gebhart/patrepeval huggingface dataset:
Acute cigarette smoke exposure induces apoptosis of alveolar macrophages (2001)

Alveolar macrophages (AMs) may play a critical role in cigarette smoke (CS)-related pulmonary diseases. This study was designed to determine whether CS induces apoptosis of AMs. In in vitro studies, mouse, rat, and human AMs and human blood monocyte-derived macrophages cultured with aqueous whole CS extracts underwent apoptosis that was detected by light and electron microscopy and terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling. The gas phase of CSE did not cause apoptosis. The CS-induced apoptosis was associated with increased oxidative stress, Bax protein accumulation, mitochondrial dysfunction, and mitochondrial cytochrome c release but was independent of p53, Fas, and caspase activation. This apoptosis was inhibited by antioxidants such as glutathione, ascorbic acid, and alpha-tocopherol. In in vivo studies where rats were exposed to the smoke from 10 cigarettes over 5 h in an exposure chamber, approximately 3% of AMs obtained by bronchoalveolar lavage after 24 h showed apoptosis. These results suggest that acute CS exposure is capable of inducing apoptosis of AMs.
A systematic review and economic model of the clinical effectiveness and cost-effectiveness of docetaxel in combination with prednisone or prednisolone for the treatment of hormone-refractory metastatic prostate cancer (2007)

This systematic review of the research suggests that docetaxel plus prednisone seems to be the most effective treatment for men with mHRPC. The economic model suggests that treatment with docetaxel plus prednisone/prednisolone is cost-effective in patients with mHRPC provided the NHS is prepared to pay 33,000 pounds per additional QALY. Future research should include the direct assessment of quality of life and utility gain associated with different treatments, including the effect of adverse events of treatment, using generic instruments, which are suitable for the purposes of cost-effectiveness analyses.
Phase I Clinical Trial of SYL040012, a Small Interfering RNA Targeting β-Adrenergic Receptor 2, for Lowering Intraocular Pressure (2013)

The objective of this study was to evaluate ocular tolerance, safety, and effect on intraocular pressure (IOP) of a topically administered small interfering RNA; SYL040012, on healthy volunteers. The study was an open-label, controlled, single-center study comprised of two intervals that enrolled 30 healthy subjects having IOP below 21 mmHg. SYL040012 was administered to one eye as a single dose to six subjects during interval 1. During interval 2 two different doses of SYL040012 were administered to one eye on a daily basis to two separate groups of 12 subjects each, over a period of 7 days. The contralateral eye was evaluated but not administered and served as control for the tolerance study. SYL040012 was well tolerated locally. No local or systemic adverse events related to the product developed in response to any of the doses studied. SYL040012 was not detected in plasma at any time point. Administration of SYL040012 over a period of 7 days reduced IOP values in 15 out of 24 healthy subjects regardless of the dose used. IOP decrease was statistically significant in response to one of the doses tested and responsiveness to SYL040012 seemed to be greater in individuals with higher baseline IOP.
Photodynamic therapy for residual neoplasms of the perianal skin (2000)

Photodynamic therapy can successfully be used after wide local excision for residual neoplasms of the perianal skin. Treatment can be rendered with acceptable morbidity.
Usual interstitial pneumonia: histologic correlation with high-resolution CT. (1992)

The authors reviewed 46 cases of idiopathic pulmonary fibrosis with usual interstitial pneumonia (UIP), correlating findings on high-resolution computed tomographic (HRCT) scans with findings in specimens obtained at open lung biopsy and autopsy. The following HRCT findings were observed: (a) an accumulation of small cystic spaces with thick walls, (b) air bronchiolograms within areas of intense lung attenuation, (c) rugged pleural surfaces, (d) irregularly thickened pulmonary vessels, (e) bronchial wall thickening, and (f) slightly increased lung attenuation. Macroscopic honeycombing correlating with small cystic spaces was demonstrated at HRCT and pathologic examination. Air bronchiolograms in the areas of intense lung attenuation (ie, microscopic honeycombing) corresponded to dilated bronchioles (greater than 1 mm in diameter) with fibrosis. Irregularly thickened vessels and bronchial walls and irregular pleural surfaces were the result of fibrosis in the periphery of the secondary pulmonary lobules. Areas of slightly increased lung attenuation seen on the HRCT scans correlated with patchy alveolar septal fibrosis or inflammation. The authors conclude that microscopic honeycombing and a perilobular distribution in UIP may be clearly identified with HRCT.
Differential tyrosine phosphorylation of inhibitory versus activating Ly-49 receptor proteins and their recruitment of SHP-1 phosphatase (1997)

