gebhart/patrepeval huggingface dataset:
<title>Document structure analysis algorithms: a literature survey</title> (2003)

Document structure analysis can be regarded as a syntactic analysis problem. The order and containment relations among the physical or logical components of a document page can be described by an ordered tree structure and can be modeled by a tree grammar which describes the page at the component level in terms of regions or blocks. This paper provides a detailed survey of past work on document structure analysis algorithms and summarize the limitations of past approaches. In particular, we survey past work on document physical layout representations and algorithms, document logical structure representations and algorithms, and performance evaluation of document structure analysis algorithms. In the last section, we summarize this work and point out its limitations.
Robust elastic nonlinear waveform inversion; application to real data (1990)

Abstract Nonlinear elastic waveform inversion has advanced to the point where it is now possible to invert real multiple-shot seismic data. The iterative gradient algorithm that we employ can readily accommodate robust minimization criteria which tend to handle many types of seismic noise (noise bursts, missing traces, etc.) better than the commonly used least-squares minimization criteria. Although there are many robust criteria from which to choose, we have tested only a few. In particular, the Cauchy criterion and the sech criterion perform very well in both noise-free and noise-added inversions of numerical data.Although the real data set, which we invert using the sech criterion, is marine (pressure sources and receivers) and is very much dominated by unconverted P waves, we can, for the most part, resolve the short wavelengths of both P impedance and S impedance. The long wavelengths of velocity (the background) are assumed known. Because we are deriving nearly all impedance information from unconverted P waves in this inversion, data acquisition geometry must have sufficient multiplicity in subsurface coverage and a sufficient range of offsets, just as in amplitude-versus-offset (AVO) inversion. However, AVO analysis is implicitly contained in elastic waveform inversion algorithms as part of the elastic wave equation upon which the algorithms are based.Because the real-data inversion is so large--over 230,000 unknowns (340,000 when density is included) and over 600,000 data values--most statistical analyses of parameter resolution are not feasible. We qualitatively verify the resolution of our results by inverting a numerical data set which has the same acquisition geometry and corresponding long wavelengths of velocity as the real data, but has semirandom perturbations in the short wavelengths of P and S impedance.
Development and regeneration of the musculoskeletal system (1998)

Log in or Register Get new issue alertsGet alerts Enter your Email address: Wolters Kluwer Health may email you for journal alerts and information, but is committed to maintaining your privacy and will not share your personal information without your express consent. For more information, please refer to our Privacy Policy. Subscribe to eTOC Secondary Logo Journal Logo All Articles Images Videos Podcasts Blogs Advanced Search Toggle navigation Register Login HomeCurrent IssuePrevious Issues Current Orthopaedic PracticeCurrent Opinion in Orthopaedics (1999-2007)Clinical Orthopaedics and Related Research (1976-2007) Published Ahead-of-PrintCOP eNewsMy CollectionsJournal Info About the JournalEditorial BoardInformation for AuthorsAdvertisingOpen AccessSubscription ServicesReprintsRights and Permissions All Articles Images Videos Podcasts Blogs Advanced Search
A unified framework for coupling measurement in object-oriented systems (1999)

The increasing importance being placed on software measurement has led to an increased amount of research developing new software measures. Given the importance of object-oriented development techniques, one specific area where this has occurred is coupling measurement in object-oriented systems. However, despite a very interesting and rich body of work, there is little understanding of the motivation and empirical hypotheses behind many of these new measures. It is often difficult to determine how such measures relate to one another and for which application they can be used. As a consequence, it is very difficult for practitioners and researchers to obtain a clear picture of the state of the art in order to select or define measures for object-oriented systems. This situation is addressed and clarified through several different activities. First, a standardized terminology and formalism for expressing measures is provided which ensures that all measures using it are expressed in a fully consistent and operational manner. Second, to provide a structured synthesis, a review of the existing frameworks and measures for coupling measurement in object-oriented systems takes place. Third, a unified framework, based on the issues discovered in the review, is provided and all existing measures are then classified according to this framework. This paper contributes to an increased understanding of the state-of-the-art.
High polymorphism level of genomic sequences flanking insertion sites of human endogenous retroviral long terminal repeats (1999)

