gebhart/patrepeval huggingface dataset:
SvpA, a novel surface virulence-associated protein required for intracellular survival of Listeria monocytogenes (2001)

A previously unknown protein, designated SvpA (surface virulence-associated protein) and implicated in the virulence of the intracellular pathogen Listeria monocytogenes, was identified. This 64 kDa protein, encoded by svpA, is both secreted in culture supernatants and surface-exposed, as shown by immunogold labelling of whole bacteria with an anti-SvpA antibody. Analysis of the peptide sequence revealed that SvpA contains a leader peptide, a predicted C-terminal transmembrane region and a positively charged tail resembling that of the surface protein ActA, suggesting that SvpA might partially reassociate with the bacterial surface by its C-terminal membrane anchor. An allelic mutant was constructed by disrupting svpA in the wild-type strain LO28. The virulence of this mutant was strongly attenuated in the mouse, with a 2 log decrease in the LD50 and restricted bacterial growth in organs as compared to the wild-type strain. This reduced virulence was not related either to a loss of adherence or to a lower expression of known virulence factors, which remained unaffected in the svpA mutant. It was caused by a restriction of intracellular growth of mutant bacteria. By following the intracellular behaviour of bacteria within bone-marrow-derived macrophages by confocal and electron microscopy studies, it was found that most svpA mutant bacteria remained confined within phagosomes, in contrast to wild-type bacteria which rapidly escaped to the cytoplasm. The regulation of svpA was independent of PrfA, the transcriptional activator of virulence genes in L. monocytogenes. In fact, SvpA was down-regulated by MecA, ClpC and ClpP, which are highly homologous to proteins of Bacillus subtilis forming a regulatory complex controlling the competence state of this saprophyte. The results indicate that: (i) SvpA is a novel factor involved in the virulence of L. monocytogenes, promoting bacterial escape from phagosomes of macrophages; (ii) SvpA is, at least partially, associated with the surface of bacteria; and (iii) SvpA is PrfA-independent and controlled by a MecA-dependent regulatory network.
An optimal algorithm for scheduling soft aperiodic tasks in dynamic-priority preemptive systems (1997)

The paper addresses the problem of jointly scheduling tasks with both hard and soft real time constraints. We present a new analysis applicable to systems scheduled using a priority preemptive dispatcher, with priorities assigned dynamically according to the EDF policy. Further, we present a new efficient online algorithm (the acceptor algorithm) for servicing aperiodic work load. The acceptor transforms a soft aperiodic task into a hard one by assigning a deadline. Once transformed, aperiodic tasks are handled in exactly the same way as periodic tasks with hard deadlines. The proposed algorithm is shown to be optimal in terms of providing the shortest aperiodic response time among fixed and dynamic priority schedulers. It always guarantees the proper execution of periodic hard tasks. The approach is composed of two parts: an offline analysis and a run time scheduler. The offline algorithm runs in pseudopolynomial time O(mn), where n is the number of hard periodic tasks and m is the hyperperiod/min deadline.
Automatic detection of three radio-opaque markers for prostate targeting using EPID during external radiation therapy (2002)

External radiotherapy is an option used for the treatment of the prostate cancer. In order to achieve the best results, radiation must be precisely delivered to the target volume while preserving healthy tissues and protecting organs at risk. Electronic portal imaging devices (EPID) are now available to verify the dose delivery by using the treatment radiation to obtain a portal image. The localization of the prostate, usually not visible on portal images, is performed by inserting up to three radio-opaque markers into the prostate. The identification and position of the markers relative to bone structures and beam field are used to insure the proper delivery of radiation to the prostate. We present a sequence of algorithms optimized for the automatic detection of the three radio-opaque markers on images obtained with EPID during prostate radiotherapy. A neural network is used to validate the detection of true markers in images.
Oxygen free radical generation during cardiopulmonary bypass: correlation with complement activation. (1986)

