gebhart/patrepeval huggingface dataset:
Video Compression - From Concepts to the H.264/AVC Standard (2004)

Over the last one and a half decades, digital video compression technologies have become an integral part of the way we create, communicate, and consume visual information. In this paper, techniques for video compression are reviewed, starting from basic concepts. The rate-distortion performance of modern video compression schemes is the result of an interaction between motion representation techniques, intra-picture prediction techniques, waveform coding of differences, and waveform coding of various refreshed regions. The paper starts with an explanation of the basic concepts of video codec design and then explains how these various features have been integrated into international standards, up to and including the most recent such standard, known as H.264/AVC.
Crosshole electromagnetic tomography: A new technology for oil field characterization (1995)

With the advent of crosshole seismic technology in the 1980s, a new generation of high resolution geophysical tools has become available for reservoir characterization. The chief improvement is simply that the tools are deployed in boreholes so measurements take place much closer to the region of interest.
Cloned human polyomavirus JC DNA can transform human amnion cells (1980)

The genome of the human polyomavirus JC (Mad-1 strain) was molecularly cloned in Escherichia coli by using the plasmid vector pBR322. Recombinant DNA molecules were constructed with the entire JC genome inserted either at its unique EcoRI site at 0.0 map units or at its unique BamHI site at 0.51 map units. Viral DNA from each of these recombinant plasmids was capable of transforming human amnion cells, and cell lines established from transformed foci were positive for JC tumor antigen as assayed by indirect immunofluorescence.
Interleukin (IL)-15 and IL-7 Jointly Regulate Homeostatic Proliferation of Memory Phenotype CD8+ Cells but Are Not Required for Memory Phenotype CD4+ Cells (2002)

The overall size and composition of the pool of naive and memory T cells are tightly regulated by homeostatic mechanisms. Recent work has shown that homeostasis of naive T cells is controlled by two factors, self-major histocompatibility complex (MHC)/peptide ligands and a cytokine, interleukin (IL)-7. In particular, contact with these two factors is required for naive CD4+ and CD8+ cells to undergo "homeostatic" proliferation, i.e., proliferation induced as a consequence of severe T cell depletion. In contrast to naive T cells, the factors that drive memory T cells to undergo homeostatic proliferation are poorly understood. To address this issue, purified memory phenotype CD4+ and CD8+ cells from normal mice were adoptively transferred into various gene-knockout mice rendered T cell-deficient by sublethal irradiation. Three findings are reported. First, unlike naive T cells, homeostatic proliferation of memory T cells is largely MHC independent. Second, memory CD8+ cells can utilize either IL-7 or IL-15 to undergo homeostatic proliferation; however, in the absence of both IL-7 and IL-15, homeostatic proliferation fails to occur. Third, unlike memory CD8+ cells, homeostatic proliferation of memory CD4+ cells is independent of IL-7 and IL-15 (also IL-4). Thus, the homeostatic proliferation mechanisms that control memory CD8+ cells and memory CD4+ cells are quite distinct.
Virtual networks of the future-converging public and private IN (1993)

The paper considers the evolution of private network systems towards 'private INs' and outlines the implications for public network operators deploying virtual network services. In particular the paper outlines some of the issues which must be addressed by future virtual network services.
Characterization of in vitro and in vivo hypomethylating effects of decitabine in acute myeloid leukemia by a rapid, specific and sensitive LC-MS/MS method (2007)

DNA hypermethylation is a common finding in malignant cells and has been explored as a therapeutic target for hypomethylating agents (e.g., decitabine). Detection of changes in DNA methylation might serve as a pharmacodynamic endpoint to establish the biological activity of these agents and predict clinical response. We developed and validated a rapid, sensitive and specific LC-MS/MS method for determination of global DNA methylation (GDM) in vitro and in vivo. Ratios of 5-methyl-2'-deoxycytidine (5mdC) to the internal standard 2-deoxyguanosine (2dG) in mass signal were used to quantify GDM levels. The assay was validated in a linear range from 40 fmol to 200 pmol 5mdC. The intra-day precision values ranged from 2.8 to 9.9% and the inter-day values from 1.1 to 15.0%. The accuracy of the assay varied between 96.7 and 109.5%. This method was initially applied for characterization of decitabine-induced GDM changes in in-vitro-treated leukemia cells. Following exposure to 2.5 microM decitabine, GDM decreased to approximately 50% of the baseline value. The clinical applicability of this method was then demonstrated in bone marrow samples from patients with acute myeloid leukemia treated with decitabine. Our data support the use of our LC-MS/MS method for clinical pharmacodynamic determination of changes in GDM in vivo.
Platelets contain proteins immunologically related to red cell spectrin and protein 4.1 (1985)