The polymorphism at the multitude of loci adjacent to human endogenous retrovirus long terminal repeats (LTRs) was analyzed by a technique for whole genome differential display based on the PCR suppression effect that provides selective amplification and display of genomic sequences flanking interspersed repeated elements. This strategy is simple, target-specific, requires a small amount of DNA and provides reproducible and highly informative data. The average frequency of polymorphism observed in the vicinity of the LTR insertion sites was found to be about 12%. The high incidence of polymorphism within the LTR flanks together with the frequent location of LTRs near genes makes the LTR loci a useful source of polymorphic markers for gene mapping.
Developmental Specificity of the Interaction between the Locus Control Region and Embryonic or Fetal Globin Genes in Transgenic Mice with an HS3 Core Deletion (1998)

The human beta-globin locus control region (LCR) consists of five erythroid-lineage-specific DNase I-hypersensitive sites (HSs) and is required for activation of the beta-globin locus chromatin domain and globin gene expression. Each DNase I-HS of the LCR consists of a highly conserved core element and flanking sequences. To analyze the functional role of the core elements of the HSs, we deleted a 234-bp fragment encompassing the core of HS3 (HS3c) from a beta-globin locus residing on a 248-kb beta-locus yeast artificial chromosome and analyzed its function in F2 progeny of transgenic mice. Human epsilon-globin gene expression was absent at day 10 and severely reduced in the day 12 embryonic erythropoiesis of mice lacking HS3c. In contrast, gamma-globin gene expression was normal in embryonic erythropoiesis but it was absent in definitive erythropoiesis in the fetal liver. These results indicate that the core element of HS3 is necessary for epsilon-globin gene transcription in embryonic cells and for gamma-globin gene transcription in definitive cells. Normal gamma-globin gene expression in embryonic cells and the absence of gamma-globin gene expression in definitive cells show that different HSs interact with gamma-globin gene promoters in these two stages of development. Such results provide direct evidence for developmental stage specificity of the interactions between the core elements of HSs and the promoters of the globin genes.
Prevention of doxorubicin myocardial toxicity in mice by reduced glutathione. (1986)

The effect of reduced glutathione (GSH) on acute myocardial toxicity due to doxorubicin (DXR) was investigated. At 20 mg/kg i.p. DXR was 100% lethal to BALB/c X DBA/2 F1 mice. At 500 or 1000 mg/kg i.p. GSH significantly decreased the lethality (P less than 0.01). Electron micrographs of the myocardium from DXR-treated mice showed narrowing of myofibrils, edematous cytoplasm, and mitochondrial swelling which were detectable at day 2, was strongest at day 14, but had disappeared by day 56. Light microscopic examination revealed that intercellular spaces between myocardial cells were widened at day 56, indicating shrinking of myocardial cells. These changes were significantly decreased by treatment with GSH (500 mg/kg i.p.). Treatment with DXR (14 mg/kg) significantly decreased myocardial non-protein sulfhydryl content (P less than 0.02) and administration of GSH (500 mg/kg) prevented the drop of non-protein sulfhydryl levels due to DXR treatment. Thus it was considered that administration of exogenous GSH contributes to prevention of the acute myocardial toxicity of DXR by increasing extracellular GSH levels and intracellular GSH synthesis, which detoxifies DXR-oxygen metabolites. The administration of GSH did not interfere with the antineoplastic effect of DXR against L1210 mouse leukemia.
A General Framework for Weighted Gene Co-Expression Network Analysis (2005)

