gebhart/patrepeval huggingface dataset:
Relative importance of fluorescent siderophores and other factors in biological control of Gaeumannomyces graminis var. tritici by Pseudomonas fluorescens 2-79 and M4-80R (1991)

Pseudomonas fluorescens 2-79 suppresses take-all, a major root disease of wheat caused by Gaeumannomyces graminis var. tritici. The bacteria produce an antibiotic, phenazine-1-carboxylic acid (PCA), and a fluorescent pyoverdin siderophore. Previous studies have established that PCA has an important role in the biological control of take-all but that antibiotic production does not account fully for the suppressiveness of the strain. To define the role of the pyoverdin siderophore more precisely, mutants deficient in production of the antibiotic, the siderophore, or both factors were constructed and compared with the parental strain for control of take-all on wheat roots. In all cases, strains that produced PCA were more suppressive than those that did not, and pyoverdin-deficient mutant derivatives controlled take-all as effectively as their respective fluorescent parental strains. Thus, the phenazine antibiotic was the dominant factor in disease suppression and the fluorescent siderophore had little or no role. The siderophore also was of minor importance in a second strain, P. fluorescens M4-80R, that does not produce PCA. Strains 2-79 and M4-80R both produced substances distinct from the pyoverdin siderophore that were responsible for fungal inhibition in vitro under iron limitation, but these substances also had, at most, a minor role in disease suppression in situ.
Structure from motion causally integrated over time (2002)

We describe an algorithm for reconstructing three-dimensional structure and motion causally, in real time from monocular sequences of images. We prove that the algorithm is minimal and stable, in the sense that the estimation error remains bounded with probability one throughout a sequence of arbitrary length. We discuss a scheme for handling occlusions (point features appearing and disappearing) and drift in the scale factor. These issues are crucial for the algorithm to operate in real time on real scenes. We describe in detail the implementation of the algorithm, which runs on a personal computer and has been made available to the community. We report the performance of our implementation on a few representative long sequences of real and synthetic images. The algorithm, which has been tested extensively over the course of the past few years, exhibits honest performance when the scene contains at least 20-40 points with high contrast, when the relative motion is "slow" compared to the sampling frequency of the frame grabber (30 Hz), and the lens aperture is "large enough" (typically more than 30/spl deg/ of visual field).
Correlative feature analysis on FFDM (2008)

Identifying the corresponding images of a lesion in different views is an essential step in improving the diagnostic ability of both radiologists and computer-aided diagnosis (CAD) systems. Because of the nonrigidity of the breasts and the 2D projective property of mammograms, this task is not trivial. In this pilot study, we present a computerized framework that differentiates between corresponding images of the same lesion in different views and noncorresponding images, i.e., images of different lesions. A dual-stage segmentation method, which employs an initial radial gradient index (RGI) based segmentation and an active contour model, is applied to extract mass lesions from the surrounding parenchyma. Then various lesion features are automatically extracted from each of the two views of each lesion to quantify the characteristics of density, size, texture and the neighborhood of the lesion, as well as its distance to the nipple. A two-step scheme is employed to estimate the probability that the two lesion images from different mammographic views are of the same physical lesion. In the first step, a correspondence metric for each pairwise feature is estimated by a Bayesian artificial neural network (BANN). Then, these pairwise correspondence metrics are combined using another BANN to yield an overall probability of correspondence. Receiver operating characteristic (ROC) analysis was used to evaluate the performance of the individual features and the selected feature subset in the task of distinguishing corresponding pairs from noncorresponding pairs. Using a FFDM database with 123 corresponding image pairs and 82 noncorresponding pairs, the distance feature yielded an area under the ROC curve (AUC) of 0.81 +/- 0.02 with leave-one-out (by physical lesion) evaluation, and the feature metric subset, which included distance, gradient texture, and ROI-based correlation, yielded an AUC of 0.87 +/- 0.02. The improvement by using multiple feature metrics was statistically significant compared to single feature performance.
Fruits and vegetables are associated with lower lung cancer risk only in the placebo arm of the beta-carotene and retinol efficacy trial (CARET). (2003)

