gebhart/patrepeval huggingface dataset:
Inhibitor of Apoptosis Proteins Physically Interact with and Block Apoptosis Induced by <i>Drosophila</i> Proteins HID and GRIM (1998)

Reaper (RPR), HID, and GRIM activate apoptosis in cells programmed to die during Drosophila development. We have previously shown that transient overexpression of RPR in the lepidopteran SF-21 cell line induces apoptosis and that members of the inhibitor of apoptosis (IAP) family of antiapoptotic proteins can inhibit RPR-induced apoptosis and physically interact with RPR through their BIR motifs (D. Vucic, W. J. Kaiser, A. J. Harvey, and L. K. Miller, Proc. Natl. Acad. Sci. USA 94:10183-10188, 1997). In this study, we found that transient overexpression of HID and GRIM also induced apoptosis in the SF-21 cell line. Baculovirus and Drosophila IAPs blocked HID- and GRIM-induced apoptosis and also physically interacted with them through the BIR motifs of the IAPs. The region of sequence similarity shared by RPR, HID, and GRIM, the N-terminal 14 amino acids of each protein, was required for the induction of apoptosis by HID and its binding to IAPs. When stably overexpressed by fusion to an unrelated, nonapoptotic polypeptide, the N-terminal 37 amino acids of HID and GRIM were sufficient to induce apoptosis and confer IAP binding activity. However, GRIM was more complex than HID since the C-terminal 124 amino acids of GRIM retained apoptosis-inducing and IAP binding activity, suggesting the presence of two independent apoptotic motifs within GRIM. Coexpression of IAPs with HID stabilized HID levels and resulted in the accumulation of HID in punctate perinuclear locations which coincided with IAP localization. The physical interaction of IAPs with RPR, HID, and GRIM provides a common molecular mechanism for IAP inhibition of these Drosophila proapoptotic proteins.
A Transition to a Compact Form of DNA in Polymer Solutions (1971)

In the presence of over-threshold concentrations of simple neutral polymers and salts, DNA undergoes a cooperative change in its solution structure. Sedimentation studies at low DNA concentrations show that phage DNA molecules collapse into particles approaching the compactness of the contents of phage heads. The interaction between DNA and polymers is thought to be nonspecifically replusive.
[In vivo synthesis of cartilage after transplantation of chondrocytes in animal experiments (author's transl)]. (1980)

Long-term results after cartilage transplantation are not satisfactory owing to poor viability of the chondrocytes. In vitro experiments with isolated fetal and neonatal rabbit chondrocytes revealed a much better proliferative ability compared with adult cartilage derived cells. Cryopreservation of cell suspensions did not decrease the proliferative ability. In in vivo experiments, cultured neonatal, fetal, and cryopreserved rabbit chondrocytes were tested in transplants and compared with cell-free controls or radiated chondrocytes. These chondrocytic transplants showed good viability and seemed to synthesize cartilage matrix, which could be stained with safranin, whereas only fibrous tissue was found in controls.
Analyzing circuit vulnerability to hardware Trojan insertion at the behavioral level (2013)

Considerable attention has been paid to hardware Trojan detection and prevention. However, there is no existing systematic approach to investigate circuit vulnerability to hardware Trojan insertion during development. We present such an approach to investigate circuit vulnerability to Trojan insertion at the behavioral level. This novel vulnerability analysis determines a circuit's susceptibility to Trojan insertion based on statement hardness analysis as well as observability of circuit signals. Further, the Trojan detectability metric is introduced to quantitatively compare the detectability of behavioral Trojans inserted into different circuits. This creates a fair comparison for analyzing the strengths and weaknesses of Trojan detection techniques as well as helping verify trustworthiness of a third party Intellectual Property (IP).
Pediatric liver transplantation for biliary atresia: results of primary grafts in 328 recipients1 (2003)

Best results in children undergoing transplantation beyond 6 years indicate the importance of performing a KHPE as the first therapeutic step in BA; innovative surgical techniques, particularly LR donor graft, allowed successful transplantation in infants with early failure of KHPE.
On the Latency and Energy of Checkpointed Superscalar Register Alias Tables (2009)