Gene co-expression networks are increasingly used to explore the system-level functionality of genes. The network construction is conceptually straightforward: nodes represent genes and nodes are connected if the corresponding genes are significantly co-expressed across appropriately chosen tissue samples. In reality, it is tricky to define the connections between the nodes in such networks. An important question is whether it is biologically meaningful to encode gene co-expression using binary information (connected=1, unconnected=0). We describe a general framework for ;soft' thresholding that assigns a connection weight to each gene pair. This leads us to define the notion of a weighted gene co-expression network. For soft thresholding we propose several adjacency functions that convert the co-expression measure to a connection weight. For determining the parameters of the adjacency function, we propose a biologically motivated criterion (referred to as the scale-free topology criterion). We generalize the following important network concepts to the case of weighted networks. First, we introduce several node connectivity measures and provide empirical evidence that they can be important for predicting the biological significance of a gene. Second, we provide theoretical and empirical evidence that the ;weighted' topological overlap measure (used to define gene modules) leads to more cohesive modules than its ;unweighted' counterpart. Third, we generalize the clustering coefficient to weighted networks. Unlike the unweighted clustering coefficient, the weighted clustering coefficient is not inversely related to the connectivity. We provide a model that shows how an inverse relationship between clustering coefficient and connectivity arises from hard thresholding. We apply our methods to simulated data, a cancer microarray data set, and a yeast microarray data set.
Ligand-dependent Cross-talk between Steroid and Thyroid Hormone Receptors (1996)

Steroid and thyroid hormone receptors exhibit striking structural and functional similarity, suggesting that these nuclear receptors may enhance transcription of target genes by similar mechanisms. To address this issue, we studied transcriptional interference between progesterone and thyroid hormone receptors in vivo and in vitro. We observed that transcriptional interference occurred in a ligand-dependent manner between progesterone receptor-B (PR-B) and thyroid hormone receptor (TR) alpha or beta in transient transfection experiments. Ligand-occupied TRalpha or TRbeta, but not the unliganded receptor, strongly suppressed transactivation of a progesterone-responsive reporter gene by endogenous PRs in human breast carcinoma T47D cells. Ligand-dependent inhibitory cross-talk also occurred between transfected PR-B and TRalpha or TRbeta and vice versa in CV1 cells. This phenomenon did not require DNA binding by the "interfering" receptor but required it to be hormone-bound, indicating that a transcriptionally active form of the interfering receptor is essential for the interfering effect. To analyze further the mechanism of the ligand-dependent cross-talk, we reproduced transcriptional interference between PR and TR in a cell-free transcription system. We observed that the addition of triiodothyronine-bound recombinant TRbeta or a ligand binding domain (LBD) peptide(145-456) inhibited specifically transcriptional activation of a progesterone-responsive gene by endogenous PRs in nuclear extracts of T47D cells, while the basal level of transcription from a minimal TATA-promoter or transcription from an adenovirus major-late promoter remained unaffected. These results indicated that a transactivation function within the LBD of the interfering receptor TRbeta was likely to interact with a mediator protein(s), termed coactivator, that is distinct from basal transcription factors and is critical for efficient PR-induced transactivation. This concept was reinforced by biochemical evidence that treatment of T47D extracts with immobilized TRbeta LBD depleted the extract of the coactivator function in a triiodothyronine-dependent manner and markedly impaired progesterone-induced transactivation of progesterone response element-linked genes. Deletion of six amino acids(451-456) in the extreme COOH terminus of TRbeta resulted in a receptor that retained the ability to bind thyroid hormone but failed to inhibit progesterone-dependent transcription. Interestingly, these six amino acids are present in a region that is highly conserved among various nuclear hormone receptors and contains a ligand-dependent transactivation function, AF-2. Based on these results, we propose that a limiting coactivator protein(s) interacts with the AF-2 of PR or TR and mediates transactivation by the ligand-bound receptor. This regulatory molecule(s) may therefore serve as a common functional link between the pathways of hormone-inducible gene activation by various members of the nuclear receptor superfamily.
Monoclonal antibodies against oxidized low-density lipoprotein bind to apoptotic cells and inhibit their phagocytosis by elicited macrophages: Evidence that oxidation-specific epitopes mediate macrophage recognition (1999)