Despite the unexpected results from the beta-Carotene and Retinol Efficacy Trial (CARET) and similar supplementation trials showing that supplementation with beta-carotene increased, rather than decreased, lung cancer incidence, considerable interest remains in investigating how other compounds in fruits and vegetables may affect lung cancer risk. We used data from 14,120 CARET participants who completed food frequency questionnaires to examine associations of diet with lung cancer risk. After 12 years of follow-up (1989-2001), 742 participants developed lung cancer. We used Cox proportional hazards models to estimate multivariate relative risks (RRs) and 95% confidence intervals (CIs). Analyses were controlled for smoking, asbestos exposure, and other covariates. Analyses of specific botanical groups were also controlled for total fruit and vegetable intake. All models were stratified by CARET treatment arm, and all statistical tests were two-sided. Statistically significant associations of fruit and vegetable intake with lower lung cancer risk were restricted to the CARET placebo arm. The RR for highest versus lowest quintile of total fruit consumption in the placebo arm was 0.56 (95% CI, 0.39-0.81) with a two-sided P for trend = 0.003. Two specific botanical groups were associated with reduced risk of lung cancer. Compared with the lowest quintile of rosaceae fruit consumption, placebo participants in the top quintile had a RR of 0.63 (95% CI, 0.42-0.94; P for trend = 0.02); for cruciferae vegetables, the RR was 0.68 (95% CI, 0.45-1.04; P for trend = 0.01). We did not observe any statistically significant associations of fruit and vegetable intake with lung cancer risk among participants randomized to receive the CARET supplements (30 mg of beta-carotene and 25,000 IU of retinyl palmitate). This report provides evidence that plant foods have an important preventive influence in a population at high risk for lung cancer. However, persons who use beta-carotene supplements do not benefit from the protective compounds in plant foods.
Growth stresses and cracking in GaN films on (111) Si grown by metalorganic chemical vapor deposition. II. Graded AlGaN buffer layers (2005)

Growth stress and critical thickness for cracking on cooling in GaN films deposited by metalorganic chemical vapor deposition on (111) Si using graded AlGaN (from AlN to GaN) buffer layers, 0.1–2μm thick, were examined. During the growth of the graded buffer layers, the incremental growth stress was observed to change from tension (∼+1to+1.5GPa) to compression (∼−1to−1.7GPa). An interruption in the composition grading during the compressive segment, followed by continued growth of the AlGaN composition at the interruption, resulted in the eventual transition to a tensile stress in films as thick as 0.75μm. A similar stress evolution, a reduction in the value of the initial compressive stress with thickness, was observed during the growth of 1-μm-thick GaN layers on 2-μm-thick graded AlGaN buffer layers. Such stress evolution, at thickness far beyond coalescence, cannot be explained by initial grain coalescence stresses alone. A combination of compressive stress generation due to the change in AlGaN composition and tensile stress generation due to the lateral increase in grain size with thickness are used to explain these results. In the GaN layer, the thickness at which the compressive-to-tensile stress transition takes place increases and the magnitude of the final stress decreases with an increase in the thickness of the graded AlGaN buffer layer. X-ray diffraction results show that this is due to increasing accommodation of the tensile stress generating microstructural changes within the thickness of the AlGaN buffer layer, thus reducing the level of tensile stress in the subsequent GaN layer. A 1-μm-thick graded AlGaN buffer layer enabled the growth of a 1-μm-thick GaN layer that is crack-free after dicing at room temperature.
Towards development of stable formulations of a live attenuated bacterial vaccine: A preformulation study facilitated by a biophysical approach (2009)

