gebhart/patrepeval huggingface dataset:
Therapeutic Strategies Using the Aromatase Inhibitor Letrozole and Tamoxifen in a Breast Cancer Model (2004)

First-line letrozole therapy extends time for tumor progression in this model relative to the other treatment regimens tested. However, further studies are needed to determine the most effective second-line therapy for tumors that progress on letrozole.
Referring Image Segmentation via Recurrent Refinement Networks (2018)

We address the problem of image segmentation from natural language descriptions. Existing deep learning-based methods encode image representations based on the output of the last convolutional layer. One general issue is that the resulting image representation lacks multi-scale semantics, which are key components in advanced segmentation systems. In this paper, we utilize the feature pyramids inherently existing in convolutional neural networks to capture the semantics at different scales. To produce suitable information flow through the path of feature hierarchy, we propose Recurrent Refinement Network (RRN) that takes pyramidal features as input to refine the segmentation mask progressively. Experimental results on four available datasets show that our approach outperforms multiple baselines and state-of-the-art1.
Heparin‐derived oligosaccharides: Affinity for acidic fibroblast growth factor and effect on its growth‐promoting activity for human endothelial cells (1989)

The minimal structural requirements for the interaction of heparin with acidic fibroblast growth factor (aFGF) were investigated. Oligosaccharides (tetra- to decasaccharides) obtained by nitrous acid depolymerisation of standard heparin were separated by affinity chromatography on Sepharose-immobilised aFGF. The shortest fragment retained by the affinity column at 0.2 M NaCl and eluted at 1 M NaCl was a "regular" hexasaccharide, a trimer of the most abundant disaccharide sequence in heparin. More complex octa- and decasaccharides were also retained by the column. The oligosaccharides eluted by 1 M NaCl from the affinity column ("high-affinity" oligosaccharides) and those washed from the column at 0.2 M NaCl ("low-affinity" oligosaccharides) were compared for their capacity to protect aFGF from proteolysis and to potentiate its mitogenic activity. At a low ionic strength, all oligosaccharides tested, except the "regular" disaccharide, protected aFGF against trypsin and collagenase digestion. At higher ionic strength (greater than 0.2 M NaCl), only high-affinity oligosaccharides showed a protective effect. The high-affinity oligosaccharides (hexa- to decasaccharides) potentiated the mitogenic activity of aFGF, as measured by [3H]thymidine incorporation into DNA of human fibroblasts. The effect of the oligosaccharides on human endothelial cell proliferation was more complex: inhibition of proliferation was observed in the presence of serum and low concentrations of aFGF (1-5 ng/ml) and potentiation in the presence of higher concentrations of aFGF. The potentiating effect increased as a function of molecular size of the heparin fragments and, for a given size, as a function of the anionic charge of the oligosaccharide. Our results suggest that inhibition of cell proliferation by heparin may result from interference with an autocrine basic FGF-like activity.
Effects of Rapamycin on Cultured Hepatocyte Proliferation and Gene Expression (1992)

Rapamycin, a potent immunosuppressive drug that disrupts normal signal-transduction processes, inhibited hepatocyte proliferation without evidence of inherent cytotoxicity in rat hepatocytes cultured in conventional medium or in a medium enriched with epidermal growth factor. The antiproliferative effect was dose dependent, uninfluenced by the concentration of epidermal growth factor in the medium and long lasting after a brief exposure. The effect of rapamycin was unaltered by the concomitant presence of FK 506 in the medium, suggesting that different binding affinities of these two drugs or even a separate rapamycin binding site may exist. Hepatocytes harvested 12 and 24 hr after partial hepatectomy were progressively less responsive to the antiproliferative effect of rapamycin. The gene expression of transforming growth factor-beta was reduced under in vivo rapamycin treatment, but at the same time the gene expression of albumin and glyceraldehyde-3-phosphate dehydrogenase was unchanged or increased. The experiments confirm that rapamycin has inherent growth-control qualities, and they strengthen the hypothesis that the recently defined immunophilin network is central to many aspects of cellular growth control.
Role of Rho Family Proteins in Phospholipase D Activation by Growth Factors (1997)

