion upon cross-linking. This report demonstrates a reductionist approach to developing new polymeric materials on the basis of principles learned from nature.
Reductase Enzyme Expression Across the National Cancer Institute Tumor Cell Line Panel: Correlation With Sensitivity to Mitomycin C and EO9 (1996)

Comparison of biochemical, molecular biological, and chemosensitivity data obtained from screening a large number of cell lines (e.g., the NCI tumor cell line panel) may facilitate investigation of factors influencing drug antitumor activity. The knowledge gained may be of value in the development of new anticancer agents or in the selection of patients to receive specific therapies.
Wound Healing Mechanisms (1982)

MARGARET E. FLYNN, RN, MA, is an infection control practitioner at St. Francis Hospital, Roslyn, N. Y. DAVID T. ROVEE, PhD, is manager of Wound Care Research division of Johnson & Johnson, New Brunswick, N. J. NANCY A. ANDERSON, RN, MPH, manager of Professional Relations and DIANE POWELL, RN, MA, former manager of Professional Relations at Johnson & Johnson, served as consultants for this feature.
A Reconfigurable and Biologically Inspired Paradigm for Computation Using Network‐On‐Chip and Spiking Neural Networks (2009)

FPGA devices have emerged as a popular platform for the rapid prototyping of biological Spiking Neural Networks (SNNs) applications, offering the key requirement of reconfigurability. However, FPGAs do not efficiently realise the biologically plausible neuron and synaptic models of SNNs, and current FPGA routing structures cannot accommodate the high levels of interneuron connectivity inherent in complex SNNs. This paper highlights and discusses the current challenges of implementing scalable SNNs on reconfigurable FPGAs. The paper proposes a novel field programmable neural network architecture (EMBRACE), incorporating low‐power analogue spiking neurons, interconnected using a Network‐on‐Chip architecture. Results on the evaluation of the EMBRACE architecture using the XOR benchmark problem are presented, and the performance of the architecture is discussed. The paper also discusses the adaptability of the EMBRACE architecture in supporting fault tolerant computing.
Conditional fast expression and function of multimeric TRPV5 channels using Shield-1 (2008)

A recently described novel controllable method to regulate protein expression is based on a mutated FK506-binding protein-12 (mtFKBP) that is unstable and rapidly degraded in mammalian cells. This instability can be conferred to other proteins directly fused to mtFKBP. Binding of a synthetic cell-permeant ligand (Shield-1) to mtFKBP reverses the instability, allowing conditional expression of mtFKBP-fused proteins. We adapted this strategy to study multimeric plasma membrane proteins using the ion channel TRPV5 as model protein. mtFKBP-TRPV5 forms functional ion channels and its expression can be controlled in a time- and dose-dependent fashion using Shield-1. Moreover, in the presence of Shield-1, mtFKBP-TRPV5 formed heteromultimeric channels with untagged TRPV5, which were codegraded upon washout of Shield-1, providing a strategy to study multimeric plasma membrane protein complexes without the need to destabilize all individual subunits.
Expanded human cord blood‐derived endothelial progenitor cells salvage infarcted myocardium in rats with acute myocardial infarction (2010)

1. Cell transplantation has promise as a therapeutic option for restoring impaired heart function after acute myocardial infarction (AMI). However, the optimal cell type to use remains controversial. We investigated the therapeutic efficacy and feasibility of intramyocardial transplantation of human umbilical cord blood-derived endothelial progenitor cells (hUCB-EPC) in rats with AMI. 2. The Wistar rats myocardial infarction model was established by ligating the left anterior descending artery. The labelled hUCB-EPC were transplanted through intramyocardial injection. Left ventricular function was assessed using a pressure-volume catheter and echocardiogram. Anti-VIII immunohistochemistry staining was used to reflect the degree of angiogenesis in peri-infarcted areas by calculating the average capillary density. The fibrosis degree of infarcted myocardium was analysed by Masson staining and the collagen volume fraction was calculated. 3. The labelled donor endothelial progenitor cells were detected in the new microvessels in host myocardium by double-positive staining with CM-Dil and FITC-UEA-l. An increase in left ventricular ejection fraction, left ventricular fractional shortening, left ventricular end-systolic pressure, first derivative of left ventricular pressure (+dP/dtmax and -dP/dtmax), as well as a decrease in the left ventricular end-diastolic pressure in rats with cell therapy indicated a significant improvement in global heart function. The cell therapy group had increased microvessel formation and a decreased degree of myocardial fibrosis compared to the control group. Moreover, the degree of myocardial fibrosis was less than that of the control group. 4. The improved global heart function and decreased cardiac fibrosis in rats with AMI implies the potential benefit of hUCB-EPC transplantation.
The NF-κB signal transduction pathway in aortic endothelial cells is primed for activation in regions predisposed to atherosclerotic lesion formation (2000)

Atherosclerotic lesions form at distinct sites in the arterial tree, suggesting that hemodynamic forces influence the initiation of atherogenesis. If NF-kappaB plays a role in atherogenesis, then the activation of this signal transduction pathway in arterial endothelium should show topographic variation. The expression of NF-kappaB/IkappaB components and NF-kappaB activation was evaluated by specific antibody staining, en face confocal microscopy, and image analysis of endothelium in regions of mouse proximal aorta with high and low probability (HP and LP) for atherosclerotic lesion development. In control C57BL/6 mice, expression levels of p65, IkappaBalpha, and IkappaBbeta were 5- to 18-fold higher in the HP region, yet NF-kappaB was activated in a minority of endothelial cells. This suggested that NF-kappaB signal transduction was primed for activation in HP regions on encountering an activation stimulus. Lipopolysaccharide treatment or feeding low-density lipoprotein receptor knockout mice an atherogenic diet resulted in NF-kappaB activation and up-regulated expression of NF-kappaB-inducible genes predominantly in HP region endothelium. Preferential regional activation of endothelial NF-kappaB by systemic stimuli, including hypercholesterolemia, may contribute to the localization of atherosclerotic lesions at sites with high steady-state expression levels of NF-kappaB/IkappaB components.