Development of optimal formulation conditions stabilizing live attenuated bacterial vaccines is impeded by traditional methods used for viability measurement. To facilitate preformulation studies of such vaccines, spectroscopic techniques capable of providing real-time and high throughput information have been employed to obtain a global stability profile for a live attenuated Ty21a bacterial typhoid vaccine over a wide range of pH (4 to 8) and temperature (10 to 85 degrees C). Using the data obtained from fluorescence and circular dichroism techniques, an empirical phase diagram (EPD) has been subsequently constructed, which suggests that Ty21a cells exist in at least four apparent physical phases related to different viability states, with the most stable phase at pH 6 and 7 at temperatures below 30 degrees C. A slightly basic pH (pH 8) appears to decrease the fluidity of the cell membrane, whereas acidic pH conditions are detrimental to membrane integrity over the entire temperature range. Based on the above stability profile, a fluorescence-based high throughput screening assay has been developed to test the stabilizing effects of various compounds at different concentrations. Amongst other promising stabilizers, 10% sucrose and 0.15 M glutamic acid display the greatest protective effects, with an increase of about 10 degrees C in the transition temperature of Ty21a cells. Preliminary studies have also been performed on foam dried formulations as an alternative approach to further stabilize Ty21a cells. The data show that 10% sucrose and trehalose both increase the in-process and storage stabilities of the cells.
10   μ m minority-carrier diffusion lengths in Si wires synthesized by Cu-catalyzed vapor-liquid-solid growth (2009)

The effective electron minority-carrier diffusion length, Ln,eff, for 2.0 μm diameter Si wires that were synthesized by Cu-catalyzed vapor-liquid-solid growth was measured by scanning photocurrent microscopy. In dark, ambient conditions, Ln,eff was limited by surface recombination to a value of ≤0.7 μm. However, a value of Ln,eff=10.5±1 μm was measured under broad-area illumination in low-level injection. The relatively long minority-carrier diffusion length observed under illumination is consistent with an increased surface passivation resulting from filling of the surface states of the Si wires by photogenerated carriers. These relatively large Ln,eff values have important implications for the design of high-efficiency, radial-junction photovoltaic cells from arrays of Si wires synthesized by metal-catalyzed growth processes.
Otterman: A Novel Approach of Spark Auto-tuning by a Hybrid Strategy (2018)

Spark has become a very attractive platform for big data analytics in recent years due to its unique advantages such as parallelism, fault tolerance, and complexity associated with clusters setup. On the spark platform, users can adjust parameter configurations according to different job requirements and specific applications to optimize performance. This leads to a problem that we can't ignore, Spark already has more than 180 parameters, and its huge combination of parameters means that we can't rely on manual tuning to grasp the impact of all parameters on performance. In order to solve the problem of relying heavily on expert experience and manual operation, we propose Otterman, a parameters optimization approach based on the combination of Simulated Annealing algorithm and Least Squares method, which can help us dynamically adjust parameters according to job types to obtain optimal configuration to improve performance. Simulated Annealing can find the optimal solution, but has poor convergence. We make use of the Least Squares method to effectively improve the speed at which the former converges to the optimal solution. Otterman is simple and easy to perform, with no additional cost. The effectiveness of the approach is verified by experiments, the results show that Otterman's average performance has increased by 30% compared to the default parameters configuration, with an accuracy of about 68%.
Future Directions in the Pharmacologic Therapy of Chronic Obstructive Pulmonary Disease (2005)

Current therapy for chronic obstructive pulmonary disease (COPD) fails to alter its relentless progression. This remains a significant challenge and unmet need. A recent advance is the demonstration that treatment with a fixed dose of an inhaled corticosteroid and a long-acting beta2-agonist in COPD improves lung function and quality of life, and reduces exacerbation more effectively than either drug alone. Other improvements include the introduction of tiotropium, a once-daily anticholinergic. In advanced clinical development are other once-daily bronchodilators and combinations of anticholinergic drugs and beta2-agonists. Increased understanding of the pathogenesis of COPD has led to novel drugs aimed at inhibiting targets, including phosphodiesterase 4, proteases, and various inflammatory mediators. Furthermore, COPD is increasingly seen as a systemic disorder or, indeed, may be a pulmonary manifestation of a complex pathophysiologic response to chronic inhalation of toxic irritants and associated with aging. Future therapy may involve better understanding of how best to target existing drugs used to treat cardiovascular disorders associated with smoking, such as atherosclerosis and hypercoagulability, and the development of new drugs that target systemic and metabolic manifestations that either result from or coexist with chronic lung inflammation, hypoxia, and cardiovascular disease in COPD.
Activating En Passant (2007)