Killer cell inhibitory receptors represent a family of p58/70-Ig-like proteins expressed on the surface of human NK cells. Engagement of class I MHC by killer cell inhibitory receptors turns off the lytic machinery of NK cells. This receptor/ligand interaction results in phosphorylation of intracellular tyrosine residues of p58/70 proteins. Murine NK cells express surface receptors of an unrelated family of type II lectin-like proteins, Ly-49, that have similar functions. Ly-49A, -C, and -G2 represent murine inhibitory receptors. However, Ly-49D functions as an activation receptor on the surface of NK cells. This dichotomy of function between Ly-49 family members suggested different signaling events upon receptor/ligand interaction. Here we demonstrate that: 1) in transfected Cos7 and murine NK cells, Ly-49A, -C, and -G2 are phosphorylated following pervanadate stimulation, whereas Ly-49D is not; 2) mAb-induced receptor ligation mediates tyrosine phosphorylation of Ly-49A and -G2, but not Ly-49D; 3) SHP-1 coprecipitates with Ly-49A and -G2 following receptor phosphorylation; and 4) tyrosine phosphorylation of Ly-49 inhibitory receptors depends on tyrosine residues restricted to the immunoreceptor tyrosine-based inhibitory motif. Our data further support the involvement of immunoreceptor tyrosine-based inhibitory motifs as crucial sequences regulating receptor-mediated inhibitory functions in NK cells.
Exubera Inhaled Insulin in Patients with Type 1 and Type 2 Diabetes: The First 12 Months (2009)

Our 12-month audit data demonstrate that the initiation of inhaled insulin in this difficult-to-treat group of patients resulted in a significant improvement in glycemic control. The subsequent withdrawal of an alternative and acceptable form of insulin treatment now presents a renewed challenge for our patients and healthcare professionals.
Computation-Guided Rational Design of a Peptide Motif That Reacts with Cyanobenzothiazoles via Internal Cysteine–Lysine Relay (2018)

Site-selective protein modification based on covalent reactions of peptide tags and small molecules is a key capability for basic research as well as for the development of new therapeutic bioconjugates. Here, we describe the computation-guided rational design of a cysteine- and lysine-containing 11-residue peptide sequence that reacts with 2-cyanobenzothiazole (CBT) derivatives. Our data show that the cysteine residue reversibly reacts with the nitrile group on the CBT moiety to form an intermediate thioimidate, which undergoes irreversible SN transfer to the lysine residue, yielding an amidine-linked product. The concepts outlined herein lay a foundation for future development of peptide tags in the context of site-selective modification of lysine residues within engineered microenvironments.
In vitro replication, packaging, and transcription of the segmented double-stranded RNA genome of bacteriophage phi 6: studies with procapsids assembled from plasmid-encoded proteins (1990)

The genome of the lipid-containing bacteriophage phi 6 contains three segments of double-stranded RNA (dsRNA). We prepared cDNA copies of the viral genome and cloned this material in plasmids that replicate in Escherichia coli and Pseudomonas phaseolicola, the natural host of phi 6. These plasmids direct the formation of viral proteins and the assembly of structures similar to viral procapsids containing proteins P1, P2, P4, and P7. We found that these particles are capable of taking up viral single-stranded RNA and synthesizing the minus strands to produce dsRNA structures. Once the dsRNA is formed, it is then used as a template for the production of viral plus strands in a reaction that resembles normal transcription. The particles were also capable of directly transcribing exogenous dsRNA. The replicase reactions were specific for phi 6 RNA, were specific for procapsids, and resulted in substantial incorporation of product dsRNA into particles. These results offer strong support to a model in which genomic packaging is done by preformed procapsids.
The expanding range of parvoviruses which infect humans (2010)

