gebhart/patrepeval huggingface dataset:
Design and Evaluation of 16S rRNA-Targeted Peptide Nucleic Acid Probes for Whole-Cell Detection of Members of the Genus Listeria (2005)

Six fluorescein-labeled peptide nucleic acid oligomers targeting Listeria-specific sequences on the 16S ribosomal subunit were evaluated for their abilities to hybridize to whole cells by fluorescence in situ hybridization (FISH). Four of these probes yielded weak or no fluorescent signals after hybridization and were not investigated further. The remaining two FISH-compatible probes, LisUn-3 and LisUn-11, were evaluated for their reactivities against 22 Listeria strains and 17 other bacterial strains belonging to 10 closely related genera. Hybridization with BacUni-1, a domain-specific eubacterial probe, was used as a positive control for target accessibility in both Listeria spp. and nontarget cells. RNase T1 treatment of select cell types was used to confirm that positive fluorescence responses were rRNA dependent and to examine the extent of nonspecific staining of nontarget cells. Both LisUn-3 and LisUn-11 yielded rapid, bright, and genus-specific hybridizations at probe concentrations of approximately 100 pmol ml(-1). LisUn-11 was the brightest probe and stained all six Listeria species. LisUn-3 hybridized with all Listeria spp. except for L. grayi, for which it had two mismatched bases. A simple ethanolic fixation yielded superior results with Listeria spp. compared to fixation in 10% buffered formalin and was applicable to all cell types studied. This study highlights the advantages of peptide nucleic acid probes for FISH-based detection of gram-positive bacteria and provides new tools for the rapid detection of Listeria spp. These probes may be useful for the routine monitoring of food production environments in support of efforts to control L. monocytogenes.
Influence of Polyethylene Glycol Chain Length on the Physicochemical and Biological Properties of Poly(ethylene imine)-graft-Poly(ethylene glycol) Block Copolymer/SiRNA Polyplexes (2006)

Polyplexes between siRNA and poly(ethylene imine) (PEI) derivatives are promising nonviral carriers for siRNA. The polyplex stability is of critical importance for efficient siRNA delivery to the cytoplasm. Here, we investigate the effect of PEGylation at a constant ratio ( approximately 50%) on the biophysical properties of the polyplexes. Particle size, zeta potential, and stability against heparin as well as RNase digestion and reporter gene knockdown under in vitro conditions of different siRNA polyplexes were characterized. Stability and size of siRNA polyplexes were clearly influenced by PEI-PEG structure, and high degrees of substitution such as PEI(25k)-g-PEG(550)(30) resulted in large (300-400 nm), diffuse complexes (AFM) which showed condensation behavior only at high N/P ratios. All other polyplexes and the PEI control showed similar sizes (150 nm) and compact structures in AFM, with complete condensation reached at N/P ratio of 3. Stability of siRNA polyplexes against heparin displacement and RNase digestion could be modified by PEGylation. Protection against RNase digestion was highest for PEI(25k)-g-PEG(5k)(4) and PEI(25k)-g-PEG(20k)(1), while siRNA/PEI provided insufficient protection. In knockdown experiments using NIH/3T3 fibroblasts stably expressing beta-galactosidase, it was shown that PEG chain length had a significant influence on biological activity of siRNA. Polyplexes with siRNA containing PEI(25k)-g-PEG(5k)(4) and PEI(25k)-g-PEG(20k)(1) yielded similar efficiencies of ca. 70% knockdown as lipofectamine controls. Confocal microscopy demonstrated enhanced cellular uptake of siRNA into cytosol by polyplexes formation with PEI copolymers. In conclusion, both the chain length and graft density of PEG were found to strongly influence siRNA condensation and stability and hence affect the knockdown efficiency of PEI-PEG/siRNA polyplexes.
Real-time 3-D model-based navigation system for endoscopic paranasal sinus surgery (1999)

