gebhart/patrepeval huggingface dataset:
Increased Plasma Vascular Endothelial Growth Factor (VEGF) as a Surrogate Marker for Optimal Therapeutic Dosing of VEGF Receptor-2 Monoclonal Antibodies (2004)

A major obstacle compromising the successful application of many of the new targeted anticancer drugs, including angiogenesis inhibitors, is the empiricism associated with determining an effective biological/therapeutic dose because many of these drugs express optimum therapeutic activity below the maximum tolerated dose, if such a dose can be defined. Hence, surrogate markers are needed to help determine optimal dosing. Here we describe such a molecular marker, increased plasma levels of vascular endothelial growth factor (VEGF), in normal or tumor-bearing mice that received injections of an anti-VEGF receptor (VEGFR)-2 monoclonal antibody, such as DC101. Rapid increases of mouse VEGF (e.g., within 24 hours) up to 1 order of magnitude were observed after single injections of DC101 in non-tumor-bearing severe combined immunodeficient or nude mice; similar increases in human plasma VEGF were detected in human tumor-bearing mice. RAFL-1, another anti-VEGFR-2 antibody, also caused a significant increase in plasma VEGF. In contrast, increases in mouse VEGF levels were not seen when small molecule VEGFR-2 inhibitors were tested in normal mice. Most importantly, the increases in plasma VEGF were induced in a dose-dependent manner, with the maximum values peaking when doses previously determined to be optimally therapeutic were used. Plasma VEGF should be considered as a possible surrogate pharmacodynamic marker for determining the optimal biological dose of antibody drugs that block VEGFR-2 (KDR) activity in a clinical setting.
Flavin-Catalyzed Generation of Diimide:  An Environmentally Friendly Method for the Aerobic Hydrogenation of Olefins (2005)

The first green and practical method for "aerobic hydrogenation" involving the use of hydrazine and an organocatalyst is described. Olefins can be hydrogenated by treatment with hydrazine in the presence of a 5-ethyl-3-methyllumiflavinium perchlorate (FlEt+.ClO4-) catalyst under O2 atmosphere to give the corresponding hydrogenated products in excellent yields along with environmentally benign water and molecular nitrogen as the only waste products.
Sense-antisense gene-pairs in breast cancer and associated pathological pathways (2015)

More than 30% of human protein-coding genes form hereditary complex genome architectures composed of sense-antisense (SA) gene pairs (SAGPs) transcribing their RNAs from both strands of a given locus. Such architectures represent important novel components of genome complexity contributing to gene expression deregulation in cancer cells. Therefore, the architectures might be involved in cancer pathways and, in turn, be used for novel drug targets discovery. However, the global roles of SAGPs in cancer pathways has not been studied. Here we investigated SAGPs associated with breast cancer (BC)-related pathways using systems biology, prognostic survival and experimental methods. Gene expression analysis identified 73 BC-relevant SAGPs that are highly correlated in BC. Survival modelling and metadata analysis of the 1161 BC patients allowed us to develop a novel patient prognostic grouping method selecting the 12 survival-significant SAGPs. The qRT-PCR-validated 12-SAGP prognostic signature reproducibly stratified BC patients into low- and high-risk prognostic subgroups. The 1381 SAGP-defined differentially expressed genes common across three studied cohorts were identified. The functional enrichment analysis of these genes revealed the GABPA gene network, including BC-relevant SAGPs, specific gene sets involved in cell cycle, spliceosomal and proteasomal pathways. The co-regulatory function of GABPA in BC cells was supported using siRNA knockdown studies. Thus, we demonstrated SAGPs as the synergistically functional genome architectures interconnected with cancer-related pathways and associated with BC patient clinical outcomes. Taken together, SAGPs represent an important component of genome complexity which can be used to identify novel aspects of coordinated pathological gene networks in cancers.
Multimodal learning using convolution neural network and Sparse Autoencoder (2017)

