gebhart/patrepeval huggingface dataset:
Recombinant Human Erythropoietin Influences Revascularization and Healing in a Rat Model of Random Ischaemic Flaps (2002)

In order to ascertain whether erythropoietin plays a role in early and late repair processes following ischaemic skin flap injury, a dorsal, caudally based skin flap was created in rats. The rats were successively divided into four groups. Group 1 was not treated. The other groups were treated with a subcutaneous administration of 0.9% NaCl saline solution (group 2), a subcutaneous administration of vehicle (group 3) or a subcutaneous administration of 300 IU/kg/day of recombinant human erythropoietin (group 4). We evaluated the possible relationships between neutrophil accumulation, myeloperoxidase activity and content in flap tissue, flap survival, flap temperature (using telethermography) and flap revascularization (using videocapillaroscopy). Necrosis in the flap was significantly less extensive in group 4 than in groups 1, 2 and 3. A significant increase in neutrophil infiltration occurred between the 1st and 24th hour in these groups, but this was not observed in group 4. These findings were confirmed by biochemical data of myeloperoxidase activity and malonyldialdehyde content. Between the 1st and 7th days, we recorded an increase of about 20% in flap temperature in groups 1, 2 and 3, whereas no significant variation was observed in group 4. On the 7th day, videocapillaroscopic findings showed an increase in the mean vascularization index in group 4. Our findings suggest that recombinant human erythropoietin administration can improve the wound healing process, in both early and late stages of injury, by reducing inflammatory response, increasing the density of capillaries in ischaemic flaps and allowing earlier repair of a damaged area.
Fault simulation and modelling of microelectromechanical systems (2000)

High-reliability and safety-critical markets for microelectromechanical systems are driving new proposals for the integration of efficient built-in test and monitoring functions. The realisation of this technology will require support tools and validation methodologies including fault simulation and testability analysis and full closed-loop simulation techniques to ensure cost and quality targets. This article proposes methods to extend the capabilities of mixed signal and analogue integrated circuit fault simulation techniques to MEMS by including failure mode and effect analysis data and using behavioural modelling techniques compatible with electrical simulators.
Recognition of the Minor Groove of DNA by Hairpin Polyamides Containing α-Substituted-β-Amino Acids (2000)

Incorporation of the flexible amino acid β-alanine (β) into hairpin polyamides composed of N-methylpyrrole (Py) and N-methylimidazole (Im) amino acids is required for binding to DNA sequences longer than seven base pairs with high affinity and sequence selectivity. Pairing the α-substituted-β-amino acids (S)-isoserine (SIs), (R)-isoserine (RIs), β-aminoalanine (Aa), and α-fluoro-β-alanine (Fb) side-by-side with β in hairpin polyamides alters DNA binding affinity and selectivity relative to the parent polyamide containing a β/β pairing. Quantitative DNase I footprinting titration studies on a restriction fragment containing the sequences 5‘-TGCNGTA-3‘ (N = A, T, G, and C) show that the polyamide ImPySIsImPy-γ-PyPyβImPy-β-Dp (SIs/β pairing) binds to N = T (Ka = 4.5 × 109 M-1) in preference to N = A (Ka = 6.2 × 108 M-1). This result stands in contrast to the essentially degenerate binding of the parent ImPyβImPy-γ-PyPyβImPy-β-Dp (β/β pairing) to N = T and N = A, and to the slight preference of ImPyβImPy-γ-PyPySIsImPy-β-Dp (β/SIs pairing) to N = A over N = T. Additionally, this study reveals that incorporation of RIs, Aa, and Fb into polyamides significantly reduces binding affinity. Therefore, DNA binding in the minor groove is sensitive to the stereochemistry, steric bulk, and electronics of the substituent at the α-position of β-amino acids in hairpin polyamides containing β/β pairs.
Multiyear Research, Development and Demonstration Plan (2012)

