gebhart/patrepeval huggingface dataset:
Activation of Two Osmotin-Like Protein Genes by Abiotic Stimuli and Fungal Pathogen in Transgenic Potato Plants (1995)

Osmotin-like proteins are encoded by at least six members of a multigene family in Solanum commersonii. A genomic clone (lambda pGEM2a-7) that contains two osmotin-like protein genes (OSML13 and OSML81) arranged in the same transcriptional orientation has been isolated. Restriction mapping and sequence analysis indicated that the two intronless genes correspond to the previously characterized pA13 and pA81 cDNAs. To study the transcriptional activation of OSML13 and OSML81 promoters, the 5' flanking DNA sequence (-1078 to +35 of OSML13 and -1054 to +41 of OSML81) was fused to the beta-glucoronidase (GUS) coding region, and the chimeric gene fusions were introduced into wild potato (S. commersonii) plants via Agrobacterium-mediated transformation. Analysis of the chimeric gene expression in transgenic potato plants showed that both 5' flanking DNA sequences are sufficient to impart GUS inducibility by abscisic acid, NaCl, salicylic acid, wounding, and fungal infection. Low temperature activated both chimeric genes only slightly. Infection with Phytophthora infestans resulted in strong GUS expression from both chimeric genes primarily in the sites of pathogen invasion, suggesting a limited diffusion of fungal infection-mediated signals. The expression patterns of both osmotin-like protein genes implicate their dual functions in osmotic stress and plant pathogen defense.
Loss of in vitro cytotoxicity of cisplatin after storage as stock solution in cell culture medium at various temperatures (1997)

Cisplatin is a potent cytotoxic drug in vitro when stored under appropriate conditions. These findings are of relevance for in vitro studies with cisplatin.
Effect of feeding an encapsulated source of butyric acid (ButiPEARL) on the performance of male Cobb broilers reared to 42 d of age (2015)

The objective of this research was to determine the optimal level of an encapsulated butyric acid (ButiPEARL) based on the performance of male Cobb broilers reared to 42 d of age and to investigate its effects on intestinal morphology. Experiment 1 ( EXP 1: ) consisted of 4 treatments with 12 replicate pens that contained 45 broilers, and Experiment 2 ( EXP 2: ) consisted of 6 treatments with 8 replicate pens that contained 50 broilers. Birds were weighed by pen on d 0, 21, 35, and 42. In EXP 1, the treatments were as follows: 1) control ( C: ); 2) C + 100 g ButiPEARL/ton; 3) C + 200 g ButiPEARL/ton; and 4) C + 300 g ButiPEARL/ton. In EXP 2, the treatments were identical to EXP 1, with 2 additional treatments: 5) C + 400 g ButiPEARL/ton and 6) C + 500 g ButiPEARL/ton. In EXP 1, two 42-d-old broilers per pen were randomly selected for duodenal and jejunal tissue collection. Only the samples from the broilers fed the C or 300 g ButiPEARL treatments were analyzed for histology in EXP 1. For EXP 2, on d 21 and 35, two broilers per pen were randomly selected for duodenal, jejunal, and ileal tissue collection. For EXP 1 and 2, BW gain increased linearly with increasing butyric acid levels (P < 0.027 and P < 0.001, respectively). For EXP 1 and 2, feed conversion linearly improved with increasing butyric acid from 0 to 42 d (P < 0.001 and P < 0.001, respectively). In EXP 1, there were no differences in any intestinal morphology at 42 d between broilers fed the C or 300 g ButiPEARL treatments. In EXP 2, there were no differences in villus height at 21 or 35 d of age with any level of butyric acid. Based on the results of this research related to BW gain and feed conversion, the recommended optimum dosage level for ButiPEARL in broilers reared to 42 d of age is up to 500 g/ton.
GASTRIN RECEPTOR ANTAGONIST Cl‐988 INHIBITS GROWTH OF HUMAN COLON CANCER IN VIVO AND IN VITRO (1996)

This was the first study in cancer with this potent gastrin receptor antagonist, CI-988. The results suggest that CI-988 may be of use in inhibiting the growth of colorectal cancer.
Phase I, open-label, multi-ascending dose trial of avelumab (MSB0010718C), an anti-PD-L1 monoclonal antibody, in Japanese patients with advanced solid tumors. (2015)