In the last decade, pattern recognition methods using neuroimaging data for the diagnosis of Alzheimer's disease (AD) have been the subject of extensive research. Deep learning has recently been a great interest in AD classification. Previous works had done almost on single modality dataset, such as Magnetic Resonance Imaging (MRI) or Positron Emission Tomography (PET), shown high performances. However, identifying the distinctions between Alzheimer's brain data and healthy brain data in older adults (age > 75) is challenging due to highly similar brain patterns and image intensities. The corporation of multimodalities can solve this issue since it discovers and uses the further complementary of hidden biomarkers from other modalities instead of only one, which itself cannot provide. We therefore propose a deep learning method on fusion multimodalities. In details, our approach includes Sparse Autoencoder (SAE) and convolution neural network (CNN) train and test on combined PET-MRI data to diagnose the disease status of a patient. We focus on advantages of multimodalities to help providing complementary information than only one, lead to improve classification accuracy. We conducted experiments in a dataset of 1272 scans from ADNI study, the proposed method can achieve a classification accuracy of 90% between AD patients and healthy controls, demonstrate the improvement than using only one modality.
Ureaplasmas and Human Disease (1990)

(1990). Ureaplasmas and Human Disease. Critical Reviews in Microbiology: Vol. 17, No. 3, pp. 161-168.
Detection of<i>Phytophthora capsici</i>in Pepper and Cucurbit Crops in Ohio with Two Commercial Immunoassay Kits (1994)

Phytophthora capsici was shown to be the principal species associated with Phytophthora blight of peppers and cucurbits in Ohio during 1992 and 1993. Both A 1 (31.5%) and A 2 (64.2%) compatibility types were found in peppers, and only A 2 isolates were obtained from cucurbits. Phytophthora cactorum was recovered from two cucurbit samples. The Alert Phytophthora «flow-through» immunoassay and the Agri-Screen multiwell ELISA kit E for Phytophthora were compared for their efficacy. The former detected P. capsici in pepper and cucurbit crops, and had the advantage of being rapid (10 min) and easy to perform. The latter was effective in detecting P. capsici in pepper tissue, but absorbance values for healthy cucurbit tissues were relatively high
Oseltamivir for treatment and prophylaxis of influenza infection (2009)

Oseltamivir is effective in reducing symptom burden in those with influenza A or B infection, and is preventative against developing infection after exposure. Emergence of naturally occurring or post-treatment oseltamivir-resistant influenza as well as an avian influenza pandemic may limit its future use as a monotherapeutic antiviral treatment agent.
Vaccinia Virus Entry, Exit, and Interaction with Differentiated Human Airway Epithelia (2007)

Variola virus, the causative agent of smallpox, enters and exits the host via the respiratory route. To better understand the pathogenesis of poxvirus infection and its interaction with respiratory epithelia, we used vaccinia virus and examined its interaction with primary cultures of well-differentiated human airway epithelia. We found that vaccinia virus preferentially infected the epithelia through the basolateral membrane and released viral progeny across the apical membrane. Despite infection and virus production, epithelia retained tight junctions, transepithelial electrical conductance, and a steep transepithelial concentration gradient of virus, indicating integrity of the epithelial barrier. In fact, during the first four days of infection, epithelial height and cell number increased. These morphological changes and maintenance of epithelial integrity required vaccinia virus growth factor, which was released basolaterally, where it activated epidermal growth factor 1 receptors. These data suggest a complex interaction between the virus and differentiated airway epithelia; the virus preferentially enters the cells basolaterally, exits apically, and maintains epithelial integrity by stimulating growth factor receptors.
Sapphire-fiber-based white-light interferometric sensor for high-temperature measurements (2005)

We present a fiber-optic temperature sensor with a single-crystal sapphire fiber as the light guide and a sapphire wafer as the sensing element. Temperature is determined by measurement of the thermal dependence of the wafer's optical thickness by use of white-light interferometry. We applied digital signal processing techniques to analyze the sensor's spectrum. A prototype sensor was tested to 1600 degrees C and demonstrated excellent reproducibility. An accuracy of +/- 0.2% full scale was obtained. The sensor is simple, small, and flexible, with potential advantages of batch fabrication and easy calibration.
Cutting Edge: Endotoxin Tolerance in Mouse Peritoneal Macrophages Correlates with Down-Regulation of Surface Toll-Like Receptor 4 Expression (2000)

