gebhart/patrepeval huggingface dataset:
Characterization of Nonrandom Chromosomal Gains and Losses in Multiple Myeloma by Comparative Genomic Hybridization (1998)

Clonal chromosomal changes in multiple myeloma (MM) and related disorders are not well defined, mainly due to the low in vivo and in vitro mitotic index of plasma cells. This difficulty can be overcome by using comparative genomic hybridization (CGH), a DNA-based technique that gives information about chromosomal copy number changes in tumors. We have performed CGH on 25 cases of MM, 4 cases of monoclonal gammopathy of uncertain significance, and 1 case of Waldenstrom's macroglobulinemia. G-banding analysis of the same group of patients demonstrated clonal chromosomal changes in only 13 (43%), whereas by CGH, the number of cases with clonal chromosomal gains and losses increased to 21 (70%). The most common recurrent changes detected by CGH were gain of chromosome 19 or 19p and complete or partial deletions of chromosome 13. +19, an anomaly that has so far not been detected as primary or recurrent change by G-banding analysis of these tumors, was noted in 2 cases as a unique change. Other recurrent changes included gains of 9q, 11q, 12q, 15q, 17q, and 22q and losses of 6q and 16q. We have been able to narrow the commonly deleted regions on 6q and 13q to bands 6q21 and 13q14-21. Gain of 11q and deletion of 13q, which have previously been associated with poor outcome, can thus be detected by CGH, allowing the use of this technique for prognostic evaluation of patients, without relying on the success of conventional cytogenetic analysis.
Interventions for acute internal hordeolum (2013)

We did not find any evidence for or against the effectiveness of nonsurgical interventions for the treatment of hordeolum. Controlled clinical trials would be useful in determining which interventions are effective for the treatment of acute internal hordeolum.
Immune Response Against Angiosarcoma Following Lower Fluence Rate Clinical Photodynamic Therapy (2008)

Tumor response to photodynamic therapy (PDT) is dependent on treatment parameters used. In particular, the light fluence rate may be an important determinant of the treatment outcome. In this clinical case report, we describe the response of angiosarcoma to PDT carried out using different fluence rates and drug and light doses. A patient with recurrent multifocal angiosarcoma of the head and neck was recruited for PDT. A new generation chlorin-based photosensitizer, Fotolon, was administered at a dose of 2.0 to 5.7 mg/kg. The lesions were irradiated with 665 nm laser light for a light dose of 65 to 200 J/cm2 delivered at a fluence rate of 80 or 150 mW/cm2. High dose PDT carried out at a high fluence rate resulted in local control of the disease for up to a year; however, the disease recurred and PDT had to be repeated. PDT of new lesions carried out at a lower fluence rate resulted in tumor eradication. More significantly, it also resulted in spontaneous remission of neighboring and distant untreated lesions. Repeat PDT carried out on a recurrent lesion at a lower fluence rate resulted in eradication of both treated and untreated lesions despite the lower total light dose delivered. Immunohistochemical examination of biopsy samples implies that PDT could have activated a cell-mediated immune response against untreated lesions. Subsequent histopathological examination of the lesion sites showed negative for disease. Our clinical observations show that lower fluence rate PDT results in better outcome and also indicate that the fluence rate, rather than the total light dose, is a more crucial determinant of the treatment outcome. Specifically, lower fluence rate PDT appears to activate the body's immune response against untreated lesions.
Poxvirus pathogenesis (1991)