3023 Background: The programmed death-1 receptor (PD-1) and its ligand (PD-L1) are key therapeutic targets in the reactivation of the immune response against multiple cancers. Avelumab* (MSB0010718C) is a fully human anti-PD-L1 IgG1 antibody currently being investigated in phase I/II trials. Here we report on the safety and tolerability of avelumab in a phase I dose escalation study (NCT01943461) in Japanese patients (pts) with advanced solid tumors. Methods: Dose escalation (3+3 design) was performed for 3 dose levels (DL 3, 10, and 20 mg/kg). The dose limiting toxicity (DLT) evaluation period was 3 weeks. Results: A total of 17 pts (4 gastric, 4 melanoma, 3 NSCLC, 2 CRC, 2 GIST, 1 esophageal, 1 MBC) were enrolled, with 5, 6, and 6 pts treated with avelumab at 3, 10, and 20 mg/kg, Q2W, respectively. Median age was 62 years (range 30–74) and all had ECOG PS 0 or 1, with a median of 4 prior lines of therapy (range 1–9). Treatment-emergent adverse events (TEAEs) occurred in 16/17 pts (94.1%), of which 11 (64.7%) were treatment-related. The most frequent related TEAEs (≥ 10%) were infusion-related reactions (5, 29.4%), stomatitis (4, 23.5%), maculopapular rash (4, 23.5%), decreased white blood cell count (3, 17.6%), pyrexia (2, 11.8%), headache (2, 11.8%), and anemia (2, 11.8%). Two pts had grade 3 TEAEs (not related). No pt experienced a DLT. Two pts had confirmed partial responses (1 melanoma, 1 esophageal), and 5 had stable disease for > 3 months. To date, 12 pts (70.6%) have discontinued treatment: 10 (58.8%) for progression, 1 (5.9%) for death, and 1 (5.9%) for other reason. Five pts (29.4%) remain on treatment. All 17 pts were evaluable for PK analysis. Half-life was 88.6, 121.8, and 114.0 h for dose levels 3, 10, and 20 mg/kg, respectively. The parameters Cmax and AUC were approximately proportional with dose, showed low variability, and were similar to those previously obtained in Caucasian pts. Conclusions: Avelumab can be safely administered to Japanese pts in doses up to 20 mg/kg Q2W. Additional phase II/III studies to evaluate the clinical activity of avelumab at 10 mg/kg Q2W in select tumor types are currently being planned. *Proposed INN. Clinical trial information: NCT01943461.
Deep Image Matting (2017)

Image matting is a fundamental computer vision problem and has many applications. Previous algorithms have poor performance when an image has similar foreground and background colors or complicated textures. The main reasons are prior methods 1) only use low-level features and 2) lack high-level context. In this paper, we propose a novel deep learning based algorithm that can tackle both these problems. Our deep model has two parts. The first part is a deep convolutional encoder-decoder network that takes an image and the corresponding trimap as inputs and predict the alpha matte of the image. The second part is a small convolutional network that refines the alpha matte predictions of the first network to have more accurate alpha values and sharper edges. In addition, we also create a large-scale image matting dataset including 49300 training images and 1000 testing images. We evaluate our algorithm on the image matting benchmark, our testing set, and a wide variety of real images. Experimental results clearly demonstrate the superiority of our algorithm over previous methods.
Discriminative training methods for hidden Markov models (2002)

We describe new algorithms for training tagging models, as an alternative to maximum-entropy models or conditional random fields (CRFs). The algorithms rely on Viterbi decoding of training examples, combined with simple additive updates. We describe theory justifying the algorithms through a modification of the proof of convergence of the perceptron algorithm for classification problems. We give experimental results on part-of-speech tagging and base noun phrase chunking, in both cases showing improvements over results for a maximum-entropy tagger.
34.1: Advanced Four‐Mask Process Architecture for the a‐Si TFT Array Manufacturing Method (2002)

Abstract In order to simplify a‐Si TFT array manufacturing process, advanced 4 mask process of low resistant metal and new pixel electrode with improved unit process was developed. Slit photolithography with continuous dry etching process on the basis of metal dry etching cleared chronic problems of currently adopted 4 mask process and new combination of material and etchant for wet etching process made it possible to achieve stabilized wet etching and reduce total process steps. Our final version of a‐Si TFT process architecture applicable to both notebook and monitor devices, will reinforce competitive power of TFT‐LCD by improved displaying performance and ultimate process simplification.
A Simple Synthesis of Stable Heterocyclic Phosphorus Ylides Derived from NH-Acids (2002)