To determine the relationships among complement activation, pulmonary leukosequestration, and oxygen free radical generation, we prospectively studied 15 patients undergoing cardiopulmonary bypass for myocardial revascularization. Plasma levels of C3a, C4a, and hydrogen peroxide (a marker of oxygen free radical generation) were measured before, during, and after extracorporeal circulation. The results confirm that cardiopulmonary bypass activates complement via the alternate (C3a) pathway. This first phase of complement activation was accompanied by an increase in plasma H2O2 (from 80 +/- 8 to 155 +/- 13 microM/ml; p less than .001) and by pulmonary sequestration of polymorphonuclear leukocytes. Protamine administration after cardiopulmonary bypass further activated complement via the classical (C4a) pathway but was not accompanied by a change in plasma hydrogen peroxide. We hypothesize that both complement activation and excess oxygen free radical generation contribute to the pathophysiology of extracorporeal circulation.
Metaphase and interphase cytogenetics with Alu-PCR-amplified yeast artificial chromosome clones containing the BCR gene and the protooncogenes c-raf-1, c-fms, and c-erbB-2. (1992)

A human yeast artificial chromosome (YAC) library was screened by polymerase chain reaction with oligonucleotide primers defined for DNA sequences of the BCR gene and the protooncogenes c-raf-1, c-fms, and c-erbB-2. Alu-PCR-generated human DNA sequences were obtained from the respective YAC clones and used for fluorescence in situ hybridization experiments under suppression conditions. After chromosomal in situ suppression hybridization to GTG-banded human prometaphase chromosomes, seven of nine initially isolated YAC clones yielded strong signals exclusively in the chromosome bands containing the respective genes. Two clones yielded additional signals on other chromosomes and were excluded from further tests. The band-specific YACs were successfully applied to visualize specific structural chromosome aberrations in peripheral blood cells from patients with myelodysplasia exhibiting del(5)(q13q34), chronic myeloid leukemia and acute lymphocytic leukemia with t(9;22)(q34;q11), acute promyelocytic leukemia (M3) with t(15;17)(q22;q21), and in a cell line established from a proband with the constitutional translocation t(3;8)(p14.2;q24). In addition to the analysis of metaphase spreads, we demonstrate the particular usefulness of these YAC clones in combination with whole chromosome painting to analyze specific chromosome aberrations directly in the interphase nucleus.
[Value of thallium-201 scintigraphy in assessment of neoadjuvant chemotherapy for osteosarcoma]. (2009)

The alteration ratio changes significantly after neoadjuvant chemotherapy and has a significantly positive correlation with tumor necrosis ratio. Thallium-201 scintigraphy is helpful in the evaluation of neoadjuvant chemotherapy for osteosarcoma.
Novel missense and frameshift mutations in the activin receptor‐like kinase‐1 gene in hereditary hemorrhagic telangiectasia (1998)

Hereditary Hemorrhagic Telangiectasia (HHT) is an autosomal dominant disorder characterized by multisystemic vascular dysplasia and recurrent hemorrhage. One of the causative genes is the activin receptor-like kinase-1 (ALK-1) gene located on chromosome 12q13. ALK-1 is an endothelial cell type I receptor for the TGF-β superfamily of ligands. As a number of mutations have been identified in the kinase domain of ALK-1, we initiated a mutation analysis specifically targeting the first four coding exons of ALK-1 in order to determine if mutations in the extracellular and transmembrane domains are also present in HHT. Six new mutations have been identified. Three frameshift mutations were identified in exons encoding the extracellular and transmembrane domains. These mutations would grossly truncate the ALK-1 protein and are thus classic null alleles. Three new missense mutations within the exons encoding the extracellular domain, in addition to two previously described missense mutations, are located at or near highly conserved cysteines. These mutations may disrupt intra- or inter-molecular disulfide bridges required for ligand binding. The combined data suggest that both severe and subtle changes in the ALK-1 amino acid sequence can lead to receptor dysfunction and result in the HHT disease phenotype. Hum Mutat 12:137, 1998. © 1998 Wiley-Liss, Inc.
Characterization of the Mycobacterium tuberculosis erp gene encoding a potential cell surface protein with repetitive structures (1995)