This paper presents a three-dimensional (3-D)-model-based navigation system for endoscopic sinus surgery treating paranasal sinusitis. Endoscopic surgery is becoming more common because of its low invasiveness. Its problem with disorientation, however, is one of the toughest barriers for the novice and may lead even an expert to commit serious surgical errors, e.g., causing cerebrospinal fluid (CSF) leakage or blinding the patient. To prevent such complications and optimize training, our system aids in navigation by showing a single perspective view of the patient and the endoscope models. This virtual endoscope has a viewing cone with a simulated light to indicate the viewing direction and visual field in real-time. The system's three clipping planes automatically follow the endoscope and help keep the surgeon aware of the endoscope's actual position. An experiment comparing the system to conventional navigation using a triplanar display showed that the perspective view was referenced very frequently, giving a positive impressions, while the triplanar display was almost completely ignored, apparently because it was too difficult to interpret immediately.
Alterations of DNA content in human endometrial stromal cells transfected with a temperature-sensitive SV40: tetraploidization and physiological consequences (1992)

The normal genomic stability of human cells is reversed during neoplastic transformation. The SV40 large T antigen alters the DNA content in human endometrial stromal cells in a manner that relates to neoplastic progression. Human endometrial stromal cells were transfected with a plasmid containing the A209 temperature-sensitive mutant of SV40 (tsSV40), which is also defective in the viral origin of replication. Ninety-seven clonal transfectants from seven different primary cell strains were isolated. Initial analysis revealed that 20% of the clonal populations (19/97) had an apparent diploid DNA content, 35% (34/97) had an apparent tetraploid DNA content, and the remainder were mixed populations of diploid and tetraploid cells. No aneuploid populations were observed. Diploid tsSV40 transformed cells always give rise to a population of cells with a tetraploid DNA content when continuously cultured at the permissive temperature. The doubling of DNA content can be vastly accelerated by the sudden reintroduction of large T antigen activity following a shift from non-permissive to permissive temperature. Tetraploid tsSV40 transfected cells have a lower capacity for anchorage-independent growth and earlier entry into 'crisis' than diploid cells. These results indicate that during the pre-crisis, extended lifespan phase of growth, the SV40 large T antigen causes a doubling of DNA content. This apparent doubling of DNA content does not confer growth advantage during the extended lifespan that precedes 'crisis'.
KRAS Mutations and Primary Resistance of Lung Adencarcinomas to Gefitnib or Erlotinib (2005)

This was Varmus's first research article in PLoS, the open-access online publishing venture that he helped to establish in 2000.
Streetscore -- Predicting the Perceived Safety of One Million Streetscapes (2014)

Social science literature has shown a strong connection between the visual appearance of a city's neighborhoods and the behavior and health of its citizens. Yet, this research is limited by the lack of methods that can be used to quantify the appearance of streetscapes across cities or at high enough spatial resolutions. In this paper, we describe 'Streetscore', a scene understanding algorithm that predicts the perceived safety of a streetscape, using training data from an online survey with contributions from more than 7000 participants. We first study the predictive power of commonly used image features using support vector regression, finding that Geometric Texton and Color Histograms along with GIST are the best performers when it comes to predict the perceived safety of a streetscape. Using Streetscore, we create high resolution maps of perceived safety for 21 cities in the Northeast and Midwest of the United States at a resolution of 200 images/square mile, scoring ~1 million images from Google Streetview. These datasets should be useful for urban planners, economists and social scientists looking to explain the social and economic consequences of urban perception.
FERROKINETICS IN MAN (1970)

FINCH, C. A.; DEUBELBEISS, K.; COOK, J. D.; ESCHBACH, J. W.; BARKER, L. A.; FUNK, D. D.; MARSAGLIA, G.; HILLMAN, R. S.; SLICHTER, S.; ADAMSON, J. W.; GANZONI, A.; GIBLETT, E. R. Author Information
Shedding of Pandemic (H1N1) 2009 Virus among Health Care Personnel, Seattle, Washington, USA (2011)

The Centers for Disease Control and Prevention (CDC) recommends that health care personnel (HCP) infected with pandemic influenza (H1N1) 2009 virus not work until 24 hours after fever subsides without the use of antipyretics. During an influenza outbreak, we examined the association between viral shedding and fever among infected HCP. Participants recorded temperatures daily and provided nasal wash specimens for 2 weeks after symptom onset. Specimens were tested by using PCR and culture. When they met CDC criteria for returning to work, 12 of 16 HCP (75%) (95% confidence interval 48%-93%) had virus detected by PCR, and 9 (56%) (95% confidence interval 30%-80%) had virus detected by culture. Fever was not associated with shedding duration (p = 0.65). HCP might shed virus even when meeting CDC exclusion guidelines. Further research is needed to clarify the association between viral shedding, symptoms, and infectiousness.
Carbon Monoxide Inhibits Human Airway Smooth Muscle Cell Proliferation via Mitogen-Activated Protein Kinase Pathway (2002)