The Fuel Cell Technologies Office Multi-Year Research, Development, and Demonstration (MYRD&D) Plan describes the goals, objectives, technical targets, tasks, and schedules for all activities within the Fuel Cell Technologies (FCT) Office, which is part of the U.S. Department of Energy's Office of Energy Efficiency and Renewable Energy. The MYRD&D Plan is a living document, which is revised periodically to reflect progress in the technologies, revisions to developmental timelines and targets, updates based on external reviews, and changes in the scope of the FCT Office. The document was first published in 2003, and revised in 2005. The document was significantly revised in 2012 to reflect scientific advancements and the changing technological landscape. Any revisions made to the MYRD&D Plan are conducted through a rigorous Change Control process as documented in the Systems Integration section of this report. The hydrogen and fuel cell activities within DOE continue to receive extensive review by stakeholders in the hydrogen and fuel cell community, including panels of the National Research Council and the National Academy of Engineering.
Polyclonal human T-cell activation by silicate in vitro. (1994)

Silica (SiO2) or related substances such as silicone ([-R2Si-O-]n), which is used in plastic surgery, or asbestos (e.g. chrysotile; 3MgO.2SiO2.H2O) have 'adjuvant effects'. In a study of scleroderma patients in Germany more than 78% had experienced exposure to silicate dust. T-cell receptor (TcR) V beta gene analysis on CD4- CD8- double-negative alpha beta T cells from scleroderma patients, using polymerase chain reaction (PCR), showed that certain V beta genes, V beta 5, V beta 7 and V beta 17, were predominantly expressed in the cells. We found that certain V beta repertoires, V beta 5.3 and V beta 6.7, were predominantly expressed on fractionated T cells with a high Ca2+ level that had been stimulated by chrysotile in vitro. The intracellular Ca2+ level in human peripheral blood mononuclear cells (PBMC) increased after incubation with silica or chrysotile. Interleukin-2 (IL-2) release from PMBC also rose significantly with chrysotile stimulation, but no change was observed when major histocompatibility complex (MHC) class II DP/DR positive cells were depleted. Therefore, our results support the possibility that silicate acts as a superantigen.
Methicillin-resistant staphylococci. (1988)

Strains of staphylococci resistant to methicillin were identified immediately after introduction of this drug. Methicillin-resistant strains have unusual properties, the most notable of which is extreme variability in expression of the resistance trait. The conditions associated with this heterogeneous expression of resistance are described. Methicillin resistance is associated with production of a unique penicillin-binding protein (PBP), 2a, which is bound and inactivated only at high concentrations of beta-lactam antibiotics. PBP2a appears to be encoded by the mec determinant, which also is unique to methicillin-resistant strains. The relationships between PBP2a and expression of resistance and implications for the mechanism of resistance are discussed. The heterogeneous expression of methicillin resistance by staphylococci poses problems in the detection of resistant strains. Experience with several susceptibility test methods is reviewed and guidelines for performance of these tests are given. Treatment of infections caused by methicillin-resistant staphylococci is discussed. Vancomycin is the treatment of choice. Alternatives have been few because methicillin-resistant strains often are resistant to multiple antibiotics in addition to beta-lactam antibiotics. New agents which are active against methicillin-resistant staphylococci are becoming available, and their potential role in treatment is discussed.
Detection and tracking of gas plumes in LWIR hyperspectral video sequence data (2013)

Automated detection of chemical plumes presents a segmentation challenge. The segmentation problem for gas plumes is difficult due to the diffusive nature of the cloud. The advantage of considering hyperspectral images in the gas plume detection problem over the conventional RGB imagery is the presence of non-visual data, allowing for a richer representation of information. In this paper we present an effective method of visualizing hyperspectral video sequences containing chemical plumes and investigate the effectiveness of segmentation techniques on these post-processed videos. Our approach uses a combination of dimension reduction and histogram equalization to prepare the hyperspectral videos for segmentation. First, Principal Components Analysis (PCA) is used to reduce the dimension of the entire video sequence. This is done by projecting each pixel onto the first few Principal Components resulting in a type of spectral filter. Next, a Midway method for histogram equalization is used. These methods redistribute the intensity values in order to reduce icker between frames. This properly prepares these high-dimensional video sequences for more traditional segmentation techniques. We compare the ability of various clustering techniques to properly segment the chemical plume. These include K-means, spectral clustering, and the Ginzburg-Landau functional.
PARP-1 Inhibition as a Targeted Strategy to Treat Ewing's Sarcoma (2012)