Human platelets were tested for the presence of proteins immunologically cross-reactive with red cell spectrin and protein 4.1. As assessed by indirect immunofluorescence microscopy, platelets were specifically reactive with affinity-purified rabbit antisera against red cell spectrin and protein 4.1. The immunoreactive platelet constituents were further analyzed by sodium dodecyl sulfate- polyacrylamide gel electrophoresis, followed by electrophoretic transfer to nitrocellulose paper and immunoperoxidase staining. We found that whole platelets, membranes, and cytoskeletal preparations isolated by Triton X-100 extraction contain small amounts of proteins reacting with anti-spectrin or anti-protein 4.1 antiserum. The immunoreactive spectrin-like platelet protein has an apparent molecular weight of 240,000 and comigrates with the alpha-subunit of red cell spectrin. The major immunoreactive protein 4.1-like constituent has an apparent molecular weight of 78,000, which is slightly less than that of red cell protein 4.1. We conclude that platelets contain a spectrin- like protein which, by analogy with red cell spectrin, may have a role in membrane-cytoskeletal attachment. The properties and function of the platelet protein 4.1-like constituent are not yet known.
Using multivariate adaptive regression splines to predict the distributions of New Zealand's freshwater diadromous fish (2005)

Summary 1. Relationships between probabilities of occurrence for fifteen diadromous fish species and environmental variables characterising their habitat in fluvial waters were explored using an extensive collection of distributional data from New Zealand rivers and streams. Environmental predictors were chosen for their likely functional relevance, and included variables describing conditions in the stream segment where sampling occurred, downstream factors affecting the ability of fish to move upriver from the sea, and upstream, catchment‐scale factors mostly affecting variation in river flows. 2. Analyses were performed using multivariate adaptive regression splines (MARS), a technique that uses piece‐wise linear segments to describe non‐linear relationships between species and environmental variables. All species were analysed using an option that allows simultaneous analysis of community data to identify the combination of environmental variables best able to predict the occurrence of the component species. Model discrimination was assessed for each species using the area under the receiver operating characteristic curve (ROC) statistic, calculated using a bootstrap procedure that estimates performance when predictions are made to independent data. 3. Environmental predictors having the strongest overall relationships with probabilities of occurrence included distance from the sea, stream size, summer temperature, and catchment‐scale drivers of variation in stream flow. Many species were also sensitive to variation in either the average and/or maximum downstream slope, and riparian shade was an important predictor for some species. 4. Analysis results were imported into a Geographic Information System where they were combined with extensive environmental data, allowing spatially explicit predictions of probabilities of occurrence by species to be made for New Zealand's entire river network. This information will provide a valuable context for future conservation management in New Zealand's rivers and streams.
Multiple immunoglobulin heavy-chain gene transcripts in Abelson murine leukemia virus-transformed lymphoid cell lines. (1982)

Lymphoid cells transformed by Abelson murine leukemia virus (A-MuLV) contain three classes of RNA transcripts from immunoglobulin mu genes. P mu-mRNAs (productive) correspond to the normal 2.7-kilobase (kb) membrane (mu m) and 2.4-kb secreted (mu s) mu mRNA species both in size and coding capacity and occur at approximately equal abundance in most mu-positive (pre-B-like) A-MuLV transformants. A mu-mRNAs (aberrant) generally fall into one of two categories--aberrantly small 2.3-kb mu m and 2.0-kb mu s mRNAs which encode aberrantly small mu polypeptide chains, or normal-sized, V H-containing mu RNAs which do not encode immunologically identifiable mu polypeptide chains. In one case, the latter type of A mu-mRNA was demonstrated to result from an in-phase termination codon in the D segment of the mu mRNA. Also, most, if not all, A-MuLV transformants express members of a 3.0 to 1.9-kb set of C mu-containing, but V H-negative S mu-RNAs (for sterile), the expression of which may occur simultaneously with but independently of P mu-mRNAs or A mu-mRNAs. The S mu-RNA sequences do not encode immunologically identifiable mu chains and can be produced by cells with unrearranged heavy-chain alleles, such as T-lymphocytes, although the structure of the S mu-RNAs from T-lymphoid cells appears to be different from that of B-lymphoid cell S mu-RNAs. Certain A-MuLV transformants also express gamma-RNA sequences that are probably analogous to the three different forms of mu RNA. These data support the concept that heavy-chain allelic exclusion, like that of light chains, is not mediated by control at the DNA or RNA levels but is probably a consequence of feedback control from cytoplasmic mu chains.
Beta protein of bacteriophage lambda promotes renaturation of DNA. (1981)