Poxviruses are a highly successful family of pathogens, with variola virus, the causative agent of smallpox, being the most notable member. Poxviruses are unique among animal viruses in several respects. First, owing to the cytoplasmic site of virus replication, the virus encodes many enzymes required either for macromolecular precursor pool regulation or for biosynthetic processes. Second, these viruses have a very complex morphogenesis, which involves the de novo synthesis of virus-specific membranes and inclusion bodies. Third, and perhaps most surprising of all, the genomes of these viruses encode many proteins which interact with host processes at both the cellular and systemic levels. For example, a viral homolog of epidermal growth factor is active in vaccinia virus infections of cultured cells, rabbits, and mice. At least five virus proteins with homology to the serine protease inhibitor family have been identified and one, a 38-kDa protein encoded by cowpox virus, is thought to block a host pathway for generating a chemotactic substance. Finally, a protein which has homology with complement components interferes with the activation of the classical complement pathway. Poxviruses infect their hosts by all possible routes: through the skin by mechanical means (e.g., molluscum contagiosum infections of humans), via the respiratory tract (e.g., variola virus infections of humans), or by the oral route (e.g., ectromelia virus infection of the mouse). Poxvirus infections, in general, are acute, with no strong evidence for latent, persistent, or chronic infections. They can be localized or systemic. Ectromelia virus infection of the laboratory mouse can be systemic but inapparent with no mortality and little morbidity, or highly lethal with death in 10 days. On the other hand, molluscum contagiosum virus replicates only in the stratum spinosum of the human epidermis, with little or no involvement of the dermis, and does not spread systemically from the site of infection. The host response to infection is progressive and multifactorial. Early in the infection process, interferons, the alternative pathway of complement activation, inflammatory cells, and natural killer cells may contribute to slowing the spread of the infection. The cell-mediated response involving learned cytotoxic T lymphocytes and delayed-type hypersensitivity components appears to be the most important in recovery from infection. A significant role for specific antiviral antibody and antibody-dependent cell-mediated cytotoxicity has yet to be demonstrated in recovery from a primary infection, but these responses are thought to be important in preventing reinfection.
Signals through 4-1BB are costimulatory to previously activated splenic T cells and inhibit activation-induced cell death (1997)

Previously, we and others showed that signals relayed through the murine T cell Ag 4-1BB enhance primary T cell responses, and that blocking the interaction of 4-1BB with its ligand results in decreased responses to polyclonal activators and to alloantigens. Because 4-1BB expression is induced following primary stimulation, we investigated the role of signaling through this molecule in the reactivation of proliferating T cells. To this end, preactivated, 4-1BB-expressing T cells were restimulated in the presence of plate-immobilized mAbs directed against 4-1BB or the prototypic costimulatory molecule CD28. In this work, we show that in the presence of either signal, T cells respond to TCR cross-linking with strong proliferative responses and cytokine production; moreover, our findings indicate that T cell proliferation partially correlates with surface 4-1BB expression. In addition, our results suggest that Ab-mediated costimulatory signals can act independently of potential accessory B7-CD28/CTLA-4 (cytotoxic T lymphocyte Ag-4) interactions. Importantly, the characteristic DNA fragmentation and apoptotic cell death observed after TCR re-engagement are inhibited comparably in the presence of either 4-1BB or CD28 signaling.
Carcinogenicity of ambient air pollution: use of biomarkers, lessons learnt and future directions. (2015)

The association between ambient air pollution (AAP) exposure and lung cancer risk has been investigated in prospective studies and the results are generally consistent, indicating that long-term exposure to air pollution can cause lung cancer. Biomarkers can enhance research on the health effects of air pollution by improving exposure assessment, increasing the understanding of mechanisms, and enabling the investigation of individual susceptibility. In this review, we assess DNA adducts as biomarkers of exposure to AAP and early biological effect, and DNA methylation as biomarker of early biological change and discuss critical issues arising from their incorporation in AAP health impact evaluations, such as confounding, individual susceptibilities, timing, intensity and duration of exposure, and investigated tissue. DNA adducts and DNA methylation are treated as paradigms. However, the lessons, learned from their use in the examination of AAP carcinogenicity, can be applied to investigations of other biomarkers involved in AAP carcinogenicity.
Selection of a Colorado Potato Beetle (Coleoptera: Chrysomelidae) Strain Resistant to Bacillus thuringiensis (1993)

For the first time, resistance to the CRYIIIA coleopteran specific delta endotoxin of Bacillus thuringiensis var. san diego or tenebrionis is reported. Colorado potato beetles, Leptinotarsa decemlineata (Say), were selected in the laboratory after exposure in potato fields in Michigan. After 12 generations of selection, the selected strain was 59 times more resistant than the unselected strain and 24-35 times more resistant than other susceptible or insecticide-resistant strains. We observed no cross-resistance between organophosphate, carbamate, or pyrethroid resistance and B. thuringiensis resistance. No difference in movement induced by B. thuringiensis or initial feeding behavior was observed between selected and unselected strains, although a shift toward petiole feeding behavior was observed in adults (of both strains) that were stressed by B. thuringiensis. The selected strain oviposited at a reduced rate of 0.1 ±0.15 (mean ± SD) egg masses per day) on treated foliage; the unselected strain was oostatic. Based on these results, it is recommended that resistance management strategies be developed and deployed for both conventionally applied B. thuringiensis products and B. thuringiensis transgenic plants.
Nanoparticles-cell association predicted by protein corona fingerprints (2016)