The gaseous molecule carbon monoxide (CO) is elevated in the breath of individuals with asthma. The physiologic function of CO in asthma is poorly understood. Here we demonstrate that CO (250 ppm) markedly inhibits human airway smooth muscle cell (HASMC) proliferation, arresting cells at the G0/G1 phase. This CO-induced cell growth arrest of HASMC was associated with upregulation of p21 and downregulation of cyclin D1 expression. It is generally believed that the signaling pathway by which CO affects biologic processes is primarily mediated via the guanylyl cyclase/3',5'-Guanylate cyclic monophosphate (cGMP) pathway. To examine whether guanylyl cyclase/cGMP was involved in CO-induced growth arrest of HASMC, Rp-8-Br-cGMP, a selective inhibitor of cGMP-dependent protein kinase and ODQ, a selective inhibitor of soluble guanylate cyclase, were administered to HASMC in the presence of CO. Interestingly, CO-induced cell growth arrest was not reversed by these inhibitors. We next examined whether the extracellular signal-regulated kinase (ERK) 1/ERK2 mitogen-activated protein kinase (MAPK) signaling pathway may regulate the antiproliferative effect of CO. We first showed time-dependent activation of the various MAPKs in HASMC in response to serum, including phosphorylated ERK1/ERK2, p38, and JNK and then demonstrated that CO exerted negligible effect on activated p38 and JNK; however, ERK activation was significantly attenuated in the presence of CO. These data suggest that CO can inhibit HASMC proliferation via the ERK1/ERK2 MAPK pathway, independent of a guanylyl cyclase/cGMP independent pathway. CO may act as an important mediator of remodeling of human airways in asthma via its ability to regulate cell growth of airway smooth muscle cells.
On the synthesis of azetidines from 3-hydroxypropylamines (1983)

P. G. Sammes and S. Smith, J. Chem. Soc., Chem. Commun., 1983, 682 DOI: 10.1039/C39830000682
Parallel Reaction Monitoring: A Targeted Experiment Performed Using High Resolution and High Mass Accuracy Mass Spectrometry (2015)

The parallel reaction monitoring (PRM) assay has emerged as an alternative method of targeted quantification. The PRM assay is performed in a high resolution and high mass accuracy mode on a mass spectrometer. This review presents the features that make PRM a highly specific and selective method for targeted quantification using quadrupole-Orbitrap hybrid instruments. In addition, this review discusses the label-based and label-free methods of quantification that can be performed with the targeted approach.
Radioimmunolocalization of human carcinoma xenografts with B72.3 second generation monoclonal antibodies. (1988)

The B72.3 reactive antigen, TAG-72, has been purified and a series of second generation monoclonal antibodies (MAbs), designated CC (colon cancer), have been characterized by a range of in vitro immunological assays. Six CC MAbs (CC11, CC30, CC46, CC49, CC83, and CC92) were chosen for analyses of the in vivo binding to a human colon carcinoma xenograft. All 6 MAbs were previously shown to be distinct from B72.3 and each other by a series of reciprocal competition radio-immunoassays, and all were shown to have a Ka higher than that of B72.3. In this study we demonstrate that all six CC MAbs evaluated are superior to B72.3 in an in vivo tumor targeting model, using human colon carcinoma (LS-174T) xenografts in athymic mice, in terms of both the percentage of the injected dose of radiolabeled MAb delivered per g of tumor and tumor:normal tissue ratios. Differences in the in vivo binding patterns and pharmacokinetics among the CC MAbs are also evaluated. Thus, in light of the fact that B72.3 has been shown to successfully target approximately 75% of primary and metastatic carcinoma lesions in a variety of different carcinoma types in over 300 patients, these studies serve as further evidence to support the clinical evaluation of the second generation CC MAbs, either alone or in combination with B72.3.
A PV window awning system on the University of Texas Houston Health Science Center using AC-modules (2002)