Ewing's sarcoma family of tumors (ESFT) refers to aggressive malignancies which frequently harbor characteristic EWS-FLI1 or EWS-ERG genomic fusions. Here, we report that these fusion products interact with the DNA damage response protein and transcriptional coregulator PARP-1. ESFT cells, primary tumor xenografts, and tumor metastases were all highly sensitive to PARP1 inhibition. Addition of a PARP1 inhibitor to the second-line chemotherapeutic agent temozolamide resulted in complete responses of all treated tumors in an EWS-FLI1-driven mouse xenograft model of ESFT. Mechanistic investigations revealed that DNA damage induced by expression of EWS-FLI1 or EWS-ERG fusion genes was potentiated by PARP1 inhibition in ESFT cell lines. Notably, EWS-FLI1 fusion genes acted in a positive feedback loop to maintain the expression of PARP1, which was required for EWS-FLI-mediated transcription, thereby enforcing oncogene-dependent sensitivity to PARP-1 inhibition. Together, our findings offer a strong preclinical rationale to target the EWS-FLI1:PARP1 intersection as a therapeutic strategy to improve the treatment of ESFTs.
Prevalence of Newly Generated Naive Regulatory T Cells (Treg) Is Critical for Treg Suppressive Function and Determines Treg Dysfunction in Multiple Sclerosis (2007)

The suppressive function of regulatory T cells (T(reg)) is impaired in multiple sclerosis (MS) patients. The mechanism underlying the T(reg) functional defect is unknown. T(reg) mature in the thymus and the majority of cells circulating in the periphery rapidly adopt a memory phenotype. Because our own previous findings suggest that the thymic output of T cells is impaired in MS, we hypothesized that an altered T(reg) generation may contribute to the suppressive deficiency. We therefore determined the role of T(reg) that enter the circulation as recent thymic emigrants (RTE) and, unlike their CD45RO(+) memory counterparts, express CD31 as typical surface marker. We show that the numbers of CD31(+)-coexpressing CD4(+)CD25(+)CD45RA(+)CD45RO(-)FOXP3(+) T(reg) (RTE-T(reg)) within peripheral blood decline with age and are significantly reduced in MS patients. The reduced de novo generation of RTE-T(reg) is compensated by higher proportions of memory T(reg), resulting in a stable cell count of the total T(reg) population. Depletion of CD31(+) cells from T(reg) diminishes the suppressive capacity of donor but not patient T(reg) and neutralizes the difference in inhibitory potencies between the two groups. Overall, there was a clear correlation between T(reg)-mediated suppression and the prevalence of RTE-T(reg), indicating that CD31-expressing naive T(reg) contribute to the functional properties of the entire T(reg) population. Furthermore, patient-derived T(reg), but not healthy T(reg), exhibit a contracted TCR Vbeta repertoire. These observations suggest that a shift in the homeostatic composition of T(reg) subsets related to a reduced thymic-dependent de novo generation of RTE-T(reg) with a compensatory expansion of memory T(reg) may contribute to the T(reg) defect associated with MS.
Neonatal FcR Expression in Bone Marrow-Derived Cells Functions to Protect Serum IgG from Catabolism (2007)

The neonatal FcR (FcRn) is a receptor that protects IgG from catabolism and is important in maintaining high serum Ab levels. A major site of expression of FcRn is vascular endothelial cells where FcRn functions to extend the serum persistence of IgG by recycling internalized IgG back to the surface. Because FcRn is expressed in other tissues, it is unclear whether endothelial cells are the only site of IgG protection. In this study, we used FcRn-deficient mice and specific antiserum to determine the tissue distribution of FcRn in the adult mouse. In addition to its expression in the vascular endothelium of several organs, we found FcRn to be highly expressed in bone marrow-derived cells and professional APCs in different tissues. Experiments using bone marrow chimeras showed that FcRn expression in these cells acted to significantly extend the half-life of serum IgG indicating that in addition to the vascular endothelium, bone marrow-derived phagocytic cells are a major site of IgG homeostasis.
IL-2 and Related Cytokines Can Promote T Cell Survival by Activating AKT (2002)