Abstract Crystalline phosphorus ylides are obtained in excellent yields from the addition reaction between triphenylphosphine, dimethyl acetylenedicarboxylate and strong NH-acids, such as 2-acetylpyrrole, indole, ethyl 3-indolylglyoxalate and N -benzyl-2-pyrrolylglyoxamate. Dynamic NMR effects are observed in the 1 H NMR spectra of stabilized ylides obtained from 2-acetylpyrrole and indole ( j G p = 67.1 and 68.8 kJmol m 1 respectively) and are attributed to restricted rotation around the carbon-carbon partial double bond resulting from conjugation of the ylide moiety with the adjacent carbonyl group. Keywords: Acetylenic EsterNh-acidsStable Phosphorus YlidesTriphenylphosphine
Molecular abnormalities in lung cancer. (1998)

Genetic abnormalities involved in the pathogenesis of lung cancer are rapidly being delineated. Understanding molecular abnormalities in lung cancer could potentially lead to earlier diagnosis and the development of novel investigational approaches to the treatment of lung cancer.
PCR-Directed Linker Scanning Mutagenesis (2003)

Linker scanning mutagenesis is a powerful method with which to assay the contribution of individual DNA sequence elements within a transcriptional control region (1). By replacing discrete segments of DNA with heterologous segments of the same length, the topological and spatial organization of the DNA helix is maintained. This allows the contribution of individual DNA-binding motifs to be determined in the context of the native DNA helix configuration. Although most commonly employed in the analysis of promoter and enhancer regions, linker scanning mutagenesis has also been adapted for the analysis of protein coding regions (2).
The development of a six‐item short‐form of the state scale of the Spielberger State—Trait Anxiety Inventory (STAI) (1992)

Two studies are reported describing the development of a short-form of the state scale of the Spielberger State-Trait Anxiety Inventory (STAI) for use in circumstances where the full-form is inappropriate. Using item-remainder correlations, the most highly correlated anxiety-present and anxiety-absent items were combined, and correlated with scores obtained using the full-form of the STAI. Correlation coefficients greater than .90 were obtained using four and six items from the STAI. Acceptable reliability and validity were obtained using six items. The use of this six-item short-form produced scores similar to those obtained using the full-form. This was so for several groups of subjects manifesting a range of anxiety levels. This short-form of the STAI is therefore sensitive to fluctuations in state anxiety. When compared with the full-form of the STAI, the six-item version offers a briefer and just as acceptable scale for subjects while maintaining results that are comparable to those obtained using the full-form of the STAI.
A highly selective charge transfer fluoroionophore for Cu2+ (2005)

A dual fluorescent charge transfer fluoroionophore (1) with its ionophore incorporated in the electron acceptor was developed and was found to show a highly selective fluorescent response to Cu2+ with a dramatic enhancement in its CT emission.
p38 mitogen-activated protein kinase activation during platelet storage: consequences for platelet recovery and hemostatic function in vivo (2009)

Platelets undergo several modifications during storage that reduce their posttransfusion survival and functionality. One important feature of these changes, which are known as platelet storage lesion, is the shedding of the surface glycoproteins GPIb-alpha and GPV. We recently demonstrated that tumor necrosis factor-alpha converting enzyme (TACE/ADAM17) mediates mitochondrial injury-induced shedding of adhesion receptors and that TACE activity correlates with reduced posttransfusion survival of these cells. We now confirm that TACE mediates receptor shedding and clearance of platelets stored for 16 hours at 37 degrees C or 22 degrees C. We further demonstrate that both storage and mitochondrial injury lead to the phosphorylation of p38 mitogen-activated kinase (MAPK) in platelets and that TACE-mediated receptor shedding from mouse and human platelets requires p38 MAP kinase signaling. Protein kinase C, extracellular regulated-signal kinase MAPK, and caspases were not involved in TACE activation. Both inhibition of p38 MAPK and inactivation of TACE during platelet storage led to a markedly improved posttransfusion recovery and hemostatic function of platelets in mice. p38 MAPK inhibitors had only minor effects on the aggregation of fresh platelets under static or flow conditions in vitro. In summary, our data suggest that inhibition of p38 MAPK or TACE during storage may significantly improve the quality of stored platelets.
Temperature-independent strain sensorusing a chirped Bragg grating in a tapered optical fibre (1995)