The design for a photovoltaic (PV) window awning system on the University Center Tower (UCT) of the University of Texas Houston Health Science Center in Houston, Texas is discussed. The system is nominally 7-kilowatt using 28 individual AC modules. The paper describes the new more powerful version of the SunSine(R) AC modules and the awning system design. Also presented in this paper are the custom features of the modules and mounting brackets that make them blend with the building. Significant design decisions were made to balance competing objectives: overall awning visibility, shading effectiveness and annual energy production by the AC modules.
Anticoagulant therapy--1974 (1974)

THE national impact of thrombosis should not be underestimated. Arterial thromboembolism is a major, if not the primary, contributor to the number 1 (acute myocardial infarction), number 3 (stroke), and the number 4 (renal) causes of death in the United States. In addition, thromboembolic episodes are frequently associated (either causally or as a complication) with rheumatic or atherosclerotic valvular diseases, arrythmias, congestive heart failure, and intimal damage in the carotid artery, the aorta-iliac region, and the arteries of the lower extremities. Some infections and severe blood dyscrasias also may be associated with arterial thrombosis. Venous thromboembolism causes approximately 300,000 patients annually to be hospitalized in the United States, of which more than 50,000 die. The cost of the hospitalization of the 250,000 survivors has been calculated to be approximately $750 million per year. These figures do not include the morbidity and cost for patients with venous thrombosis alone, nor the
Somatic Cell Nuclear Transfer in Humans: Pronuclear and Early Embryonic Development (2001)

Human therapeutic cloning requires the reprogramming of a somatic cell by nuclear transfer to generate autologous totipotent stem cells. We have parthenogenetically activated 22 human eggs and also performed nuclear transfer in 17 metaphase II eggs. Cleavage beyond the eight-cell stage was obtained in the parthenogenetic-activated eggs, and blastocoele cavities were observed in six. Three somatic cell-derived embryos developed beyond the pronuclear stage up to the six-cell stage. The ability to create autologous embryos represents the first step towards generating immune-compatible stem cells that could be used to overcome the problem of immune rejection in regenerative medicine.
A Novel Skew Detection Technique Based on Vertical Projections (2011)

Document skew detection is often done by the use of horizontal projections. In this paper, we introduce a new document skew detection approach that is based on vertical projections as well as bounding box minimization criterion. We motivated by the fact that the majority of the Latin characters have vertical strokes. We claim that the proposed approach is more efficient and gives more accurate results compared with the state-of-the-art skew detection algorithm based on horizontal projections since it is noise and warp resistant. For these reasons, it can be efficiently applied to historical machine printed documents. Experimental results on a database with representative historical printed documents prove the efficiency of the proposed approach. Moreover, an analysis of the performance of the main elements of the proposed technique is also done.
Reversing T-cell Dysfunction and Exhaustion in Cancer (2016)

In the context of chronic antigen exposure in chronic viral infections and cancer, T cells become exhausted/dysfunctional. These exhausted T cells exhibit defective proliferative capacities and cytokine production, but are not totally inert and may exert lytic functions. Importantly, exhausted T cells upregulate multiple inhibitory receptors/immune checkpoints that bind to their ligands expressed by tumor cells and antigen-presenting cells in the tumor microenvironment (TME). Immune checkpoint blockades with anti-CTL antigen 4 (CTLA-4) and/or anti-programmed death 1 (PD-1) mAbs successfully reinvigorate tumor-infiltrating T lymphocytes and provide persistent clinical benefits to a large number of patients with advanced cancer. This great and long-awaited success for the immunotherapy of cancer has infused considerable enthusiasm in the field of oncology and fostered the development of combinatorial strategies to target the multiple mechanisms of tumor-induced T-cell dysfunction. Here, we review the critical immunoregulatory mechanisms driving T-cell exhaustion in the TME. We also discuss the development of promising combinatorial immunotherapies to counteract the mechanisms of tumor-induced T-cell dysfunction to improve the clinical efficacy of current immune checkpoint blockades. As our understanding of the mechanisms supporting tumor-induced T-cell dysfunction improves based upon preclinical and clinical studies, we expect that novel combinatorial immunotherapies will emerge to improve the clinical outcome of patients with advanced cancers.
Identification of a major determinant of mouse neurovirulence of dengue virus type 2 using stably cloned genomic-length cDNA. (1998)