The first human parvoviruses to be described (1960s) were the adeno-associated viruses (AAVs, now classed as dependoviruses), originally identified as contaminants of cell cultures, followed by parvovirus B19 (B19V) in 1974, the first parvovirus to be definitively shown to be pathogenic. More recently two new groups of parvoviruses, the human bocaviruses (HuBoV) and the Parv4 viruses have been identified. These four groups of human viruses are all members of different genera within the Parvovirus family, and have very different biology, epidemiology and disease associations from each other. This review will provide an overview of the virological, pathogenic and clinical features of the different human paroviruses, and how these new viruses and their variants fit into the current understanding of parvovirus infection.
Chromatin organization and transcriptional activation of Hox genes (2010)

Spatially and temporally programmed expression of the Hox genes along the antero-posterior (A-P) axis is essential for correct pattern formation during embryonic development. An accumulating body of evidence indicates the pivotal role of spatial chromatin organization for the coordination of gene regulation. Recently, chromosome conformation capture (3C) technique has been developed and opened a new way to study chromosomal interactions in the nucleus. In this study, we describe 3C method we applied in F9 embryonic teratocarcinoma cells and demonstrate that the chromosomal interactions at Hox loci are successfully detected. Interestingly, at Hoxc loci, the abundance of intrachromosomal interactions with neighboring fragments was drastically decreased when the genes are expressed. These results indicate the possibility of the dynamic pattern of chromosomal interaction in association with the transcriptional regulation of Hox genes.
Effective and efficient malware detection at the end host (2009)

Malware is one of the most serious security threats on the Internet today. In fact, most Internet problems such as spam e-mails and denial of service attacks have malware as their underlying cause. That is, computers that are compromised with malware are often networked together to form botnets, and many attacks are launched using these malicious, attacker-controlled networks. With the increasing significance of malware in Internet attacks, much research has concentrated on developing techniques to collect, study, and mitigate malicious code. Without doubt, it is important to collect and study malware found on the Internet. However, it is even more important to develop mitigation and detection techniques based on the insights gained from the analysis work. Unfortunately, current host-based detection approaches
Remarkably Size-Regulated Cell Invasion by Artificial Viruses. Saccharide-Dependent Self-Aggregation of Glycoviruses and Its Consequences in Glycoviral Gene Delivery (2003)

We here report a novel example of artificial glycoviral vectors constructed via number- and size-controlled gene (pCMVluc, 7040 bp) coating with micellar glycocluster nanoparticles (GNPs) of calix[4]resorcarene-based macrocyclic glycocluster amphiphiles having eight or five saccharide moieties with terminal alpha-glucose (alpha-Glc), beta-glucose (beta-Glc), or beta-galactose (beta-Gal) residues. The resulting glycoviruses are compactly packed (approximately 50 nm) and well charge-shielded (zeta approximately equal 0 mV), undergo saccharide-dependent (alpha-Glc > beta-Gal >> beta-Glc) self-aggregation, and transfect cell (Hela and HepG2) cultures as triggered by the pinocytic form of endocytosis. The semilogarithmic linear size-activity correlation suggests that size-restricted pinocytosis (<100 nm) is effective only for monomeric viruses. The activities of oligomeric and otherwise poorly active beta-Gal-functionalized viruses toward hepatic HepG2 cells are approximately 10(2)-times higher than expected on the size basis, owing to the receptor-mediated specific pathway involving the asialoglycoprotein receptors on the hepatic cell surfaces. The scope and prospect of artificial glycoviruses are discussed.
A modular and extensible RNA-based gene-regulatory platform for engineering cellular function (2007)