A novel, temperature-independent strain sensor is demonstrated using a chirped fibre grating in a tapered optical fibre. The effective bandwidth of the grating is uniquely dependent on strain and is essentially temperature-independent. The interrogation simply involves monitoring the back-reflected intensity from the grating. A strain resolution of 0.1% over a strain measurement range of 4066 µɛ has been experimentally achieved.
Effective Medium Theory of the Porosity Dependence of Bulk Moduli (2001)

Effective medium theory is used to obtain a closed‐ form expression for the porosity dependence of the bulk moduli of ceramics. The theory is illustrated with an application to data for high‐purity alumina that spans a volume fraction of porosity ranging from 0.5% to 90%.
Use of Confocal Microscopy To Analyze the Rate of Vancomycin Penetration through Staphylococcus aureus Biofilms (2005)

ABSTRACT When bacteria assume the biofilm mode of growth, they can tolerate levels of antimicrobial agents 10 to 1,000 times higher than the MICs of genetically equivalent planktonic bacteria. The properties of biofilms that give rise to antibiotic resistance are only partially understood. Inhibition of antibiotic penetration into the biofilm may play a role, but this has not been proven directly. In this report, penetration of the glycopeptide antibiotic vancomycin into viable Staphylococcus aureus biofilms was analyzed by confocal scanning laser microscopy using a fluorescently labeled derivative of the drug. We found that while vancomycin bound to free-floating bacteria in water within 5 min, it took more than 1 h to bind to cells within the deepest layers of a biofilm. These results indicate that the antibiotic is transported through the depth of the biofilm but that the rate is significantly reduced with respect to its transport through flowing water. This suggests that, whereas planktonic bacteria were rapidly exposed to a full bolus of vancomycin, the bacteria in the deeper layers of the biofilm were exposed to a gradually increasing dose of the drug due to its reduced rate of penetration. This gradual exposure may allow the biofilm bacteria to undergo stress-induced metabolic or transcriptional changes that increase resistance to the antibiotic. We also investigated the role of poly- N -acetylglucosamine, an important component of the S. aureus biofilm matrix, and found that its production was not involved in the observed decrease in the rate of vancomycin penetration.
Lung Epithelial NF- κ B and Stat1 Signaling in Response to CD8 + T Cell Antigen Recognition (2006)

CD8+ T cell recognition of viral antigens presented by lung epithelial cells is important in the clearance of respiratory viral infection but may cause considerable injury to the lung. We have shown that a critical event of this type of injury is the activation of target epithelial cells and expression of chemokines by these cells. In this study, epithelial gene expression and transcription factor activation triggered by specific CD8+ T cell antigen recognition was examined in vitro and in vivo. T cell recognition triggers expression profiles of tumor necrosis factor-alpha (TNF-alpha)-dependent and interferon-gamma (IFN-gamma)-dependent genes in epithelial target cells. Consistent with these profiles, transcription factors nuclear factor-kappaB (NF-kappaB) and activator protein-1 (AP-1) were activated in lung epithelial cells of wild-type (WT) mice but not TNF receptor 1 (TNFR1)-deficient mice after CD8+ T cell recognition in vivo. In contrast, Stat1 activation and Stat1-dependent genes, such as IFN regulatory factor-1 (IRF-1) and guanylate-binding protein-2 (GBP-2), were induced to a similar extent in epithelial cells of both WT and TNFR1-deficient mice, indicating that this pathway is insufficient to induce pulmonary immunopathology in the absence of NF-kappaB-dependent transcriptional activation. Antibody neutralization of TNF-alpha abrogated epithelial monocyte chemotactic protein-1 (MCP-1) and macrophage inflammatory protein-2 (MIP-2) production in vitro as well as pulmonary immunopathology in vivo, confirming the primary importance of this cytokine in CD8+ T cell-mediated immunopathology.
Corneal Ablation by Nanosecond, Picosecond, and Femtosecond Lasers at 532 and 625 nm (1989)