The protein encoded by the red beta gene of bacteriophage lambda was found to promote reannealing of complementary single strands of DNA. Reannealing activity was optimal at pH 6.0 and required a divalent cation. A threshold temperature of at least 15 degrees C was necessary in order to detect activity. The reaction was linear with time for about 20 min, but the extent of reaction was dependent upon the amount of beta protein added. Reannealing of complementary single strands was confirmed by measuring increased lability of DNA to lambda exonuclease. When protein preparations from red- lysogens were tested for ability to promote reannealing, high activity was observed in a mutant altered in the gene for exonuclease, but there was low activity in a mutant altered in the gene for beta protein.
Interference ofPseudomonas aeruginosasignalling and biofilm formation for infection control (2010)

Pseudomonas aeruginosa is the best described bacterium with regards to quorum sensing (QS), in vitro biofilm formation and the development of antibiotic tolerance. Biofilms composed of P. aeruginosa are thought to be the underlying cause of many chronic infections, including those in wounds and in the lungs of patients with cystic fibrosis. In this review, we provide an overview of the molecular mechanisms involved in QS, QS-enabled virulence, biofilm formation and biofilm-enabled antibiotic tolerance. We now have substantial knowledge of the multicellular behaviour of P. aeruginosa in vitro. A major task for the future is to investigate how such in vitro data correlate with the in vivo behaviour of P. aeruginosa, and how to treat chronic infections of this bacterium in patients.
The Digestion of Human Hair Keratin by Microsporum canis Bodin (1953)

SUMMARY: Microsporum canis Bodin, the causative agent of animal ringworm in children and adults, is able to digest human hair keratin in vitro. The process of degradation has been followed by microscopic observation and an analysis of the resulting amino-acids which accumulate in the medium after growth on human hair has been made by chromatographic techniques.
BRCA1 interacts with Nrf2 to regulate antioxidant signaling and cell survival (2013)

Oxidative stress plays an important role in cancer development and treatment. Recent data implicate the tumor suppressor BRCA1 in regulating oxidative stress, but the molecular mechanism and the impact in BRCA1-associated tumorigenesis remain unclear. Here, we show that BRCA1 regulates Nrf2-dependent antioxidant signaling by physically interacting with Nrf2 and promoting its stability and activation. BRCA1-deficient mouse primary mammary epithelial cells show low expression of Nrf2-regulated antioxidant enzymes and accumulate reactive oxygen species (ROS) that impair survival in vivo. Increased Nrf2 activation rescues survival and ROS levels in BRCA1-null cells. Interestingly, 53BP1 inactivation, which has been shown to alleviate several defects associated with BRCA1 loss, rescues survival of BRCA1-null cells without restoring ROS levels. We demonstrate that estrogen treatment partially restores Nrf2 levels in the absence of BRCA1. Our data suggest that Nrf2-regulated antioxidant response plays a crucial role in controlling survival downstream of BRCA1 loss. The ability of estrogen to induce Nrf2 posits an involvement of an estrogen-Nrf2 connection in BRCA1 tumor suppression. Lastly, BRCA1-mutated tumors retain a defective antioxidant response that increases the sensitivity to oxidative stress. In conclusion, the role of BRCA1 in regulating Nrf2 activity suggests important implications for both the etiology and treatment of BRCA1-related cancers.
Localization of an NH2-terminal Disease-causing Mutation Hot Spot to the “Clamp” Region in the Three-dimensional Structure of the Cardiac Ryanodine Receptor (2007)