A genomic-length cDNA clone corresponding to the RNA of dengue virus type 2 (DEN-2) New Guinea C strain (NGC) was constructed in a low copy number vector. The cloned cDNA was stably propagated in Escherichia coil and designated pDVWS501. RNA transcripts produced in vitro from the cDNA using T7 RNA polymerase yielded infectious virus (MON501) upon electroporation into BHK-21 cells. When compared with parental NGC virus, MON501 replicated to similar levels in Aedes albopictus C6/36 cells and showed similar neurovirulence in suckling mice. In contrast, a second genomic-length cDNA clone (pDVWS310) used as an intermediate in the construction of pDVWS501 produced virus (MON310) that replicated well in C6/36 cells but was not neurovirulent in mice. MON310 contained the prM and E genes of the non-neurovirulent PUO-218 strain in an NGC background. There were seven amino acid differences between the prM and E proteins of MON310 and MON501. The differences were generally conservative, with the exception of E residue 126, which was Glu in MON310 and Lys in MON501. To examine the role of this residue in mouse neurovirulence, substitutions of Glu --> Lys and Lys --> Glu were made in MON310 and MON501, respectively. The properties of these mutants clearly demonstrated that Lys at E residue 126 is a major determinant of DEN-2 mouse neurovirulence.
Adipsin and Complement Factor D Activity: An Immune-Related Defect in Obesity (1989)

Adipsin is a serine protease that is secreted by adipocytes into the bloodstream; it is deficient in several animal models of obesity, representing a striking example of defective gene expression in this disorder. Recombinant mouse adipsin was purified and its biochemical and enzymatic properties were studied in order to elucidate the function of this protein. Activated adipsin has little or no proteolytic activity toward most substrates but has the same activity as human complement factor D, cleaving complement factor B when it is complexed with activated complement component C3. Like authentic factor D, adipsin can activate the alternative pathway of complement, resulting in red blood cell lysis. Decreased (58 to 80 percent) complement factor D activity, relative to lean controls, was observed as a common feature of several experimental models of obesity, including the ob/ob, db/db, and monosodium glutamate (MSG)-injected mouse and the fa/fa rat. These results suggest that adipsin and the alternative pathway of complement may play an unexpected but important role in the regulation of systemic energy balance in vivo.
Pleasure principles: A review of research on hedonic consumption (2012)

Abstract Thirty years ago, Hirschman and Holbrook (1982) advocated greater attention to hedonic consumption and the myriad ways in which consumers seek pleasure and enjoyment. A thorough review finds that the topic has much appeal and that consumer research has made significant progress toward understanding some of its parameters. However, many questions remain unanswered, particularly with regard to understanding the sources of pleasure, the manner in which consumers seek it, and the ways in which consumers might alter their hedonic consumption decisions to maximize pleasure and happiness. We assess three decades of research on hedonic consumption, emphasizing areas of greatest potential for future exploration.
The 5' Terminal Oligopyrimidine Tract Confers Translational Control on Top Mrnas in a Cell Type-and Sequence Context-Dependent Manner (1997)

TOP mRNAs are vertebrate transcripts which contain a 5'terminal oligopyrimidine tract (5'TOP), encode for ribosomal proteins and elongation factors 1alpha and 2, and are candidates for growth-dependent translational control mediated through their 5'TOP. In the present study we show that elongation factor 2 (EF2) mRNA is translationally regulated in a growth-dependent manner in cells of hematopoietic origin, but not in any of three different non-hematopoietic cell lines studied. Human beta1-tubulin mRNA is a new member of the family which contains all the hallmarks of a typical TOP mRNA, yet its translation is refractory to growth arrest of any of the examined cell lines. Transfection experiments indicate that the first 29 and 53 nucleotides of the mRNAs encoding EF2 and beta1-tubulin, respectively, contain all the translational cis-regulatory elements sufficient for ubiquitously conferring growth-dependent translational control on a reporter mRNA. These results suggest that the distinct translational regulation of TOP mRNAs reflects downstream sequences which can override the regulatory features of the 5'TOP in a cell type-specific manner. This notion is further supported by the fact that mutations within the region immediately downstream of the 5'TOP of rpS16 mRNA confer onto the resulting transcripts growth-dependent translational control with a cell type specificity similar to that displayed by EF2 mRNA.