Apoptosis is recognized as important for normal cellular homeostasis in multicellular organisms. Although there have been great advances in our knowledge of the molecular events regulating apoptosis, much less is known about the receptors on phagocytes responsible for apoptotic cell recognition and phagocytosis or the ligands on apoptotic cells mediating such recognition. The observations that apoptotic cells are under increased oxidative stress and that oxidized low-density lipoprotein (OxLDL) competes with apoptotic cells for macrophage binding suggested the hypothesis that both OxLDL and apoptotic cells share oxidatively modified moieties on their surfaces that serve as ligands for macrophage recognition. To test this hypothesis, we used murine monoclonal autoantibodies that bind to oxidation-specific epitopes on OxLDL. In particular, antibodies EO6 and EO3 recognize oxidized phospholipids, including 1-palmitoyl 2-(5-oxovaleroyl) phosphatidylcholine (POVPC), and antibodies EO12 and EO14 recognize malondialdehyde-lysine, as in malondialdehyde-LDL. Using FACS analysis, we demonstrated that each of these EO antibodies bound to apoptotic cells but not to normal cells, whereas control IgM antibodies did not. Confocal microscopy demonstrated cell-surface expression of the oxidation-specific epitopes on apoptotic cells. Furthermore, each of these antibodies inhibited the phagocytosis of apoptotic cells by elicited peritoneal macrophages, as did OxLDL. In addition, an adduct of POVPC with BSA also effectively prevented phagocytosis. These data demonstrate that apoptotic cells express oxidation-specific epitopes-including oxidized phospholipids-on their cell surface, and that these serve as ligands for recognition and phagocytosis by elicited macrophages.
Treatment of Infections Associated with Surgical Implants (2004)

About half of all nosocomial infections are associated with indwelling devices. Infections associated with implanted surgical devices are particularly difficult to deal with because they can require prolonged antibiotic treatment and repeated surgical procedures. This review summarizes the diagnostic challenges and explains the approaches to managing infections that are associated with various devices, including prosthetic heart valves, vascular grafts, pacemakers and defibrillators, and joint prostheses.
Theoretic applicability of antisense-mediated exon skipping for Duchenne muscular dystrophy mutations (2009)

Antisense-mediated exon skipping aiming for reading frame restoration is currently a promising therapeutic application for Duchenne muscular dystrophy (DMD). This approach is mutation specific, but as the majority of DMD patients have deletions that cluster in hotspot regions, the skipping of a small number of exons is applicable to relatively large numbers of patients. To assess the actual applicability of the exon skipping approach, we here determined for deletions, duplications and point mutations reported in the Leiden DMD mutation database, which exon(s) should be skipped to restore the open reading frame. In theory, single and double exon skipping would be applicable to 79% of deletions, 91% of small mutations, and 73% of duplications, amounting to 83% of all DMD mutations. Exon 51 skipping, which is being tested in clinical trials, would be applicable to the largest group (13%) of all DMD patients. Further research is needed to determine the functionality of different in-frame dystrophins and a number of hurdles has to be overcome before this approach can be applied clinically. Hum Mutat 0, 1–7, 2009. © 2009 Wiley-Liss, Inc.
Mapping and partial characterization of proteases expressed by a CHO production cell line (2006)

The proteolytic activities expressed by a Chinese hamster ovary (CHO) cell line in the cultivation supernatant during the production of recombinant factor VIII were mapped with a broad spectrum protease assay and a series of different types of protease inhibitors. The destabilizing effect on the product emanated from a metalloproteinase, which could be effectively blocked by chelating agents to lead to product stabilization. Amino acid sequences of the isolated metalloproteinase were found to have sequence homology with matrix metalloproteinases (MMPs) MMP3, MMP10, and MMP12. Several species with metalloproteinase activity were characterized and found to be related to each other. The results indicate that an MMP pro-enzyme of >/=200 kDa was released from the CHO cells during the production phase. The enzyme expressed collagenase/gelatinase activity when activated. Due to autoproteolysis, a number of smaller, less specific MMPs were formed with the smallest form, a 19.4 kDa protein, being the most active. These results may be of particular relevance for other production processes using CHO cells for the expression of recombinant proteins.
Wireless home networks based on a hierarchical Bluetooth scatternet architecture (2005)