Monocytes/macrophages exposed to LPS show reduced responses to second stimulation with LPS, which is termed LPS tolerance. In this study, we investigated molecular mechanism of LPS tolerance in macrophages. Mouse peritoneal macrophages pre-exposed to LPS exhibited reduced production of inflammatory cytokines in a time- and dose-dependent manner. Activation of neither IL-1 receptor-associated kinase nor NF-kappaB was observed in macrophages that became tolerant by LPS pretreatment, indicating that the proximal event in Toll-like receptor 4 (TLR4)-MyD88-dependent signaling is affected in tolerant macrophages. Although TLR4 mRNA expression significantly decreased within a few hours of LPS pretreatment and returned to the original level at 24 h, the surface TLR4 expression began to decrease within 1 h, with a gradual decrease after that, and remained suppressed over 24 h. A decrease in inflammatory cytokine production in tolerant macrophages well correlates with down-regulation of the surface TLR4 expression, which may explain one of the mechanisms for LPS tolerance.
Pseudomonas mesophilica, a New Species of Pink Bacteria Isolated from Leaf Surfaces (1979)

Eleven strains of pink-pigmented bacteria, isolated from the leaf surface of Lolium perenne (perennial rye grass), were compared with six marker strains and 50 pink-pigmented isolates from a variety of habitats. The organisms were examined for 146 unit characters, and the data were analyzed by the simple matching and Jaccard coefficients and the average-linkage algorithm. The Lolium strains formed a single, well-defined cluster. These isolates were gram-negative, oxidative rods which were motile by means of one to three polar flagella; the guanine-plus-cytosine content of the deoxyribonucleic acid of a representative strain was 65.8 ± 0.5 mol%. The organisms were classified in the genus Pseudomonas but could not be assigned to any previously defined species. A new species, Pseudomonas mesophilica, is proposed for these organisms; the type strain is A47 (= ATCC 29983 = ICPB 4095).
Complete amino acid sequences of five dimeric and four monomeric forms of metallothionein from the edible mussel <i>Mytilus edulis</i> (1993)

Cadmium-induced metallothioneins from the common sea mussel, Mytilus edulis, were shown to comprise of two groups of isoforms having apparent molecular masses of 10 kDa and 20 kDa. The 10-kDa group was resolved by anion-exchange chromatography into four fractions while the 20-kDa group was resolved into three fractions using this method. After metal removal and S-methylation of the cysteine residues using methyl-p-nitrobenzenesulphonate the complete amino acid sequences were determined. Five isoforms of the 20-kDa group were shown to possess monomeric units consisting of 71 amino acids. These proteins were distinct from the four 72-amino-acid proteins of the 10-kDa group. The FASTA algorithm has been used to compare the degree of similarity between the mussel metallothionein MT-10-IV isoform and other metallothioneins. The mussel MT-10-IV isoform exhibited substantial similarity to other molluscan metallothioneins. Moreover, the mussel metallothionein exhibited more similarity to vertebrate metallothioneins than to those of non-molluscan invertebrates, thus suggesting that the mussel metallothioneins are class I metallothioneins.
Isolation of products and intermediates of pancreatic prosomatostatin processing: use of fast atom bombardment mass spectrometry as an aid in analysis of prohormone processing (1987)