Treatment of fibroblasts with growth factors results in activation of phospholipase D (PLD). In order to determine the role of the Rho family of small GTPases in growth factor-mediated PLD activation, we used cells transfected with wild type and mutant Rac1. In response to epidermal growth factor (EGF), PLD activity was greatly increased in Rat1 fibroblasts expressing wild type Rac1 (wtRac1), and completely abrogated in cells expressing dominant negative N17Rac1, consistent with Rac1 mediating the action of this growth factor. In contrast, in cells treated with platelet-derived growth factor (PDGF) or phorbol ester, the wtRac1 cells showed little or no enhancement of PLD activity, and the response was not affected in the N17Rac1 cells, implying that Rac1 played a minimal role in the activation of PLD by PDGF or protein kinase C. Both growth factors produced an attenuated PLD response in cells expressing constitutively active V12Rac1, but these cells showed other changes, including altered morphology, increased basal PLD, and decreased growth factor receptor autophosphorylation. The effects of EGF and PDGF on phosphoinositide phospholipase C activity were not enhanced in cells expressing wtRac1 or inhibited in those expressing N17Rac1. In cells expressing constitutively active V12Rac1, basal phosphoinositide phospholipase C was elevated, but there were no significant effects of EGF or PDGF. We used C3 transferase of Clostridium botulinum, which ADP-ribosylates and inactivates RhoA, to investigate the involvement of RhoA in the activation of PLD by PDGF. Cells expressing wtRac1 and N17Rac1 showed a decreased PLD in response to PDGF when treated with C3 transferase, indicating a role for RhoA. In summary, these data indicate a major role for Rac1 in the activation of PLD by EGF, but not PDGF or protein kinase C.
Microfluidic Exploration of the Phase Diagram of a Surfactant/Water Binary System (2007)

We investigate the behavior of a binary surfactant solution (AOT/water) as it is progressively concentrated in microfluidic evaporators. We observe in time a succession of phase transitions from a dilute solution up to a dense state, which eventually grows and invades the microchannels. Analyzing these observations, we show that, with a few experiments and a limited amount of material, our microdevices permit a semiquantitative screening of the equilibrium phase diagram as well as a few kinetic observations.
Intelligent media agents in interactive television systems (2002)

Future interactive television applications are the upcoming front-end to interactive radio, television, video rental, home shopping, multimedia communication, and information retrieval. The challenge of an interactive television system is not that the medium is digital, nor the ability of browsing media resources, nor reception of multiple kinds of media. Users do not need more information than today. The colleague is to provide information which corresponds to users' interests and needs. This paper describes the vision of a multimedia iTV system whose appearance is personally adapted for each user. The concept personal iTV systems is presented by explaining the task of personalization and the technical fundamentals of intelligent assistance.
Breast Cancer — Loss of PTEN Predicts Resistance to Treatment (2004)

A new study uncovers a mechanism by which trastuzumab (Herceptin) counters the progression of cancer. The findings point to a subgroup of patients who are likely to have a response to treatment.
Disregulated Expression of the Th2 Cytokine Gene in Patients with Intraoral Squamous Cell Carcinoma (2003)

It has been seen that advanced stage oral squamous cell carcinoma is associated with impaired T-cell function and higher antibody response. In order to find out if such immune disregulation is associated with alteration of T-helper (Th) type CD4+ T-cell phenotype leading to altered cytokine production, we studied the Th-like cytokine profile in 35 oral squamous cell carcinoma patients and 21 normal controls. Concomitant expression of both Th1 and Th2 cytokine genes was studied by reverse transcription and Polymerase Chain Reaction (PCR) based amplification (RT-PCR) of mRNA extracted from freshly isolated peripheral blood mononuclear cells (PBMC) using specific primers for Interferon (IFN)-gamma, Interleukin (IL)-2, IL-4 and IL-10. Almost 63% of oral cancer patients showed polarization of a Th-like cytokine response as compared to 33% of the normal controls while 66.6% of normal controls showed a predominantly non-polarized Th0 response. Expression of IFN-gamma and IL-2 genes was more commonly seen in the early stage of the disease (p < 0.02) whereas majority of advanced stage tumours was associated with enhanced expression of IL-4 and IL-10 but not IFN-gamma and IL-2 genes. Patients with lymphnode metastases and poorly differentiated tumours expressed IL-4 and IL-10 more frequently with concomitant suppression of IFN-gamma and IL-2 genes. It seems therefore, that the development of oral squamous cell carcinoma leads to polarization of cytokine gene expression that is skewed towards the Th1-like response in the early stage. However, increasing tumour load and lymphnode invasion suppresses Th1 cytokine genes, thus skewing it toward a Th2-like cytokine response.
Retrieval of reflections from seismic background‐noise measurements (2007)

The retrieval of the earth's reflection response from cross‐correlations of seismic noise recordings can provide valuable information, which may otherwise not be available due to limited spatial distribution of seismic sources. We cross‐correlated ten hours of seismic background‐noise data acquired in a desert area. The cross‐correlation results show several coherent events, which align very well with reflections from an active survey at the same location. Therefore, we interpret these coherent events as reflections. Retrieving seismic reflections from background‐noise measurements has a wide range of applications in regional seismology, frontier exploration and long‐term monitoring of processes in the earth's subsurface.
Basic Science Symposium I: Bone Graft Substitutes (2008)