A region between residues 414 and 466 in the cardiac ryanodine receptor (RyR2) harbors more than half of the known NH(2)-terminal mutations associated with cardiac arrhythmias and sudden death. To gain insight into the structural basis of this NH(2)-terminal mutation hot spot, we have determined its location in the three-dimensional structure of RyR2. Green fluorescent protein (GFP), used as a structural marker, was inserted into the middle of this mutation hot spot after Ser-437 in the RyR2 sequence. The resultant GFP-RyR2 fusion protein, RyR2(S437-GFP,) was expressed in HEK293 cells and characterized using Ca(2+) release, [(3)H]ryanodine binding, and single cell Ca(2+) imaging studies. These functional analyses revealed that RyR2(S437-GFP) forms a caffeine- and ryanodine-sensitive Ca(2+) release channel that possesses Ca(2+) and caffeine dependence of activation indistinguishable from that of wild type (wt) RyR2. HEK293 cells expressing RyR2(S437-GFP) displayed a propensity for store overload-induced Ca(2+) release similar to that in cells expressing RyR2-wt. The three-dimensional structure of the purified RyR2(S437-GFP) was reconstructed using cryo-electron microscopy and single particle image processing. Subtraction of the three-dimensional reconstructions of RyR2-wt and RyR2(S437-GFP) revealed the location of the inserted GFP, and hence the NH(2)-terminal mutation hot spot, in a region between domains 5 and 9 in the clamp-shaped structure. This location is close to a previously mapped central disease-causing mutation site located in a region between domains 5 and 6. These results, together with findings from previous studies, suggest that the proposed interactions between the NH(2)-terminal and central regions of RyR2 are likely to take place between domains 5 and 6 and that the clamp-shaped structure, which shows substantial conformational differences between the closed and open states, is highly susceptible to disease-causing mutations.
Targeting of non-small cell lung cancer using HMFG1-99mTc monoclonal antibodies. (1993)

Anti HMFG1 monoclonal antibodies labeled with 99mTc were used for the detection of non-small cell lung cancers and their metastases in 18 patients (12 squamous cell cancers, 2 large cell lung cancers, 1 adenocarcinoma and 3 undifferentiated non-small cell lung cancer). According to performed therapy all patients were divided into three groups: group 1 consisted of 13 patients who had not received chemotherapy or radiotherapy before immunoscintigraphy (IS), group 2 included 3 patients who had undergone IS during external beam radiotherapy, and group 3 (two patients) who had received both chemotherapy and radiotherapy before IS. After antibody administration planar scintigraphy of the head and neck, chest in anterior and posterior projection, anterior abdomen, pelvis, thighs and calves was obtained at 10 minutes, 5 hours and 24 hours. The scans were interpreted semi-quantitatively using T/NT ratio. In the first group IS was found true positive in 5/13 patients (38%), and T/NT ratio ranged from 1.3-1.5. In the second group all three patients were true positive and T/NT ratio ranged from 1.76 to 2.1. In the third group both patients were found false negative. Successful metastases detection was found in 4/13 patients (30%).
Neutrophil elastase and cathepsin G stimulate secretion from cultured bovine airway gland serous cells. (1990)

To investigate the hypothesis that neutrophil proteases stimulate airway gland secretion, we studied the effect of human cathepsin G and elastase on secretion of 35S-labeled macromolecules from cultured bovine airway gland serous cells. Both proteases stimulated secretion in a concentration-dependent fashion with a threshold of greater than or equal to 10(-10) M. Elastase was more potent than cathepsin G, causing a maximal secretory response of 1,810 +/- 60% over baseline at 10(-8) M. The maximal response to cathepsin G (1,810 +/- 70% over baseline at 10(-7) M) was similar to the maximal response to elastase. These responses were greater than 10-fold larger than the response to other agonists such as histamine. Protease-induced secretion was noncytotoxic and required catalytically active enzymes. The predominant sulfated macromolecule released by proteases was chondroitin sulfate proteoglycan. Immunocytochemical staining demonstrated chondroitin sulfate in cytoplasmic granules and decreased granular staining after stimulation of cells with elastase. The neutrophil proteases also degraded the proteoglycan released from serous cells. Cathepsin G and elastase in supernatant obtained by degranulation of human peripheral neutrophils also caused a secretory response. Thus, neutrophil proteases stimulate airway gland serous cell secretion of chondroitin sulfate proteoglycan and degrade the secreted product. These findings suggest a potential role for neutrophil proteases in the pathogenesis of increased and abnormal submucosal gland secretions in diseases associated with inflammation and neutrophil infiltration of the airways.
Analysis of immune deviation elicited by antigens injected into the subretinal space. (1998)