Using the phoA gene fusion methodology adapted to mycobacteria, several Mycobacterium tuberculosis DNA fragments encoding exported proteins were recently identified. In this paper, the molecular cloning, genomic positioning, nucleotide sequence determination and transcriptional start site mapping of a new M. tuberculosis gene, identified by this methodology, are reported. This gene was called erp (for exported repetitive protein) and has a sequence similar to that of the Mycobacterium leprae 28 kDa antigen irg gene M. tuberculosis erp gene contains a putative iron box close to the mapped transcriptional start site. The predicted Erp protein displays a typical N-terminal signal sequence, a hydrophobic domain at the C-terminus and harbours repeated amino acid motifs. These structural features are reminiscent of cell-wall-associated surface proteins from Gram-positive bacteria. We found that these repeats are conserved among M. tuberculosis isolates, and are absent from the published M. leprae irg gene sequence. In addition to being present in M. leprae, erp sequences were found in other members of the M. tuberculosis complex, but not in other mycobacteria tested. These results suggest that erp might encode a cell surface component shared by major pathogenic mycobacteria.
Remodeling in Asthma and Chronic Obstructive Lung Disease (2001)

Asthma and chronic obstructive lung disease (COPD) are both inflammatory conditions of the lung associated with structural "remodeling" inappropriate to the maintenance of normal lung function. The clinically observed distinctions between asthma and COPD are reflected by differences in the remodeling process, the patterns of inflammatory cells and cytokines, and also the predominant anatomic site at which these alterations occur. In asthma the epithelium appears to be more fragile than that of COPD, the epithelial reticular basement membrane (RBM) is significantly thicker, there is marked enlargement of the mass of bronchial smooth muscle, and emphysema does not occur in the asthmatic nonsmoker. In COPD, there is epithelial mucous metaplasia, airway wall fibrosis, and inflammation associated with loss of surrounding alveolar attachments to the outer wall of small airways: bronchiolar smooth muscle is increased also. Emphysema is a feature of severe COPD: in spite of the destructive process, alveolar wall thickening and focal fibrosis may be detected. The hypertrophy of submucosal mucus-secreting glands is similar in extent in asthma and COPD. The number of bronchial vessels and the area of the wall occupied by them increase in severe corticosteroid-dependent asthma: it is likely that these increases also occur in severe COPD as they do in bronchiectasis. Pulmonary vasculature is remodeled in COPD. In asthma several of these structural alterations begin early in the disease process, even in the child. In COPD the changes begin later in life and the associated inflammatory response differs from that in asthma. The following synopsis defines and compares the key remodeling processes and proposes several hypotheses.
Quantitative Comparisons of Image Registration Techniques Based on High-Resolution MRI of the Brain (1994)

We conclude that fiducial markers such as stereotaxic Z frames that are not rigidly fixed to a patient's skull are inaccurate compared with other registration techniques, Talairach coordinate transformations provide surprisingly good registration, and minimizing the variance of MRI-MRI, PET-PET, or MRI-PET ratio images provides significantly better registration than all other techniques tested. Registration optimization based on measurement of the similarity of spatial distributions of voxel values is superior to techniques that do not use such information.
Effectiveness of displaying energy consumption data in residential houses Analysis on how the residents respond (2005)

Providing the residents with information on their use has become a feasible option to promote savings in residential sector. The authors have constructed an interactive energy consumption information that displays consumption of the whole house and domestic appliances. The display system were set up into 10 residential houses and the effects on consumption have been analyzed in detail based on the monitored data before and after the installation of the system and also on the log of how the residents responded through the keyboard. In this paper, the amount of savings actually achieved by setting up the display system and how these savings were achieved by the residents will be described. Some of the observed facts to be shown are the following: 1. The responses of residents to the questionnaire were received for more than nine months and provided us with useful information. The participants became especially interested in the daily load curve.
Suppression of malignancy by the 3' untranslated regions of ribonucleotide reductase R1 and R2 messenger RNAs. (1996)