Autotransporters are a family of bacterial virulence proteins that are first translocated across the inner membrane and then inserted into the outer membrane. The smaller C-terminal domain adopts a β barrel structure that spans the outer membrane and serves as a transitway for the larger N-terminal “passenger” domain, which is transported through the barrel; some passenger domains are released into the extracellular space by proteolysis.
Pentacene-Based Dendrimers: Synthesis and Thin Film Photoconductivity Measurements of Branched Pentacene Oligomers (2009)

The synthesis of pentacene-based dendrimers has been achieved via esterification of 1,3,5-benzenetricarboxylic acid and unsymmetrical pentacene 4 possessing a hydroxy group. Dendrimers 1 (C(183)H(204)O(9)Si(9), 2800 g mol(-1)) and 2 (C(540)H(570)O(30)Si(24), 8214 g mol(-1)) are characterized by (1)H and (13)C NMR, IR, UV-vis, and fluorescence spectroscopy, as well as mass spectrometry. These branched oligomeric materials are benchtop stable and soluble in common organic solvents, allowing for solution cast formation of thin films. Photocurrent and photocurrent yield measurements of these films reveal improved efficiency in photogenerated conduction for dendrimers in comparison to linearly connected pentacene-based polymers.
Bispecific CD3 × CD19 diabody for T cell-mediated lysis of malignant human B cells (1998)

For the treatment of minimal residual disease in patients with leukemias and malignant lymphomas, we constructed a heterodimeric diabody specific for human CD19 on B cells and CD3epsilon chain of the T cell receptor complex. The bispecific diabody was expressed in Escherichia coli using a vector containing a dicistronic operon for co-secretion of V(H)3-V(L)19 and V(H)19-V(L)3 single-chain Fv fragments (scFv). It was purified in one step by immobilized metal affinity chromatography (IMAC) from the periplasmic extract and culture medium. Flow cytometry experiments revealed specific interactions of the diabody with both CD3 and CD19 positive cells, to which it bound with affinities close to those of the parental scFvs. It was less stable than anti-CD3 scFv but more stable than anti-CD19 scFv when incubated in human serum at 37 degrees C. In cytotoxicity tests, the diabody proved to be a potent agent for retargeting peripheral blood lymphocytes to lyse tumor cells expressing the CD19 antigen. The efficiency of cell lysis compared favorably with that obtained with a bispecific antibody (BsAb) of the same dual specificity that was prepared by the quadroma technique.
A Novel Rhetorical Structure Approach for Classifying Arabic Security Documents (2009)

Security Documents classification is aimed at securing documents from being illegally disclosed.Classifying a portion of a document as a 'secret' depends on the type of effect its disclosure will have in an organization.In this respect, Information is classified according to their critical semantic (i.e. its context or value and intended uses or audience at particular time or situation).Understanding the semantic of a document is not an easy task.The rhetorical structure theory (RST) is one of the leading theories that have been applied successfully in text processing and understanding.In this paper, we will describe a novel approach to automatically classify Arabic Security documents using RST.
Identification of the plasma membrane receptor for interleukin‐1 on mouse thymoma cells (1987)

The plasma membrane receptor for interleukin-1 (IL-1) has been characterized from mouse EL4-6.1 thymoma cells. Following binding of IL-1 to surface labeled EL4-6.1 cells, the IL-1 binding molecule was immuno-precipitated using a rabbit antiserum against the hormone. The putative IL-1 receptor is a membrane-associated glycopeptide of Mr = 82,000 containing probably two or three N-linked glycan units as indicated by its conversion into a Mr = 60,000 polypeptide upon deglycosylation with endo-beta-N-glycosidase F.
Chemokines and their Receptors as Therapeutic Targets: The Role of the SDF-1 / CXCR4 Axis (2004)