This paper investigates how the latency and energy of register alias tables (RATs) vary as a function of the number of global checkpoints (GCs), processor issue width, and window size. It improves upon previous RAT checkpointing work that ignored the actual latency and energy tradeoffs and focused solely on evaluating performance in terms of instructions per cycle (IPC). This work utilizes measurements from the full-custom checkpointed RAT implementations developed in a commercial 130-nm fabrication technology. Using physical- and architectural-level evaluations together, this paper demonstrates the tradeoffs among the aggressiveness of the RAT checkpointing, performance, and energy. This paper also shows that, as expected, focusing on IPC alone incorrectly predicts performance. The results of this study justify checkpointing techniques that use very few GCs (e.g., four). Additionally, based on full-custom implementations for the checkpointed RATs, this paper presents analytical latency and energy models. These models can be useful in the early stages of architectural exploration where actual physical implementations are unavailable or are hard to develop. For a variety of RAT organizations, our model estimations are within 6.4% and 11.6% of circuit simulation results for latency and energy, respectively. This range of accuracy is acceptable for architectural-level studies.
Fast optical thresholding with an array of optoelectronic transceiver elements (1999)

In this letter, we present an optoelectronic system for fast gray-level image decomposition into binary slices. To perform thresholding, we are making use of the differential nature of optical thyristors and compare the light level of the image pixels to that of a reference intensity. As input a gray-level image was generated using a nematic liquid crystal spatial light modulator (SLM) and as a reference intensity a VCSEL light source combined with a diffractive fan-out element was used. We also introduced a compact, large field of view telecentric optical system based on gradient refractive index lenses to image between the SLM and the array. A frame rate decomposition of a six gray-level image has been obtained at 1.8 kHz. Future prospects for system improvements are discussed.
Evolution of pathogenicity and sexual reproduction in eight Candida genomes (2009)

Candida species are the most common cause of opportunistic fungal infection worldwide. Here we report the genome sequences of six Candida species and compare these and related pathogens and non-pathogens. There are significant expansions of cell wall, secreted and transporter gene families in pathogenic species, suggesting adaptations associated with virulence. Large genomic tracts are homozygous in three diploid species, possibly resulting from recent recombination events. Surprisingly, key components of the mating and meiosis pathways are missing from several species. These include major differences at the mating-type loci (MTL); Lodderomyces elongisporus lacks MTL, and components of the a1/2 cell identity determinant were lost in other species, raising questions about how mating and cell types are controlled. Analysis of the CUG leucine-to-serine genetic-code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the Candida albicans gene catalogue, identifying many new genes.
Preclinical Assessment of the Efficacy of Mycograb, a Human Recombinant Antibody against Fungal HSP90 (2003)

Mycograb (NeuTec Pharma plc) is a human genetically recombinant antibody against fungal heat shock protein 90 (HSP90). Antibody to HSP90 is closely associated with recovery in patients with invasive candidiasis who are receiving amphotericin B (AMB). Using in vitro assays developed for efficacy assessment of chemotherapeutic antifungal drugs, Mycograb showed activity against a wide range of yeast species (MICs against Candida albicans [fluconazole [FLC]-sensitive and FLC-resistant strains], Candida krusei, Candida tropicalis, Candida glabrata, and Candida parapsilosis, 128 to 256 microg/ml). Mycograb (4 or 8 microg/ml) showed synergy with AMB, the fractional inhibitory index being 0.09 to 0.31. Synergy was not evident with FLC, except for FLC-sensitive C. albicans. Murine kinetics showed that Mycograb at 2 mg/kg produced a maximum concentration of drug in serum of 4.7 microg/ml, a half-life at alpha phase of 3.75 min, a half-life at beta phase of 2.34 h, and an area under the concentration-time curve from 0 to t h of 155 microg. min/ml. Mycograb (2 mg/kg) alone produced significant improvement in murine candidiasis caused by each species: (i). a reduction (Scheffe's test, P < 0.05) in the mean organ colony count for the FLC-resistant strain of C. albicans (kidney, liver, and spleen), C. krusei (liver and spleen), C. glabrata (liver and spleen), C. tropicalis (kidney), and C. parapsilosis (kidney, liver, and spleen) and (ii). a statistically significant increase in the number of negative biopsy specimens (Fisher's exact test, P < 0.05) for C. glabrata (kidney), C. tropicalis (liver and spleen), and C. parapsilosis (liver). AMB (0.6 mg/kg) alone cleared the C. tropicalis infection but failed to clear infections caused by C. albicans, C. krusei, C. glabrata, or C. parapsilosis. Synergy with AMB, defined as an increase (Fisher's exact test, P < 0.05) in the number of negative biopsy specimens compared with those obtained using AMB alone, occurred with the FLC-resistant strain of C. albicans (kidney), C. krusei (spleen), C. glabrata (spleen), and C. parapsilosis (liver and spleen). Only by combining Mycograb with AMB was complete resolution of infection achieved for C. albicans, C. krusei, and C. glabrata.
Energy-Efficient Pipeline Templates for High-Performance Asynchronous Circuits (2011)