Engineered biological systems hold promise in addressing pressing human needs in chemical processing, energy production, materials construction, and maintenance and enhancement of human health and the environment. However, significant advancements in our ability to engineer biological systems have been limited by the foundational tools available for reporting on, responding to, and controlling intracellular components in living systems. Portable and scalable platforms are needed for the reliable construction of such communication and control systems across diverse organisms. We report an extensible RNA-based framework for engineering ligand-controlled gene-regulatory systems, called ribozyme switches, that exhibits tunable regulation, design modularity, and target specificity. These switch platforms contain a sensor domain, comprised of an aptamer sequence, and an actuator domain, comprised of a hammerhead ribozyme sequence. We examined two modes of standardized information transmission between these domains and demonstrate a mechanism that allows for the reliable and modular assembly of functioning synthetic RNA switches and regulation of ribozyme activity in response to various effectors. In addition to demonstrating examples of small molecule-responsive, in vivo functional, allosteric hammerhead ribozymes, this work describes a general approach for the construction of portable and scalable gene-regulatory systems. We demonstrate the versatility of the platform in implementing application-specific control systems for small molecule-mediated regulation of cell growth and noninvasive in vivo sensing of metabolite production.
CLKN: Cascaded Lucas-Kanade Networks for Image Alignment (2017)

This paper proposes a data-driven approach for image alignment. Our main contribution is a novel network architecture that combines the strengths of convolutional neural networks (CNNs) and the Lucas-Kanade algorithm. The main component of this architecture is a Lucas-Kanade layer that performs the inverse compositional algorithm on convolutional feature maps. To train our network, we develop a cascaded feature learning method that incorporates the coarse-to-fine strategy into the training process. This method learns a pyramid representation of convolutional features in a cascaded manner and yields a cascaded network that performs coarse-to-fine alignment on the feature pyramids. We apply our model to the task of homography estimation, and perform training and evaluation on a large labeled dataset generated from the MS-COCO dataset. Experimental results show that the proposed approach significantly outperforms the other methods.
Surface Characterization of Hydroxyapatite and Related Calcium Phosphates by XPS and TOF-SIMS (2000)

The surfaces of six biologically interesting calcium phosphate (CaP) phases (hydroxyapatite, dibasic calcium phosphate dihydrate, dibasic calcium phosphate, monobasic calcium phosphate, beta-tribasic calcium phosphate, octacalcium phosphate) have been examined by X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (TOF-SIMS). The intensity of an O(1s) shake-up satellite correlates with the phosphate oxygen content. Together with the Ca/P and O/Ca XPS peak ratios, this feature helps provide identification of the CaP phase(s) present in the surface of unknown samples and establish their mole fractions, as proven with a bone sample. Contributions from carbonate impurities can be quantified using its C(1s) peak at 279.9 eV and subtracted from the O(1s) line shape to aid identification. Principal component analysis (PCA) has been applied successfully to analyze TOF-SIMS spectra of these six CaP phases. Multivariate analysis can help differentiate these CaP phases using the first two PCs, which are dominated by the relative intensities of only a few key ions: PO3-, O-, Ca+, CaOH+, PO2-, and OH-.
Immune dysregulation in atopic dermatitis (2006)

Atopic dermatitis (AD) is a chronic, relapsing, highly pruritic, inflammatory skin disease characterized by cutaneous hyperreactivity to environmentals triggers. Recent data suggest the presence of two different forms of AD: an extrinsic AD with elevated IgE involving 70-80% of the patients and an intrinsic AD with serum IgE not elevated and no specific IgE. Patients with extrinsic AD have elevated Th2- and decreased Thl-expressing cells in the peripheral blood, with elevated IL-4 and IL-13 expression, as well as IL-5. On the contrary, the intrinsic AD is linked with much lower levels of IL-4 and IL-13. Genetic factors are involved in the control of the disease and in the intrinsic AD the same chromosomal regions seem to be associated with psoriasis susceptibility. The AD is characterized by a complex of immunological alterations involving interactions between IgE-bearing antigen-presenting cells, T-cell activation, mast-cell degranulation, keratinocytes, eosinophils, and a combination of immediate and cellular immune responses. Inflammatory dendritic epidermal cells constitute a distinct dendritic cells population that is mainly found in AD and could induce the Th2/Thl isotopic switch contributing to AD chronic phase. Therapy is based on interventation in the pathophysiology of atopic eczema and elimination of exogenous provocation factors.
"Introduction:Verbalizing the Visual and Visualizing the Verbal (2010)