Major products and an intermediate in the proteolytic processing pathway of preprosomatostatin I from anglerfish (Lophius americanus) were purified and characterized. Proteolytic mapping by fast atom bombardment mass spectrometry was used to rapidly locate regions of the peptides whose masses deviated from those deduced from the cDNA sequence. Amino acid analysis and partial Edman sequencing were also used to confirm the structures. The protein structural data indicate a Glu for Gly substitution at position 83 of preprosomatostatin I (aPPSS-I, numbering from the initiator Met) relative to the cDNA sequence. Two of the peptides isolated, aPPSS-I (26-52) (7.5 nmol X g-1) and aPPSS-I (26-92) (49.5 nmol X g-1), define signal cleavage as occurring between Cys-25 and Ser-26. A partial sequence was obtained from fragment ions in the mass spectrum of a peptide corresponding to aPPSS-I (94-105) (58 nmol X g-1). The 14-residue somatostatin [SS-14 corresponding to aPPSS-I (108-121)] has previously been isolated [Noe, B. D., Spiess, J., Rivier, J. E., & Vale, W. (1979) Endocrinology (Baltimore) 105, 1410-1415]. Taken together, these peptides suggest a pathway for prosomatostatin I processing in which the residues corresponding to SS-14 and the immediately preceding 14 residues are cleaved from the prohormone via endoproteolysis (order of cleavage not determined). The fragment aPPSS-I (94-105) was isolated in lower yield than SS-14 and may represent a secondary site of cleavage. Subsequent cleavage at arginine-53 results in the minor peptide aPPSS-I (26-52).(ABSTRACT TRUNCATED AT 250 WORDS)
Changes in T‐cell subsets identify responders to FcR‐nonbinding anti‐CD3 mAb (teplizumab) in patients with type 1 diabetes (2015)

The mechanisms whereby immune therapies affect progression of type 1 diabetes (T1D) are not well understood. Teplizumab, an FcR nonbinding anti-CD3 mAb, has shown efficacy in multiple randomized clinical trials. We previously reported an increase in the frequency of circulating CD8(+) central memory (CD8CM) T cells in clinical responders, but the generalizability of this finding and the molecular effects of teplizumab on these T cells have not been evaluated. We analyzed data from two randomized clinical studies of teplizumab in patients with new- and recent-onset T1D. At the conclusion of therapy, clinical responders showed a significant reduction in circulating CD4(+) effector memory T cells. Afterward, there was an increase in the frequency and absolute number of CD8CM T cells. In vitro, teplizumab expanded CD8CM T cells by proliferation and conversion of non-CM T cells. Nanostring analysis of gene expression of CD8CM T cells from responders and nonresponders versus placebo-treated control subjects identified decreases in expression of genes associated with immune activation and increases in expression of genes associated with T-cell differentiation and regulation. We conclude that CD8CM T cells with decreased activation and regulatory gene expression are associated with clinical responses to teplizumab in patients with T1D.
From a Mess to Graphic Maps: Visualization of Large-Scale Heterogeneous Networks (2010)

This paper describes a visualization design for network information representation. The aim of the design is to provide graphical presentations of large-scale and complex networks and help network administrators to manage large-scale networks easily and detect failures on networks promptly. Central to the design is the visualization of network topologies with rich information about the device and connections within the network visually displayed. Based on the design, a prototype application has been implemented using the NetBeans platform, and it has been run over a university-scale network to test the performance.
Nonlinear Low Frequency Phenomenological Engine Modeling and Analysis (1987)

The paper contains a bibliography and discussion of recent activity in nonthermodynamic (low frequency) internal combustion engine model development where spark advance, fuel, throttle, and exhaust gas recirculation are the elected control variables. Modeling considerations are delineated and the modeling relationship to experimental verification is discussed. Examples with explicit methods of parameter determination and dynamic validation are presented.
A preliminary randomized study of growth hormone administration in Becker and Duchenne muscular dystrophies (2003)

The 3-month GH therapy in patients with DMD and BMD induces a hypertrophic response associated with a significant reduction of brain natriuretic peptide plasma levels and a slight improvement of systolic function, no changes in skeletal muscle function, and no side effects.
Image interpretation using multi-relational grammars (2002)

An approach to computational vision that is based on multiple levels of interpretation is presented. The step between each level is seen as taking place in three stages-parsing (in which features and groups of features in an image are given labels), interpreting (in which several interpretations are built, assuring that each feature is given at most one explanation in terms of a higher-level label), and pruning (in which some interpretations are discarded because of global constraints). The parsing and pruning steps are guided by multirelational grammars, a generalization of ordinary attribute grammars and of graph grammars. A bottom-up parsing algorithm for this class of grammars is presented, and their usefulness in image interpretation is illustrated by examples using both synthetic and real-world data.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Land Use and the Internal Operation of Farms (1939)