Bone graft substitutes is a general term to describe any material used to aid in regeneration of bone, such as in a fracture, or in promotion of bone, such as in a spine fusion. There is a wide spectrum of materials used today for the purpose of grafting; however, their ultimate goal remains the
Improved maize reference genome with single-molecule technologies (2017)

Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome, our assembly features a 52-fold increase in contig length and notable improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed more than 130,000 intact transposable elements, allowing us to identify transposable element lineage expansions that are unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by single-molecule real-time sequencing. In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes.
Statistical analysis of sensor-based milk parlour data to support dairy cow production and health management. (1997)

Sensor measurements can be used in dairy farming for the detection of heat and diseases. A new model has been developed to process the measured variables in a combined way. It is based on time series models for yield, temperature, conductivity and activity, and a probability distribution for the concentrates leftovers. The parameters of the time series models and the probabilities are fitted on-line for each cow after each milking by Kalman filters. This makes it possible to combine the variables and to generate cow-specific alerts. Some results are given.
The adeno-associated virus (AAV) Rep protein acts as both a repressor and an activator to regulate AAV transcription during a productive infection (1997)

Adeno-associated virus (AAV) uses three promoters, p5, p19, and p40, to regulate viral gene expression. The p5 and p19 promoters direct the synthesis of the viral regulatory proteins, Rep78 and -68 and Rep52 and -40, respectively. The p5 Rep proteins bind a linear 22-bp sequence, the Rep binding element (RBE), that is within both the terminal repeat (TR) and the p5 promoter. In the absence of helper virus, all four Rep proteins have been shown to reduce transcription from the viral p5 and p19 promoters. In this report, we focus on the roles of these proteins and the RBEs in controlling transcription during a productive infection, that is, in the presence of adenovirus. We find that in the presence of adenovirus, the p5 RBE represses p5 transcription while the RBE in the TR activates p5. However, both the TR RBE and the p5 RBE transactivate the p19 and p40 promoters. The fact that the p5 RBE-Rep complex can transactivate p19 and p40 while repressing p5 suggests that Rep78/68 is both a repressor and a transactivator. Rep repression of p5 is specific for the p5 RBE, as other p5 promoter elements do not support this activity. We also demonstrate that in the presence of adenovirus, the p19 Rep proteins, which do not bind to the RBE, can eliminate repression of the p5 promoter by Rep78 and Rep68. This may occur by the association of Rep52 with Rep78 or Rep68 to produce a Rep78/68-Rep52 protein complex which can be detected in vivo by immunoprecipitation. Finally, two Rep mutants that were deficient in RBE binding and transactivation but positive for p5 repression were identified. These mutants may define interaction domains involved in making contacts with other proteins that facilitate repression. These observations suggest a mechanism for controlling the p5 and p19 mRNA levels during a productive AAV infection.
Something of value--energy from wood on rangelands. (1981)

This material was digitized as part of a cooperative project between the Society for Range Management, the National Agricultural Library, and the University of Arizona Libraries.
Intein-mediated purification of cytotoxic endonuclease I-TevI by insertional inactivation and pH-controllable splicing (2002)

An intein-mediated approach was developed for expression and affinity purification of a protein that is lethal to Escherichia coli. The protein, I-TevI, is an intron-encoded endonuclease. The approach involved the insertional inactivation of I-TevI with a controllable mini-intein placed in front of a cysteine required for splicing (an I-TevI::intein fusion). The purification was facilitated by a chitin-binding domain inserted into the mini-intein. Affinity purification of the I-TevI::intein fusion precursor on a chitin column was followed by pH-controllable splicing to restore the structure and function of I-TevI. To study the impact of the insertion context on I-TevI inactivation, the chimeric intein was inserted independently in front of seven cysteines of I-TevI. One of the seven intein integrants yielded I-TevI of high activity. This technique is, in principle, generalizable to the expression and purification of other cytotoxic proteins and is amenable to scale-up.
Modern-Day Clinical Course of Type 1 Diabetes Mellitus After 30 Years' Duration (2009)

The frequencies of serious complications in patients with T1DM, especially when treated intensively, are lower than that reported historically.
Interfacial Energy Effects on the Electric Field Alignment of Symmetric Diblock Copolymers (2003)

The alignment of diblock copolymer microdomains by an electric field depends on the segmental interaction between two blocks and the difference in the interfacial energies of each block with the substrate. Morphologies having mixed orientations are predicted when the difference in the interfacial energies of the two blocks is large. By modifying a surface with random copolymer brushes, interfacial energies were controlled and the influence of interfacial energy on the orientation of the copolymer microdomains by an electric field was examined. Complete alignment of the lamellar microdomains was achieved only when the interfacial interactions were balanced. In all other cases, lamellae adjacent to the substrate were oriented parallel to the substrate surface, whereas in the center of the sample the lamellae oriented in the direction of the applied field. These results can be ascribed to a pathway-dependent alignment and a high energetic barrier to achieve complete reorientation of the lamellae adjacent to the surface.
Impact of the next generation DNA sequencers. (2009)