We present two novel energy-efficient pipeline templates for high throughput asynchronous circuits. The proposed templates, called N-P and N-Inverter pipelines, use a single-track handshake protocol. There are multiple stages of logic within each pipeline. The proposed techniques minimize handshake overheads associated with input tokens and intermediate logic nodes within a pipeline template. Each template can pack a significant amount of logic in a single stage, while still maintaining a fast cycle time of only 18 transitions. Noise and timing robustness constraints of our pipelined circuits are quantified across all process corners. We present completion detection scheme based on wide NOR gates, which results in significant latency and energy savings especially as the number of outputs increase. To fully quantify all design trade-offs, three separate pipeline implementations of an 8x8-bit Booth-encoded array multiplier are presented. Compared to a standard QDI pipeline implementation, the N-Inverter and N-P pipeline implementations reduced the energy-delay product by 38.5% and 44% respectively. The overall multiplier latency was reduced by 20.2% and 18.7%, while the total transistor width was reduced by 35.6% and 46% with N-Inverter and N-P pipeline templates respectively.
Textbook of EndourologyPhiladelphia: W. B. Saunders Co.1997. 650 pages. (1997)

No AccessJournal of UrologyBook Review1 Jul 1997Textbook of Endourology Robert G. MooreMD Robert G. MooreRobert G. Moore More articles by this author View All Author Informationhttps://doi.org/10.1097/00005392-199707000-00087AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Textbook of Endourology." The Journal of Urology, 158(1), p. 314 Department of Urology, Johns Hopkins Bayview Medical Center, Baltimore, Maryland.© 1997 by American Urological Association, Inc.FiguresReferencesRelatedDetails Volume 158Issue 1July 1997Page: 314 Advertisement Copyright & Permissions© 1997 by American Urological Association, Inc.MetricsAuthor Information Robert G. Moore More articles by this author Expand All Advertisement Loading ...
The NRF2‐related interactome and regulome contain multifunctional proteins and fine‐tuned autoregulatory loops (2012)

NRF2 is a well-known, master transcription factor (TF) of oxidative and xenobiotic stress responses. Recent studies uncovered an even wider regulatory role of NRF2 influencing carcinogenesis, inflammation and neurodegeneration. Prompted by these advances here we present a systems-level resource for NRF2 interactome and regulome that includes 289 protein-protein, 7469 TF-DNA and 85 miRNA interactions. As systems-level examples of NRF2-related signaling we identified regulatory loops of NRF2 interacting proteins (e.g., JNK1 and CBP) and a fine-tuned regulatory system, where 35 TFs regulated by NRF2 influence 63 miRNAs that down-regulate NRF2. The presented network and the uncovered regulatory loops may facilitate the development of efficient, NRF2-based therapeutic agents.
Real-Time Well Control Advisor (1992)