In a physiological environment (e.g., blood and interstitial fluids) nanoparticles (NPs) will bind proteins shaping a "protein corona" layer. The long-lived protein layer tightly bound to the NP surface is referred to as the hard corona (HC) and encodes information that controls NP bioactivity (e.g. cellular association, cellular signaling pathways, biodistribution, and toxicity). Decrypting this complex code has become a priority to predict the NP biological outcomes. Here, we use a library of 16 lipid NPs of varying size (Ø≈ 100-250 nm) and surface chemistry (unmodified and PEGylated) to investigate the relationships between NP physicochemical properties (nanoparticle size, aggregation state and surface charge), protein corona fingerprints (PCFs), and NP-cell association. We found out that none of the NPs' physicochemical properties alone was exclusively able to account for association with human cervical cancer cell line (HeLa). For the entire library of NPs, a total of 436 distinct serum proteins were detected. We developed a predictive-validation modeling that provides a means of assessing the relative significance of the identified corona proteins. Interestingly, a minor fraction of the HC, which consists of only 8 PCFs were identified as main promoters of NP association with HeLa cells. Remarkably, identified PCFs have several receptors with high level of expression on the plasma membrane of HeLa cells.
Nuclease Resistance and RNase H Sensitivity of Oligonucleotides Bridged by Oligomethylenediol and Oligoethylene Glycol Linkers (2001)

The properties of new chimeric oligodeoxynucleotides made of short sequences (tetramers, pentamers, octamers, and decamers) bridged by hexamethylenediol and hexaethylene glycol linkers have been investigated. These chimeric oligonucleotides showed an improved resistance toward snake venom 3'-phosphodiesterase, with an increased stability when a terminal 3'-3'-internucleotide phosphodiester bond is present. It also has been demonstrated that the hybrid complexes formed by bridged oligonucleotides and a complementary 20-mer RNA are able to elicit the activity of ribonuclease H (RNase H) from Escherichia coli. The substrate properties of chimeric oligonucleotides depend on the length of the oligonucleotide fragments bridged by linkers. Introduction of a nonnucleotide spacer into the native oligonucleotide only slightly hampers the extent of the RNA hydrolysis in the hybrid complexes, whereas a modification of the site of reaction is observed as a possible consequence of the steric disturbance due to the aliphatic linkers. Hence, these new chimeric oligonucleotides, namely, short oligonucleotide fragments bridged by nonnucleotide linkers, demonstrate a favorable combination of exonuclease resistance and high substrate activity toward RNase H. As a consequence, these chimeric oligonucleotides could be proposed as new, promising analogs to be used in the antisense strategy.
The Link between the PDL1 Costimulatory Pathway and Th17 in Fetomaternal Tolerance (2011)

Fetomaternal tolerance has been shown to depend both on regulatory T cells (Tregs) and negative signals from the PD1-PDL1 costimulatory pathway. More recently, IL-17-producing T cells (Th17) have been recognized as a barrier in inducing tolerance in transplantation. In this study, we investigate the mechanisms of PDL1-mediated regulation of fetomaternal tolerance using an alloantigen-specific CD4(+) TCR transgenic mouse model system (ABM-tg mouse). PDL1 blockade led to an increase in embryo resorption and a reduction in litter size. This was associated with a decrease in Tregs, leading to a lower Treg/effector T cell ratio. Moreover, PDL1 blockade inhibited Ag-specific alloreactive T cell apoptosis and induced apoptosis of Tregs and a shift toward higher frequency of Th17 cells, breaking fetomaternal tolerance. These Th17 cells arose predominantly from CD4(+)Foxp3(-) cells, rather than from conversion of Tregs. Locally in the placenta, similar decrease in regulatory and apoptotic markers was observed by real-time PCR. Neutralization of IL-17 abrogated the anti-PDL1 effect on fetal survival rate and restored Treg numbers. Finally, the adoptive transfer of Tregs was also able to improve fetal survival in the setting of PDL1 blockade. This is to our knowledge the first report using an alloantigen-specific model that establishes a link between PDL1, Th17 cells, and fetomaternal tolerance.
Simulating Low-Cost Cameras for Augmented Reality Compositing (2009)