Introduzione al volume Speaking Picture, dove i tre curatori si concentrano sui concetti di "speaking picture" e "Visual/Verbal" rispetto allo spettatore. It's the introduction to the volume Speaking Pictures. The three editor focus on the concepts of "speaking picture" and "Visual/Verbal" as regards the audience.
The two-photon laser-induced fluorescence of the tumor-localizing photosensitizer hematoporphyrin derivative. Resonance-enhanced 750 nm two-photon excitation into the near-UV Soret band. (1986)

The tumor-localizing photosensitizer hematoporphyrin derivative (HPD) is shown to undergo a simultaneous two-photon excitation into the near-ultraviolet Soret band system upon intense laser irradiation at 750 nm, a spectral region where there is no significant HPD one-photon absorbance in aqueous solution. Subsequent to this excitation, internal conversion and vibrational relaxation occur, resulting in the population of the vibrationless level of the first electronically excited singlet state. This state relaxes by two channels, the emission of fluorescence in the spectral region 600-700 nm and intersystem crossing into the triplet manifold, followed by near-resonant electronic energy transfer with surrounding oxygen to result in the generation of highly reactive singlet molecular oxygen (1 delta g). Evidence for the two-photon excitation consists in the observation both of the HPD fluorescence spectrum in the region of 615 nm as a result of 750 nm excitation and the quadratic dependence of this fluorescence emission intensity upon the excitation laser intensity. Since, in general, the penetration depth of ultraviolet and visible light into tissue varies directly with wavelength (red penetrating more deeply than blue), these studies suggest the possibility that two-photon-induced localization of tumor-bound HPD might facilitate the detection of deeper lying tumors than allowed by the current one-photon photolocalization method.
Opportunist mycobacteria express ligands that stimulate production of human V gamma 9V delta 2 T lymphocytes (1992)

Human gamma delta T cells are known to respond at high frequencies to pathogenic mycobacteria. Here we show that opportunistic strains of mycobacteria share with pathogenic mycobacteria the ability to trigger at high frequencies human V gamma 9V delta 2 T-cell-receptor-positive T lymphocytes. Stimulating ligands were present in part in a low-molecular-weight fraction of lysates from opportunistic mycobacteria, as has been found for pathogenic strains. These results support the view that postnatal exposure to ever-present opportunistic mycobacteria may be a driving force for the numerical expansion of the V gamma 9V delta 2 T-cell subset in adolescence.
Tubulin aggregation and disaggregation: mediation by two distinct vinblastine-binding sites. (1976)

Rat brain tubulin possesses two distinct binding sites for vinblastine per molecule: a high-affinity site with an affinity constant of 6.2 x 10(6) M-1 and a low-affinity site with an affinity constant of 8 x 10(4) M-1. The high-affinity site is labile, with a t1/237 degrees of 3.5 hr, is protected by colchicine, and is unaffected by salt, whereas the low-affinity site is stable but is inhibited by salt. Binding to both sites is rapid. The high-affinity binding constant of vinblastine to tubulin (6.2 x 10(6) M-1) corresponds to the half-maximal concentration of vinblastine needed to prevent polymerization of tubulin in vitro, whereas the low-affinity binding constant (8 x 10(4) M-1) corresponds to the half-maximal concentration of vinblastine required to aggregate tubulin. We conclude that vinblastine binding to the high- and low-affinity sites, respectively, accounts for the depolymerization and aggregation behavior of tubulin.