SDF-1 and CXCR4 are an important chemokine ligand/receptor pair, which play a crucial role in numerous biological processes including hematopoiesis, cardiogenesis, vasculogenesis, neuronal development and immune cell trafficking. They have also been implicated in various pathological conditions such as cancer, infection with the human immunodeficiency virus (HIV) and various inflammatory conditions. Numerous pharmacological agents exist that can modulate SDF-1/CXCR4-induced responses both in vitro and in vivo. The usefulness of these agents in affecting the outcome of pathological conditions influenced by the SDF-1/CXCR4 axis is currently being investigated. Whilst some of these compounds have been shown to be safe and well tolerated in phase 1 clinical trials, the full repercussions of SDF-1/CXCR4 inhibition or stimulation on normal physiological functions are yet to be appreciated. Inhibition of the SDF-1/CXCR4 axis may have positive effects in regulating tumour metastasis and growth, however, this may also negate immunological responses through dysregulated lymphocyte trafficking and contribute to disruption of hematopoiesis. As with any therapy, the usefulness of this type of intervention will require a balance between its positive effect on the disease outcome and deleterious effects on normal physiological functions. A greater understanding of the role of SDF-1 and CXCR4 in the body will allow greater manipulation of this important biological axis to affect disease outcome. Greater knowledge of the SDF-1 interaction with its receptor and the structural elements within CXCR4 mediating the different signalling events, resulting in SDF-1-induced responses, will also enhance future drug design.
Extracting meaningful information from video sequences for intelligent searches. (2005)

Video and image data are knowledge-rich sources of information, but their utility for current and future systems is limited without autonomous methods for understanding and characterizing their content. Semantic-based video understanding may benefit systems dedicated to the detection of insiders, alarm patterns, unauthorized activities in material monitoring applications, etc. A direct benefit of this technology is not only intelligent alarm analysis, but the ability to browse and perform query-based searches for useful and interesting information after video data has been acquired and stored. These searches can provide a tremendous benefit for use in intelligence agency, government, military, and DOE site investigations. This report provides an initial investigation into the algorithms and methods needed to characterize and understand video content. Such algorithms include background modeling, detecting dynamic image regions, grouping dynamic pixels into coherent objects, and robust tracking strategies. With solid approaches for addressing these problems, analysis can be performed seeking to recognize distinctive objects and their motions leading to semantic-based video searches.
Cell kinetic evaluation of human colonic aberrant crypts. (Colorectal Cancer Study Group of the University of Modena and the Health Care District 16, Modena, Italy). (1993)

Foci of aberrant crypts (ACF) have been observed on the unsectioned, methylene blue-stained mucosal surface of the human colon. Experimental evidence and the histological features of the lesions suggest that they might be early events in colon cancer development. The main objective of the present study was to evaluate cell kinetic properties of ACF in the human colon. Five samples of colon mucosa were collected immediately after operation following the administration of 500 mg of 5'-bromo-2'-deoxyuridine prior to surgery. ACF were then identified on the fixed, unsectioned, methylene blue-stained mucosal surface under a light microscope. Some specimens containing ACF were serially sectioned perpendicular to the luminal surface of the intestine, along with specimens of normal-appearing mucosa. Several sections were prepared for the immunohistochemical identification of 5'-bromo-2'-deoxyuridine-incorporating cells (in the S phase of the cell cycle). The results of this study demonstrated that aberrant crypts have more cells per crypt than normal glands. Total labeling index and labeling index values in each of the five longitudinal compartments in which each crypt was divided showed an increased total proliferative activity in all ACF examined, although limited to the lower crypt compartments in almost all aberrant crypts evaluated. These findings are in keeping with previous cell kinetic studies and observations in experimental animals and provide evidence of the involvement of human aberrant crypts in the stepwise process leading from normal mucosa to colon cancer.