The regulated elimination of T cells serves to maintain normal immune function and prevents autoimmune responses. IL-2 family cytokines play an important role in controlling the survival of immature and mature T cells. These molecules activate the protein kinase, AKT/PKB. AKT has been shown to transduce an antiapoptotic signal in numerous cell types. In this study, we show that an active form of AKT can protect T cells from apoptosis following growth factor withdrawal and that IL-2 family cytokines can promote T cell survival by activating this kinase. We also provide evidence that AKT does not block death receptor-mediated killing of lymphocytes. These data suggest that AKT may serve as a common signaling element by which members of the IL-2 family of cytokines promote T cell survival.
Analysis of the binding of Xenopus ribosomal protein L5 to oocyte 5 S rRNA. The major determinants of recognition are located in helix III-loop C. (1995)

Xenopus ribosomal protein L5 was expressed in Escherichia coli and exhibits high affinity (Kd = 2 nM) and specificity for oocyte 5 S rRNA. The pH dependence of the association constant for the complex reveals an ionization with a pK alpha value of 10.1, indicating that tyrosine and/or lysine residues are important for specific binding of L5 to the RNA. Formation of the L5.5 S rRNA complex is remarkably insensitive to ionic strength, providing evidence that nonelectrostatic interactions make significant contributions to binding. Together, these results suggest that one or more tyrosine residues may form critical contacts through stacking interactions with bases in the RNA. In order to locate recognition elements within 5 S rRNA, we measured binding of L5 to a collection of site-specific mutants. Mutations in the RNA that affected the interaction are confined to the hairpin structure comprised of helix III and loop C. Earlier experiments with a rhodium structural probe had shown that the two-nucleotide bulge in helix III and the intrinsic structure of loop C create sites in the major groove that are opened and accessible to stacking interactions with the metal complex. In the present studies, we detect a correlation between the intercalative binding of the rhodium complex to mutants in the hairpin and binding of L5, supporting the proposal that binding of the protein is mediated, in some part, by stacking interactions. Furthermore, the results from mutagenesis establish that, despite overlapping binding sites on 5 S rRNA, L5 and transcription factor IIIA utilize distinct structural elements for recognition.
Finding Actors and Actions in Movies (2013)

We address the problem of learning a joint model of actors and actions in movies using weak supervision provided by scripts. Specifically, we extract actor/action pairs from the script and use them as constraints in a discriminative clustering framework. The corresponding optimization problem is formulated as a quadratic program under linear constraints. People in video are represented by automatically extracted and tracked faces together with corresponding motion features. First, we apply the proposed framework to the task of learning names of characters in the movie and demonstrate significant improvements over previous methods used for this task. Second, we explore the joint actor/action constraint and show its advantage for weakly supervised action learning. We validate our method in the challenging setting of localizing and recognizing characters and their actions in feature length movies Casablanca and American Beauty.
Tumor Hypoxia: Definitions and Current Clinical, Biologic, and Molecular Aspects (2001)

Tissue hypoxia results from an inadequate supply of oxygen (O(2)) that compromises biologic functions. Evidence from experimental and clinical studies increasingly points to a fundamental role for hypoxia in solid tumors. Hypoxia in tumors is primarily a pathophysiologic consequence of structurally and functionally disturbed microcirculation and the deterioration of diffusion conditions. Tumor hypoxia appears to be strongly associated with tumor propagation, malignant progression, and resistance to therapy, and it has thus become a central issue in tumor physiology and cancer treatment. Biochemists and clinicians (as well as physiologists) define hypoxia differently; biochemists define it as O(2)-limited electron transport, and physiologists and clinicians define it as a state of reduced O(2) availability or decreased O(2) partial pressure that restricts or even abolishes functions of organs, tissues, or cells. Because malignant tumors no longer execute functions necessary for homeostasis (such as the production of adequate amounts of adenosine triphosphate), the physiology-based definitions of the term "hypoxia" are not necessarily valid for malignant tumors. Instead, alternative definitions based on clinical, biologic, and molecular effects that are observed at O(2) partial pressures below a critical level have to be applied.
Comparative efficacy of two oral treatments for dogs containing either afoxolaner or fluralaner against Rhipicephalus sanguineus sensu lato and Dermacentor reticulatus (2015)