Abstract A summary of the design, and design rationale, for a software Well Site Advisor (WSA) tool to prompt and train drilling personnel in taking well control actions is presented. Key features of the WSA are: (1) a seven state Kaiman filter to estimate (track) and predict well and influx parameters during well control. Estimated and predicted parameters include bottom hole pressure, volume of influx gas, volume of influx liquid, influx position, influx distribution, influx velocity (top and bottom), and expected future pressures and volumes; (2) CuSum analysis of errors between predicted and measured pressures and volumes to detect meaningful deviations indicating possible problems; (3) automated pattern recognition or classification of data trends; (4) expert system processing to finalize the diagnosis of problems and provide advice; and (5) graphical user interface and efficient coding to provide rapid data entry, interpretation, and processing. The WSA system is the final product of DEA-49, a thirty-month study funded by the Drilling Engineers Association, to develop a real-time well control advisor tool. Prior prediction systems have usually been designed for well planning functions or post-kick control analysis and were not capable of responding to events as they occur during kick control operations. This system provides real-time computer capability to accurately process, predict, and interpret kick control surface measurements (e.g., drill pipe pressure, casing pressure, pit gain, drill string weight, and pump strokes per minute) so that automated problem detection, diagnosis, and advice are possible during kick control. Test results, including simulations, test well data, and actual kicks while drilling, are very promising and are discussed.
Dexmedetomidine oromucosal gel for noise‐associated acute anxiety and fear in dogs—a randomised, double‐blind, placebo‐controlled clinical study (2017)

The aim of this randomised, double-blind, placebo-controlled, clinical-field study was to evaluate the effect of dexmedetomidine oromucosal gel at subsedative doses in alleviation of noise-associated acute anxiety and fear in dogs. On New Year's Eve, 182 dogs with a history of acute anxiety and fear associated with fireworks received treatment as needed up to five times: 89 dogs received dexmedetomidine and 93 dogs received placebo. For the primary efficacy variables, dog owners assessed the overall treatment effect as well as signs and extent of anxiety and fear. The overall treatment effect was statistically significant (P<0.0001). An excellent or good treatment effect was reported for a higher proportion of dogs treated with dexmedetomidine (64/89, 72 per cent) than those receiving placebo (34/93, 37 per cent). Additionally, dexmedetomidine-treated dogs expressed significantly (P<0.0314) fewer signs of fear and anxiety despite the noise of fireworks. No local tolerance or clinical safety concerns occurred during the study. This study demonstrated that oromucosal dexmedetomidine at subsedative doses alleviates noise-associated acute anxiety and fear in dogs.
Scatter factor/hepatocyte growth factor in brain tumor growth and angiogenesis (2005)

The multifunctional growth factor scatter factor/hepatocyte growth factor (SF/HGF) and its receptor tyrosine kinase c-Met have emerged as key determinants of brain tumor growth and angiogenesis. SF/HGF and c-Met are expressed in brain tumors, the expression levels frequently correlating with tumor grade, tumor blood vessel density, and poor prognosis. Overexpression of SF/HGF and/or c-Met in brain tumor cells enhances their tumorigenicity, tumor growth, and tumor-associated angiogenesis. Conversely, inhibition of SF/HGF and c-Met in experimental tumor xenografts leads to inhibition of tumor growth and tumor angiogenesis. SF/HGF is expressed and secreted mainly by tumor cells and acts on c-Met receptors that are expressed in tumor cells and vascular endothelial cells. Activation of c-Met leads to induction of proliferation, migration, and invasion and to inhibition of apoptosis in tumor cells as well as in tumor vascular endothelial cells. Activation of tumor endothelial c-Met also induces extracellular matrix degradation, tubule formation, and angiogenesis in vivo. SF/HGF induces brain tumor angiogenesis directly through only partly known mechanisms and indirectly by regulating other angiogenic pathways such as VEGF. Different approaches to inhibiting SF/HGF and c-Met have been recently developed. These include receptor antagonism with SF/HGF fragments such as NK4, SF/HGF, and c-Met expression inhibition with U1snRNA/ribozymes; competitive ligand binding with soluble Met receptors; neutralizing antibodies to SF/HGF; and small molecular tyrosine kinase inhibitors. Use of these inhibitors in experimental tumor models leads to inhibition of tumor growth and angiogenesis. In this review, we summarize current knowledge of how the SF/HGF:c-Met pathway contributes to brain tumor malignancy with a focus on glioma angiogenesis.
Human Pluripotent Stem Cell-Based Approaches for Myocardial Repair: From the Electrophysiological Perspective (2011)