Video see-through Augmented Reality adds computer graphics to the real world in real time by overlaying graphics onto a live video feed. To achieve a realistic integration of the virtual and real imagery, the rendered images should have a similar appearance and quality to those produced by the video camera. This paper describes a compositing method which models the artifacts produced by a small low-cost camera, and adds these effects to an ideal pinhole image produced by conventional rendering methods. We attempt to model and simulate each step of the imaging process, including distortions, chromatic aberrations, blur, Bayer masking, noise, sharpening, and color-space compression, all while requiring only an RGBA image and an estimate of camera velocity as inputs.
« Deconstructing Harry » : une évaluation des systèmes de repérage d'entités nommées (2001)

○ On appelle traditionnellement entites nommees (de l'anglais named entity) l'ensemble des noms de personnes, d'entreprises et de lieux presents dans un texte donne. On associe souvent a ces elements d'autres syntagmes reperables par des grammaires locales comme les dates, les unites monetaires, les pourcentages, etc. ○ Cet article presente un etat de l'art des systemes permettant le reperage des entites nommees. Nous proposons un protocole pour « deconstruire » un systeme et en evaluer les differentes composantes. Nous examinerons les performances d'un tel systeme muni de capacites d'apprentissage mais disposant de connaissances initiales reduites. Nous menons ces experiences dans des conditions operationnelles: les corpus vises sont de natures diverses, de taille souvent modeste et ils ne sont pas etiquetes au prealable. ○ Enfin, nous proposons des indicateurs permettant d'estimer a priori le gain que peuvent apporter des capacites d'apprentissage et de revision liees a un systeme a base de regles.
A versatile synthetic dimerizer for the regulation of protein–protein interactions (1997)

The use of low molecular weight organic compounds to induce dimerization or oligomerization of engineered proteins has wide-ranging utility in biological research as well as in gene and cell therapies. Chemically induced dimerization can be used to activate intracellular signal transduction pathways or to control the activity of a bipartite transcription factor. Dimerizer systems based on the natural products cyclosporin, FK506, rapamycin, and coumermycin have been described. However, owing to the complexity of these compounds, adjusting their binding or pharmacological properties by chemical modification is difficult. We have investigated several families of readily prepared, totally synthetic, cell-permeable dimerizers composed of ligands for human FKBP12. These molecules have significantly reduced complexity and greater adaptability than natural product dimers. We report here the efficacies of several of these new synthetic compounds in regulating two types of protein dimerization events inside engineered cells--induction of apoptosis through dimerization of engineered Fas proteins and regulation of transcription through dimerization of transcription factor fusion proteins. One dimerizer in particular, AP1510, proved to be exceptionally potent and versatile in all experimental contexts tested.
Markedly reduced effects of (−)‐isoprenaline but not of (−)‐CGP12177 and unchanged affinity of β‐blockers at Gly389‐β1‐adrenoceptors compared to Arg389‐β1‐adrenoceptors (2004)

1. Substitution of arginine by glycine at position 389, a frequent beta(1)-adrenoceptor polymorphism, reduces adenylyl cyclase stimulation by (-)-isoprenaline. beta(1)-Adrenoceptors mediate the effects of catecholamines and nonconventional partial agonists ((-)-CGP12177) through different sites. We investigated the influence of the 389 polymorphism on beta blocker affinity, as well as on the responses to (-)-isoprenaline and the nonconventional partial agonist (-)-CGP12177 on cyclic AMP levels in CHO cells expressing recombinant Arg389-beta(1)-adrenoceptors (101 fmol mg(-1) protein) or Gly389-beta(1)-adrenoceptors (94 fmol mg(-1)). 2. The affinity of beta-blockers and partial agonists, estimated from competition binding with (-)-[(125)I]-cyanopindolol, was not different for Arg389-beta(1)-adrenoceptors and Gly389-beta(1)-adrenoceptors. 3. The maximum cAMP increases by (-)-isoprenaline and (-)-CGP12177 at Gly389-beta(1)-adrenoceptors were reduced by 97 and 46%, but the potencies enhanced 2 and 0.5 log units, respectively, compared to Arg389-beta(1)-adrenoceptors. The intrinsic activity of (-)-CGP12177 with respect to the (-)-isoprenaline was 0.057 at Arg389-beta(1)-adrenoceptors and 1.05 at Gly389-beta(1)-adrenoceptors. 4. We confirm in intact CHO cells that responses to (-)-isoprenaline are markedly reduced at Gly389-beta(1)-adrenoceptors compared to Arg389-beta(1)-adrenoceptors. However, the 389 polymorphism reduces considerably less the agonist responses to (-)-CGP12177, indicating that coupling to G(s) protein is different for beta(1)-adrenoceptors activated by catecholamines than for receptors activated by nonconventional partial agonists. The affinity of beta-blockers is conserved across the Arg389Gly polymorphism.
Metabolic Adaptation in Obesity and Type II Diabetes: Myokines, Adipokines and Hepatokines (2016)