The subretinal space supports immune deviation for histoincompatible tumor cells and soluble protein antigens by actively suppressing antigen-specific DTH. Acute loss of immune privilege in the subretinal space and the VC does not cause loss of privilege in the AC, but abolition of immune privilege in the AC eliminates the capacity of the subretinal space and the VC to support immune deviation to antigens injected locally.
vacC, a virulence-associated chromosomal locus of Shigella flexneri, is homologous to tgt, a gene encoding tRNA-guanine transglycosylase (Tgt) of Escherichia coli K-12 (1994)

The genetic determinants required for invasion of epithelial cells by Shigella flexneri and for the subsequent bacterial spreading are encoded by the large virulence plasmid. Expression of the virulence genes is under the control of various genes on the large plasmid as well as on the chromosome. We previously identified one of the virulence-associated loci near phoBR in the NotI-C fragment of the chromosome of S. flexneri 2a YSH6000 and designated the locus vacC. The vacC mutant showed decreased levels of IpaC, and IpaD proteins as well as transcription of ipa, an operon essential for bacterial invasion (N. Okada, C. Sasakawa, T. Tobe, M. Yamada, S. Nagai, K. A. Talukder, K. Komatsu, S. Kanegasaki, and M. Yoshikawa, Mol. Microbiol. 5:187-195, 1991). To elucidate the molecular nature of the vacC locus, we cloned the vacC region from YSH6000 on a 1.8-kb SalI-BamHI DNA fragment. The nucleotide sequence of the 1,822-bp vacC clone was highly (&gt; 98%) homologous to the tgt region of Escherichia coli K-12, which is located at 9.3 min on the linkage map. Complementation tests indicated that the vacC function was encoded by an open reading frame expressing a 42.5-kDa protein, which corresponded to the tgt gene of E. coli K-12, coding for tRNA-guanine transglycosylase (Tgt) (K. Reuter, R. Slany, F. Ullrich, and H. Kersten, J. Bacteriol. 173:2256-2264, 1991). The cloned tgt gene from E. coli K-12 restored the virulence phenotype to the vacC mutant of YSH6000. Characterization of the vacC mutant indicated that levels of VirG, a protein essential for bacterial spreading, and VirF, the positive regulator for the expression of the virG and ipaBCD operons, decreased significantly compared with those of the wild type. Similar phenotypic changes occurred in vacC mutants constructed by insertion of a neomycin resistance gene in shigellae and enteroinvasive E. coli strains, consistent with the hypothesis that the vacC (tgt) gene contributes to the pathogenicity of Shigella flexneri.
The Marine Fishes of Broward County, Florida: Final Report of 1998-2002 Survey Results (2005)

We inventoried fishes associated with three hardbottom reef tracts that are separated by sand and run parallel to the coast in sequentially deeper water offshore Broward County, Florida. Using SCUBA and the Bohnsack-Bannerot visual point count method, we recorded fish abundance, species richness, sizes (TL), and general habitat characteristics within an imaginary 15m cylinder extending from the substrate to the surface. Sites were sampled along transects at quarter nautical mile intervals along 18 nautical miles of coastline at western and eastern edges, and crest of each of the three reef tracts. A total of 86,463 fishes belonging to 208 species and 52 families was censused from 667 sites over four years (August 1998 to November 2002). Mean species richness, mean total abundance and mean total biomass of fishes increased significantly on each reef tract moving offshore (p Differences were found within reef tracts based on edge or crest sites and position along reefs north or south of Port Everglades and Hillsboro Inlet. Sites within 5 na. mi. south of Port Everglades had lower total abundance and species richness (p Of management interest, was a scarcity or absence of groupers and snappers observed over four years. Although juvenile red grouper were frequently seen (n = 232 at 667 sites), only two were above legal minimum size. No goliath or black grouper were recorded. A total of 10 gag, yellowfin, or scamp grouper was observed; none were legal. Among six snapper species, 219 of 718 were of legal size.