Mammalian ribonucleotide reductase is rate limiting for the synthesis of DNA. The active enzyme is composed of two dissimilar components called R1 and R2, encoded by different genes. The 3' untranslated regions (3' UTRs) of R1 and R2 messages contain sequences that are important in regulating gene expression through changes in message stability. We have constructed expression plasmids containing the R1 or R2 mRNA 3' UTRs, and we show that transfection of these plasmids into highly malignant mouse 10 T1/2 cells significantly suppresses the tumorigenic properties of these cells in syngeneic mice when compared with cells transfected with the same plasmid lacking R1 or R2 3' UTR sequences or when compared with cells transfected with the same plasmid expressing a heterologous sequence as a control. Furthermore, cells expressing the R2 3' UTR exhibit significantly reduced potential to disseminate to the lungs of syngeneic animals in experimental metastasis assays. The tumor-suppressive effects of the mouse R1 and R2 3' UTRs were not confined to mouse cells, because human HeLa cells transfected with expression plasmids containing either RI or R2 3' UTRs were also significantly less tumorigenic in assays using BALB/c nu/nu mice. These studies demonstrate that the untranslated regions of ribonucleotide reductase mRNAs can function as modifiers of tumor cell development and for the more complex process of tumor dissemination. We propose that these malignancy-suppressive effects are mediated through RNA interactions with cellular components involved in growth regulation through mechanisms of posttranscriptional control of gene expression. In addition, these observations emphasize the enormous potential of untranslated RNA to act directly as modifiers of biological characteristics relevant to mechanisms of malignancy.
Characterization of hepatitis C virus structural proteins with a recombinant baculovirus expression system (1993)

We cloned and expressed the sequences encoding the structural proteins of the hepatitis C virus in a baculovirus eukaryotic expression system. Four recombinant constructs expressed sufficient hepatitis C virus-specific proteins in insect cell culture to allow analysis of protein cleavage, glycosylation and immunoreactivity. Using immunoblot analysis, we detected a 22-kD protein corresponding to the hepatitis C virus capsid protein cleaved from a larger precursor. Recombinant constructs encoding the presumptive envelope (E1) protein produced products ranging from 30 to 35 kD, whereas constructs encoding the presumptive E2/NS1 protein expressed products ranging in size from 68 to 73 kD. The recombinant envelope proteins were glycosylated, as shown by sensitivity to endoglycosidase F digestion, whereas the capsid was not. We examined the immunoreactivity of these recombinant proteins using sera from 50 patients chronically infected with HCV. Forty-seven of 50 of these sera contained antibodies against the capsid, 14 (28%) also had antibodies against E1 and at least 5 (10%) had antibody against E2/NS1. Forty-seven of 50 sera (94%) were viremic, as determined on hepatitis C virus polymerase chain reaction. The three sera that were hepatitis C virus polymerase chain reaction negative did not have envelope antibodies, whereas all sera that had envelope antibodies were also hepatitis C virus polymerase chain reaction positive. Thus antibodies to baculovirus-expressed hepatitis C virus structural proteins, including E1 and E2/NS1, are found in the presence of viremia.
Mass Spectrometry-based Proteomic Profiling of Lung Cancer (2009)

In an effort to further our understanding of lung cancer biology and to identify new candidate biomarkers to be used in the management of lung cancer, we need to probe these tissues and biological fluids with tools that address the biology of lung cancer directly at the protein level. Proteins are responsible of the function and phenotype of cells. Cancer cells express proteins that distinguish them from normal cells. Proteomics is defined as the study of the proteome, the complete set of proteins produced by a species, using the technologies of large-scale protein separation and identification. As a result, new technologies are being developed to allow the rapid and systematic analysis of thousands of proteins. The analytical advantages of mass spectrometry (MS), including sensitivity and high-throughput, promise to make it a mainstay of novel biomarker discovery to differentiate cancer from normal cells and to predict individuals likely to develop or recur with lung cancer. In this review, we summarize the progress made in clinical proteomics as it applies to the management of lung cancer. We will focus our discussion on how MS approaches may advance the areas of early detection, response to therapy, and prognostic evaluation.
The conformation of nascent polylysine and polyphenylalanine peptides on ribosomes (1991)

Polypeptide synthesis using either phenylalanine or lysine was initiated on Escherichia coli ribosomes; then the position and conformation of the nascent peptide were monitored by fluorescence techniques. To this end, fluorophores had been attached to the amino terminus of each nascent peptide, and major differences were observed as chain extension occurred. Polyphenylalanine appeared to build up as a hydrophobic mass adjacent to the peptidyl transferase center while polylysine apparently was extended directly from the ribosome into the surrounding solution. An explanation for these differences may be provided by the physical and chemical properties of each polypeptide. These properties may be responsible for the route by which each peptide exits the peptidyl transferase center as demonstrated by the different sensitivity of each to inhibition by erythromycin.
USP 30 deubiquitylates mitochondrial P arkin substrates and restricts apoptotic cell death (2015)