New generation sequencers have been developed with a strong impact on genomics. These sequencers are based on a principle different from the Sanger method, and can sequence one to several million templates in a single run, albeit read length is relatively small. The current large-scale efforts are: 1) complete genome sequencing of 1,000 individuals, the primary objective of which is identification of rare SNP variants, not identified by the international HapMap project; 2) large-scale sequencing of cancer genomes to construct a complete catalog of genomic changes. These sequencers are also being applied in the identification of new infectious agents. Steady increase in data production capacity and decrease of cost will definitely make the sequencers a powerful diagnostic tool, especially for screening of all genetic diseases. On the contrary, statistical problems inherent to large data sets need to be solved before application to specific problems in medical science.
Ligand association rates to the inner-variable-domain of a dual-variable-domain immunoglobulin are significantly impacted by linker design (2011)

The DVD-Ig (TM) protein is a dual-specific immunoglobulin. Each of the two arms of the molecule contains two variable domains, an inner variable domain and an outer variable domain linked in tandem, each with binding specificity for different targets or epitopes. One area of on-going research involves determining how the proximity of the outer variable domain affects the binding of ligands to the inner variable domain. To explore this area, we prepared a series of DVD-Ig proteins with binding specificities toward TNFα and an alternate therapeutic target. Kinetic measurements of TNFα binding to this series of DVD-Ig proteins were used to probe the effects of variable domain position and linker design on ligand on- and off-rates. We found that affinities for TNFα are generally lower when binding to the inner domain than to the outer domain and that this loss of affinity is primarily due to reduced association rate. This effect could be mitigated, to some degree, by linker design. We show several linker sequences that mitigate inner domain affinity losses in this series of DVD-Ig proteins. Moreover, we show that single chain proteolytic cleavage between the inner and outer domains, or complete outer domain removal, can largely restore inner domain TNFα affinity to that approaching the reference antibody. Taken together, these results suggest that a loss of affinity for inner variable domains in this set of DVD-Ig proteins may be largely driven by simple steric hindrance effects and can be reduced by careful linker design.
Prestack inversion of plane-layered viscoacoustic Earth parameters (1985)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 1985Prestack inversion of plane‐layered viscoacoustic Earth parametersAuthors: B. J. VerWestM. A. HooshyarB. J. VerWestARCO Resources Technology and M. A. HooshyarUniv. of Texas, Dallashttps://doi.org/10.1190/1.1892630 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail FiguresReferencesRelatedDetails SEG Technical Program Expanded Abstracts 1985ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 1985 Pages: 643 publication data© 1985 Copyright © 1985 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 07 Mar 2005 CITATION INFORMATION B. J. VerWest and M. A. Hooshyar, (1985), "Prestack inversion of plane‐layered viscoacoustic Earth parameters," SEG Technical Program Expanded Abstracts : 383-385. https://doi.org/10.1190/1.1892630 Plain-Language Summary PDF DownloadLoading ...
Directed Differentiation of Human Embryonic Stem Cells into Functional Dendritic Cells through the Myeloid Pathway (2006)

We have established a system for directed differentiation of human embryonic stem (hES) cells into myeloid dendritic cells (DCs). As a first step, we induced hemopoietic differentiation by coculture of hES cells with OP9 stromal cells, and then, expanded myeloid cells with GM-CSF using a feeder-free culture system. Myeloid cells had a CD4+CD11b+CD11c+CD16+CD123(low)HLA-DR- phenotype, expressed myeloperoxidase, and included a population of M-CSFR+ monocyte-lineage committed cells. Further culture of myeloid cells in serum-free medium with GM-CSF and IL-4 generated cells that had typical dendritic morphology; expressed high levels of MHC class I and II molecules, CD1a, CD11c, CD80, CD86, DC-SIGN, and CD40; and were capable of Ag processing, triggering naive T cells in MLR, and presenting Ags to specific T cell clones through the MHC class I pathway. Incubation of DCs with A23187 calcium ionophore for 48 h induced an expression of mature DC markers CD83 and fascin. The combination of GM-CSF with IL-4 provided the best conditions for DC differentiation. DCs obtained with GM-CSF and TNF-alpha coexpressed a high level of CD14, and had low stimulatory capacity in MLR. These data clearly demonstrate that hES cells can be used as a novel and unique source of hemopoietic and DC precursors as well as DCs at different stages of maturation to address essential questions of DC development and biology. In addition, because ES cells can be expanded without limit, they can be seen as a potential scalable source of cells for DC vaccines or DC-mediated induction of immune tolerance.