We produced corneal excisions with nanosecond (ns)-, picosecond-, and femtosecond (fs)-pulsed lasers at visible wavelengths. The threshold energy for ablation was proportional to the square root of the pulse duration and varied from 2.5 microjoules (microJ) at 100 fs to 500 microJ at 8 ns. Excisions made with picosecond and femtosecond lasers was ultrastructurally superior to those made with nanosecond lasers and, at pulse energies near threshold, showed almost as little tissue damage as excisions made with excimer lasers at 193 nm. We conclude that ultrashort-pulsed lasers at visible and near-infrared wavelengths are a possible alternative to excimer lasers for corneal surgery and might have advantages over conventional ophthalmic neodymium-YAG lasers for some intraocular applications.
SIP services and interworking with IPv6 (2001)

This paper presents a research project that has implemented a Mobile IPv6 enhanced native IPv6 network on which different TCP and UDP based protocols are used. The most important protocol is considered to be the Session Initiation Protocol, which defines the infrastructure and end client behavior for efficient end-to-end session setup. An overview of the project targets is first given and each technology used is described. Topics covered are IPv6 and Mobile IPvB, transition mechanisms and the Session Initiation Protocol (SIP). The project achievements and possible future work is also presented. A conclusion of the technologies used in the research project is given.
IL-10 production in cutaneous basal and squamous cell carcinomas. A mechanism for evading the local T cell immune response (1995)

Cytokines play a vital role in the host immune response by regulating the development and function of immunocompetent cells. To explore the possibility that tumors may alter the host response via release of immunomodulatory cytokines, we studied two different skin cancers, basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) as models. By RT-PCR, we found that the type 2 cytokines, IL-4 and IL-10, were strongly expressed in BCC compared with matched PBMC. Furthermore, IL-10 was more strongly expressed in SCC compared with benign growths. To identify the cell types responsible for production of these cytokines, tumor and tumor-infiltrating lymphocyte (TIL) cell lines were derived from BCC and SCC biopsy specimens. IL-2 and IFN-gamma mRNAs were expressed in TIL, while IL-10 mRNA were strongly expressed in BCC lines. In addition, IL-10 was detected in culture supernatants from BCC and SCC cell lines by ELISA and in tissue sections by immunohistology. TIL lines derived from these tumors demonstrated proliferative activity to autologous tumor cells in the presence of APCs, dependent on the addition of low concentrations of rIL-2 or neutralizing anti-IL-10 mAb in the culture medium. Furthermore, treatment of BCC with intralesional IFN-alpha induced tumor regression with concomitant up-regulation of IL-2 and down-regulation of IL-10 mRNA expression in lesions. These data suggest that tumor production of the cytokine, IL-10, may provide a mechanism for evading the local T cell-mediated immune response.
Generalized DNA Barcode Design Based on Hamming Codes (2012)

The diversity and scope of multiplex parallel sequencing applications is steadily increasing. Critically, multiplex parallel sequencing applications methods rely on the use of barcoded primers for sample identification, and the quality of the barcodes directly impacts the quality of the resulting sequence data. Inspection of the recent publications reveals a surprisingly variable quality of the barcodes employed. Some barcodes are made in a semi empirical fashion, without quantitative consideration of error correction or minimal distance properties. After systematic comparison of published barcode sets, including commercially distributed barcoded primers from Illumina and Epicentre, methods for improved, Hamming code-based sequences are suggested and illustrated. Hamming barcodes can be employed for DNA tag designs in many different ways while preserving minimal distance and error-correcting properties. In addition, Hamming barcodes remain flexible with regard to essential biological parameters such as sequence redundancy and GC content. Wider adoption of improved Hamming barcodes is encouraged in multiplex parallel sequencing applications.
Sooner or later!: Have e-books turned the page? (2004)

Electronic journals have become well established in their various formats in university libraries while electronic books are still struggling to find their place. The notion that âebooks are a solution in search of a problemâ still has some currency as libraries negotiate the various licensing and access issues associated with e-books. This paper will explore the theoretical and practical issues of implementing e-books in the tertiary education environment. Experiences at Bond University where the School of IT and the Library are collaborating to experiment with e-book solutions for IT students will be used to illustrate progress.