Heart diseases are a leading cause of mortality worldwide. Terminally differentiated adult cardiomyocytes (CMs) lack the innate ability to regenerate. Their malfunction or significant loss can lead to conditions from cardiac arrhythmias to heart failure. For myocardial repair, cell- and gene-based therapies offer promising alternatives to donor organ transplantation. Human embryonic stem cells (hESCs) can self-renew while maintaining their pluripotency. Direct reprogramming of adult somatic cells to become pluripotent hES-like cells (also known as induced pluripotent stem cells or iPSCs) has been achieved. Both hESCs and iPSCs have been successfully differentiated into genuine human CMs. In this review, we describe our current knowledge of the structure-function properties of hESC/iPSC-CMs, with an emphasis on their electrophysiology and Ca(2+) handling, along with the hurdles faced and potential solutions for translating into clinical and other applications (e.g., disease modeling, cardiotoxicity and drug screening).
Salicylic Acid Based Small Molecule Inhibitor for the Oncogenic Src Homology-2 Domain Containing Protein Tyrosine Phosphatase-2 (SHP2) (2010)

The Src homology-2 domain containing protein tyrosine phosphatase-2 (SHP2) plays a pivotal role in growth factor and cytokine signaling. Gain-of-function SHP2 mutations are associated with Noonan syndrome, various kinds of leukemias, and solid tumors. Thus, there is considerable interest in SHP2 as a potential target for anticancer and antileukemia therapy. We report a salicylic acid based combinatorial library approach aimed at binding both active site and unique nearby subpockets for enhanced affinity and selectivity. Screening of the library led to the identification of a SHP2 inhibitor II-B08 (compound 9) with highly efficacious cellular activity. Compound 9 blocks growth factor stimulated ERK1/2 activation and hematopoietic progenitor proliferation, providing supporting evidence that chemical inhibition of SHP2 may be therapeutically useful for anticancer and antileukemia treatment. X-ray crystallographic analysis of the structure of SHP2 in complex with 9 reveals molecular determinants that can be exploited for the acquisition of more potent and selective SHP2 inhibitors.
Association of Troponin T Detected With a Highly Sensitive Assay and Cardiac Structure and Mortality Risk in the General Population (2010)

In this population-based cohort, cTnT detected with a highly sensitive assay was associated with structural heart disease and subsequent risk for all-cause mortality.
MAPHYD - A DIGITAL MAP-BASED HYDROLOGIC MODELING SYSTEM (1989)

A digital map-based hydrologic modeling system, called MAPHYD, has been developed and applied to urban watersheds. MAPHYD incorporates automatic generation of model input data using geographic information system functions and a suite of hydrologic modeling algorithms into a user-friendly PC workstation. Interactive computer graphics techniques were used to quickly develop a watershed digital database on topography, soils, landuse, and rainfall distribution. The spatial distribution of the data are mapped as color codes which can be interpreted by the linked hydrologic response algorithms. Digital terrain modeling was accomplished to obtain slope and the direction of slope for a user-selectable grid cell resolution. Rainfall patterns were defined using radar rainfall images. Computations of runoff were based on unit hydrograph, time-area, or cascade-of-reservoirs algoritms, and various infiltration mechanisms were provided. Alternate output displays include the runoff hydrograph and the spatial distribution of runoff using an interval color scale.
Analysis of the genomic sequence encoding the 29-kDa cysteine-rich protein of Entamoeba histolytica. (1993)

By analyzing cDNA and genomic clones coding for the 29-kDa cysteine-rich protein of Entamoeba histolytica, substantial sequence differences were found to the 5'-end of a previously described full-length cDNA coding for the same protein (Reed et al., 1992), which was reported to contain an untranslated 5'-sequence of at least 171 nucleotides, unusual for E. histolytica cDNAs. We found evidence that the cDNA published by Reed et al. (1992) represents a hybridclone composed of two unrelated sequences and that the gene coding for the 29-kDa molecule comprises all of the features typical for E. histolytica genes. A data base analysis revealed substantial sequence homology of the 29-kDa protein to a class of polypeptides found in prokaryotic organisms that may be involved in the inactivation of hydrogen peroxide.