Obesity and type II diabetes are characterized by insulin resistance in peripheral tissues. A high caloric intake combined with a sedentary lifestyle is the leading cause of these conditions. Whole-body insulin resistance and its improvement are the result of the combined actions of each insulin-sensitive organ. Among the fundamental molecular mechanisms by which each organ is able to communicate and engage in cross-talk are cytokines or peptides which stem from secretory organs. Recently, it was reported that several cytokines or peptides are secreted from muscle (myokines), adipose tissue (adipokines) and liver (hepatokines) in response to certain nutrition and/or physical activity conditions. Cytokines exert autocrine, paracrine or endocrine effects for the maintenance of energy homeostasis. The present review is focused on the relationship and cross-talk amongst muscle, adipose tissue and the liver as secretory organs in metabolic diseases.
Use of Recombinant Human Bone Morphogenetic Protein-2 to Achieve Posterolateral Lumbar Spine Fusion in Humans (2002)

Study Design. A prospective randomized clinical study was conducted. Objective. To determine whether the dose and carrier that were successful in rhesus monkeys could induce consistent radiographic spine fusion in humans. Summary of Background Data. Preclinical studies have demonstrated that recombinant human bone morphogenetic protein-2 (rhBMP-2), an osteoinductive bone morphogenetic protein, is successful at generating spine fusion in rabbits and rhesus monkeys. Methods. For this study, 25 patients undergoing lumbar arthrodesis were randomized (1:2:2 ratio) based on the arthrodesis technique: autograft/Texas Scottish Rite Hospital (TSRH) pedicle screw instrumentation (n = 5), rhBMP-2/TSRH (n = 11), and rhBMP-2 only without internal fixation (n = 9). On each side, 20 mg of rhBMP-2 were delivered on a carrier consisting of 60% hydroxyapatite and 40% tricalcium phosphate granules (10 cm3/side). The patients had single-level disc degeneration, Grade 1 or less spondylolisthesis, mechanical low back pain with or without leg pain, and at least 6 months failure of nonoperative treatment. Results. All 25 patients were available for follow-up evaluation (mean, 17 months; range 12–27 months). The radiographic fusion rate was 40% (2/5) in the autograft/TSRH group and 100% (20/20) with rhBMP-2 group with or without TSRH internal fixation (P = 0.004). A statistically significant improvement in Oswestry score was seen at 6 weeks in the rhBMP-2 only group (−17.6;P = 0.009), and at 3 months in the rhBMP-2/TSRH group (−17.0;P = 0.003), but not until 6 months in the autograft/TSRH group (−17.3;P = 0.041). At the final follow-up assessment, Oswestry improvement was greatest in the rhBMP-2 only group (−28.7, P < 0.001). The SF-36 Pain Index and PCS subscales showed similar changes. Discussion. This pilot study is the first with at least 1 year of follow-up evaluation to demonstrate successful posterolateral spine fusion using a BMP-based bone graft substitute, with radiographs and CT scans as the determinant. Consistently, rhBMP-2 was able to induce bone in the posterolateral lumbar spine when delivered at a dose of 20 mg per side with or without the use of internal fixation. Patients with spondylolisthesis classified higher than Meyerding Grade 1 or with more than 5 mm of translational motion may still require internal fixation. Some patients did smoke during the postoperative period, and all in the rhBMP-2 groups still obtained solid fusions. Conclusions. Consistently, rhBMP-2 with the biphasic calcium phosphate granules induced radiographic posterolateral lumbar spine fusion with or without internal fixation in patients whose spondylolisthesis did not exceed Grade 1. Statistically greater and quicker improvement in patient-derived clinical outcome was measured in the rhBMP-2 groups.