Mitochondria play a pivotal role in the orchestration of cell death pathways. Here, we show that the control of ubiquitin dynamics at mitochondria contributes to the regulation of apoptotic cell death. The unique mitochondrial deubiquitylase, USP30, opposes Parkin-dependent ubiquitylation of TOM20, and its depletion enhances depolarization-induced cell death in Parkin-overexpressing cells. Importantly, USP30 also regulates BAX/BAK-dependent apoptosis, and its depletion sensitizes cancer cells to BH3-mimetics. These results provide the first evidence for a fundamental role of USP30 in determining the threshold for mitochondrial cell death and suggest USP30 as a potential target for combinatorial anti-cancer therapy.
Ensembles of Locally Independent Prediction Models (2020)

Ensembles depend on diversity for improved performance. Many ensemble training methods, therefore, attempt to optimize for diversity, which they almost always define in terms of differences in training set predictions. In this paper, however, we demonstrate the diversity of predictions on the training set does not necessarily imply diversity under mild covariate shift, which can harm generalization in practical settings. To address this issue, we introduce a new diversity metric and associated method of training ensembles of models that extrapolate differently on local patches of the data manifold. Across a variety of synthetic and real-world tasks, we find that our method improves generalization and diversity in qualitatively novel ways, especially under data limits and covariate shift.
Combined Intravenous and Intra-Arterial Recombinant Tissue Plasminogen Activator in Acute Ischemic Stroke (2000)

We believe that the greater-than-expected proportion of favorable outcomes in these patients with severe ischemic stroke reflects the short time to initiation of both IV and IA thrombolysis.
Le Testament de Melville (2011)

Lorsque Herman Melville meurt a New York, en 1891, il est un vieil homme a peu pres oublie. Moby-Dick, quarante ans plus tot, a coule sa carriere litteraire. C'est seulement dans les annees 1920, dans une Angleterre qui a fait l'experience de la Grande Guerre, que le public commence a s'aviser de son genie. La fievre de la redecouverte nourrit la quete d'inedits et, d'une boite en fer-blanc, surgit le recit auquel Melville a travaille durant les cinq dernieres annees de sa vie : Billy Budd. Malgre une taille limitee, celle d'une longue nouvelle, et une intrigue tres simple, Billy Budd est rapidement devenu l'un des textes les plus etudies et les plus commentes de la litterature mondiale, suscitant des debats aussi passionnes que contradictoires. La violence de la lutte entre critiques ne doit pas surprendre : Melville a tout fait pour livrer a une modernite demi-habile, pensant que tout probleme a sa solution, une de ces situations sur lesquelles elle ne peut que se casser les dents. Qu'est-ce que le mal ? Par quelles voies se repand-il ? Comment limiter son empire ? Quel sens donner a la beaute d'un etre ? Comment accueillir la grâce echue a un autre ? Autant de questions que la pensee instrumentale nous a desappris a poser et qui, lorsqu'elle les rencontre, la rendent comme folle. Autant de questions qui n'en demeurent pas moins essentielles et dont la litterature est peut-etre la mieux a meme, par ses ambiguites, de traiter sans faussete. C'est dans cet esprit que le present ouvrage se met a l'ecole de Billy Budd. Il saisit l'occasion qui nous est donnee, en explorant l'œuvre ultime de Melville, de renouer avec des interrogations dont nous ne pouvons nous passer.
Baeyer-Villiger Oxidation of β-Aryl Substituted Unsaturated Carbonyl Compounds with Hydrogen Peroxide and Catalytic Selenium Dioxide (1995)

Abstract A simple and cheap oxidative procedure using 30% H2O2 and catalytic SeO2 allows to transform 2-aralkylidenecycloalkanones and hydroxy- or alkoxybenzaldehydes to give, in high yields, enollactones and arylformates, respectively.