Wireless home networking is being addressed by numerous groups such as the HomeRF working group, and the Bluetooth consortium. Of these, Bluetooth technology promises a wider acceptance in term of home networking in the near future. The potential of easily embedding Bluetooth technology in communication devices, computing devices and home appliances make it a more attractive alternative to SWAP. Although the layer up to the data link layer has been standardized by the Bluetooth consortium, how complete home networking solutions can be realized, is still not clear. This paper addresses this aspect, and proposes a way to establish a complete home network deploying Bluetooth technology.
Vision-based obstacle detection and avoidance for the CWRU cutter Autonomous Lawnmower (2009)

This paper describes the vision-based obstacle detection system of the CWRU Cutter, an autonomous lawnmower developed for the annual “Institute of Navigation (ION) Autonomous Lawnmower Competition.” Unlike LIDAR sensors commonly found on autonomous vehicles, computer vision systems can provide similar information at drastically reduced prices. Though significantly more cost-effective than LIDAR, these systems have inherent problems due to changing lighting conditions and shadows. This paper investigates the use of image hue and intensity to create a robust, real-time vision-based obstacle detection system for use during the ION competition. Data abstraction methods used to process incoming images for easy combination of information from multiple sensors are also discussed. Using this system, CWRU Cutter correctly identified obstacles in 89% of frames containing fence, 78% of frames containing flowerbeds, and 84% of frames containing boundary lines.
Treatment of depression in HIV+men: Literature review and report of an ongoing study of testosterone replacement therapy (1996)

Our research program was designed to assess androgenic, anabolic, and mood effects of testosterone replacement therapy in human immunodeficiency virus positive (HIV+) men with significant immune suppression and hypogonadism. This article focuses on mood effects. Treatment consisted of biweekly intramuscular injections of testosterone cypionate at doses of 200 to 400 mg. Assessments included psychiatric evaluation using the Structured Clinical Interview for DSM-III-R, Hamilton Rating Scale for Depression, and Brief Symptom Inventory. This is an interim report of 73 men who completed at least eight weeks of treatment. Responders continued for four more weeks and then entered a double-blind placebo controlled discontinuation phase.At study entry, 49% had CD4 counts under 50, and 84% had an acquired immune deficiency syndrome (AIDS)-defining condition. In terms of sexual desire and function, 76% were clear-cut responders at Week 8. Of the 31 study completers who had mood problems at baseline, 26 (84%) were rated as much improved in mood. Mean changes in CD4 cell count and beta 2 microglobulin after treatment were not statistically significant. These findings suggest that testosterone replacement therapy has significant antidepressant effects for men with significant immunodeficiency and clinical manifestations of hypogonadism.
160 &#215; 244 Element PtSi Schottky-barrier IR-CCD image sensor (1985)

A 160 × 244 element IR-CCD image sensor was developed with PtSi Schottky-barrier detectors (SBD's) for thermal imaging in the 3.0-5.0-µm IR band. This imager has 80 × 40 µm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> pixels, a fill factor of 39 percent, and a chip size of 584 × 464 mil <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . It produces excellent quality thermal imaging with noise-equivalent temperature (NEΔT) of less than 0.1 K for operation at 30 frames/s with standard-TV-interlace f/2.3 optics, and one-point offset-type uniformity corrector. This paper describes the design, construction, and performance of 160 × 244 element IR-CCD imager and the characteristics of the PtSi Schottky-barrier detector elements.
Genomics of Sorghum (2008)

Sorghum (Sorghum bicolor (L.) Moench) is a subject of plant genomics research based on its importance as one of the world's leading cereal crops, a biofuels crop of high and growing importance, a progenitor of one of the world's most noxious weeds, and a botanical model for many tropical grasses with complex genomes. A rich history of genome analysis, culminating in the recent complete sequencing of the genome of a leading inbred, provides a foundation for invigorating progress toward relating sorghum genes to their functions. Further characterization of the genomes other than Saccharinae cereals may shed light on mechanisms, levels, and patterns of evolution of genome size and structure, laying the foundation for further study of sugarcane and other economically important members of the group.