The problems associated with land use are not new to the South. As early as 1746 the systems of farming followed by Southern planters were exhausting our soils and exploiting labor; during the latter half of the eighteenth century Virginia and North Carolina planters were compelled to diminish tobacco production because of depleted soils. Efforts were made to solve this problem by substituting grain for tobacco production. When this method failed, the land was abandoned and new land cleared. But as the same systems of farming and the same practices were employed on the new as on the old land, the new land was soon exhausted.2 During the post-Colonial period little, if any, effective progress was made to check the rapid exhaustion of Southern soils. It is true that John Taylor, Edmund Ruffin, Martin Phillips, and other leaders did much to improve conditions and restore confidence by their continued and active advocacy of new farming methods, new combination of crops, including clover and cowpeas, and a more effective use of lime.3 The work of these pioneers was helpful, but in spite of their efforts, the Southern planters were unable or unwilling to place their farming on a sound physical basis.
Peloruside A, a novel antimitotic agent with paclitaxel-like microtubule- stabilizing activity. (2002)

Peloruside A is a novel secondary metabolite isolated from a New Zealand marine sponge, Mycale hentscheli, that has potent paclitaxel-like microtubule-stabilizing activity and is cytotoxic at nanomolar concentrations. Its 16-membered macrolide ring is similar to that of epothilone, a drug currently under clinical investigation as an anticancer agent. Like paclitaxel, peloruside A arrests cells in the G(2)-M phase of the cell cycle and induces apoptosis. The relatively simple structure of peloruside makes it suitable for the design and synthesis of analogues with improved tumor targeting and reduced tumor cross-resistance.
Travel scrapbooks: Creating rich visual travel narratives (2009)

The convergence of the Internet and ubiquitous technologies offers an unprecedented level of convenience for information collection, accessing, and sharing through mobile devices and Web services. Mobile devices have become increasingly context aware and connected to the Internet, which lowers the barriers for capturing and sharing contextual information (e.g. location and time). Web applications are increasingly taking advantage of the so-called 'long tail', offering specialized services to a small number of users and allowing them to annotate, produce and consume relevant information. This paper presents travel scrapbooks, an online service that automatically stitches information together from various online sources based on geotagged photos from social networks, and visually presents the information to the user in the form of a scrapbook metaphor.
Relative shear modulus reconstruction for visualization with no geometrical artifact (2010)

We previously reported several useful shear modulus reconstruction methods obtained from motion or static equations and reference shear moduli that yield an absolute reconstruction of shear modulus, density or inertia using the finite difference method (FDM) or finite element method (FEM) with strain tensor measurement (i.e., methods referred to as Methods A to C and F). Methods A to C are particularly useful for three-dimensional (3D) shear modulus reconstruction in an incompressible case or in the case of an inhomogeneous Poisson’s ratio by using the mean normal stress as an unknown, whereas Method F using a typical Poisson’s ratio is particularly useful when the reconstruction dimensionality is low or when the Poisson’s ratio is homogeneous. For instance, when using FDM, although Method B permits the absolute reconstruction of a mean normal stress by using a reference mean normal stress, Methods A and C yield biased mean normal stress reconstructions using no reference value and a quasi-reference value (e.g., zero), respectively. In this report, we describe our newly developed Methods D and E obtained from Methods A to C and F, which yield a unique relative shear modulus reconstruction with no geometrical artifact. In Method D, no reference shear modulus is used with Methods A to C and F, whereas in Method E, an arbitrary finite value (e.g., unity) is used with Methods A to C and F as a quasi-reference shear modulus at one or more arbitrary points (i.e., a quasi-reference point) or in an arbitrary region (i.e., a quasi-reference region) in the region of interest. That is, both Method D and Method E permit the visualization of the shear modulus distribution without using an absolute reference value (e.g., no reference material or typical value), which is particularly useful when dealing with deeply located tissues such as the liver and heart tissues. Methods D and E use iterative methods such as the conjugate gradient method to solve algebraic equations. As confirmed from simulated phantom deformation data, each version of Method E results in a higher convergence speed and reconstruction accuracy than the corresponding Method D. Although several versions of Method D using FEM are practically useful, Method E obtainable should be used for such relative reconstructions rather than the corresponding version of Method D, in combination with Methods A to C and F.
Follies of Power (2009)

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