The present study compares the efficacy of two recent oral ectoparasiticides containing isoxazolines (NexGard(®), containing afoxolaner and administered at a monthly regimen, and Bravecto™ containing fluralaner and administered at a tri-monthly regimen) against Rhipicephalus sanguineus sensu lato and Dermacentor reticulatus ticks on dogs. 24 dogs were randomly allocated to untreated control, NexGard(®) treated, and Bravecto™ treated groups. The treatments were administered on Days 0, 28 and 56 for afoxolaner and on Day 0 for fluralaner. Tick infestations were performed weekly with 50 unfed adult ticks per each species on each dog from Days 30 to 84 (with the exception of R. sanguineus on Day 63). Ticks were counted at 24h post-infestation. The dogs from both treated groups had statistically significantly (p<0.05) less R. sanguineus and D. reticulatus ticks compared to the untreated dogs on all assessment days. Percent efficacy against R. sanguineus ranged from 86.4% to 99.5% at 24h post-infestation for NexGard(®) and from 65.7% to 100% for Bravecto™. Statistically significantly (p<0.05) less R. sanguineus ticks were recorded for NexGard(®) treated dogs compared to Bravecto™ treated dogs on Day 78. Percent efficacy against D. reticulatus ranged from 85.2% to 99.6% at 24h post-infestation for NexGard(®) and from 63.4% to 99.1% for Bravecto™. Statistically significantly (p<0.05) less D. reticulatus ticks were recorded for NexGard(®) treated dogs compared to Bravecto™ treated dogs on Days 71, 78 and 85.
Chroma Binary Similarity and Local Alignment Applied to Cover Song Identification (2008)

We present a new technique for audio signal comparison based on tonal subsequence alignment and its application to detect cover versions (i.e., different performances of the same underlying musical piece). Cover song identification is a task whose popularity has increased in the music information retrieval (MIR) community along in the past, as it provides a direct and objective way to evaluate music similarity algorithms. This paper first presents a series of experiments carried out with two state-of-the-art methods for cover song identification. We have studied several components of these (such as chroma resolution and similarity, transposition, beat tracking or dynamic time warping constraints), in order to discover which characteristics would be desirable for a competitive cover song identifier. After analyzing many cross-validated results, the importance of these characteristics is discussed, and the best performing ones are finally applied to the newly proposed method. Multiple evaluations of this one confirm a large increase in identification accuracy when comparing it with alternative state-of-the-art approaches.
Vertical organic light emitting transistor (2007)

The authors demonstrate a vertical organic light emitting transistor achieved by stacking a capacitor on top of an organic light emitting diode (OLED). This unique device has dual functions, emitting light as an OLED and switching current as a transistor. When the capacitor is under bias, the storage charges on the thin electrode shared by two cells modulate the charge injection of the OLED active cell, hence controlling the current flow and subsequently tuning the light emission. Due to the vertical integration, this device can be operated at low voltage, which provides a solution for OLED display applications.
PD-L1 Expression Correlates with Tumor-Infiltrating Lymphocytes and Response to Neoadjuvant Chemotherapy in Breast Cancer (2014)

Programmed death 1 ligand 1 (PD-L1) is an immune regulatory molecule that limits antitumor immune activity. Targeting of PD-L1 and other immune checkpoint proteins has shown therapeutic activity in various tumor types. The expression of PD-L1 and its correlation with response to neoadjuvant chemotherapy in breast cancer has not been studied extensively. Our goal was to assess PD-L1 expression in a cohort of breast cancer patients treated with neoadjuvant chemotherapy. Pretreatment biopsies from 105 patients with breast cancer from Yale New Haven Hospital that subsequently received neoadjuvant chemotherapy were assessed for PD-L1 protein expression by automated quantitative analysis with a rabbit monoclonal antibody (E1L3N) to the cytoplasmic domain of PD-L1. In addition, tumor-infiltrating lymphocytes (TIL) were assessed on hematoxylin and eosin slides. PD-L1 expression was observed in 30% of patients, and it was positively associated with hormone-receptor-negative and triple-negative status and high levels of TILs. Both TILs and PD-L1 measured in the epithelium or stroma predicted pathologic complete response (pCR) to neoadjuvant chemotherapy in univariate and multivariate analyses. However, because they are strongly associated, TILs and PD-L1 cannot both be included in a significant multivariate model. PD-L1 expression is prevalent in breast cancer, particularly hormone-receptor-negative and triple-negative patients, indicating a subset of patients that may benefit from immune therapy. Furthermore, PD-L1 and TILs correlate with pCR, and high PD-L1 predicts pCR in multivariate analysis.