gebhart/patrepeval huggingface dataset:
A block-based gradient descent search algorithm for block motion estimation in video coding (1996)

A block-based gradient descent search (BBGDS) algorithm is proposed in this paper to perform block motion estimation in video coding. The BBGDS evaluates the values of a given objective function starting from a small centralized checking block. The minimum within the checking block is found, and the gradient descent direction where the minimum is expected to lie is used to determine the search direction and the position of the new checking block. The BBGDS is compared with full search (FS), three-step search (TSS), one-at-a-time search (OTS), and new three-step search (NTSS). Experimental results show that the proposed technique provides competitive performance with reduced computational complexity.
Antifungal Activity of Bacillus Species Against Fusarium and Analysis of the Potential Mechanisms Used in Biocontrol (2018)

<i>Fusarium</i> is a complex genus of ascomycete fungi that consists of plant pathogens of agricultural relevance. Controlling <i>Fusarium</i> infection in crops that leads to substantial yield losses is challenging. These economic losses along with environmental and human health concerns over the usage of chemicals in attaining disease control are shifting focus toward the use of biocontrol agents for effective control of phytopathogenic <i>Fusarium</i> spp. In the present study, an analysis of the plant-growth promoting (PGP) and biocontrol attributes of four bacilli (<i>Bacillus simplex</i> 30N-5, <i>B. simplex</i> 11, <i>B. simplex</i> 237, and <i>B. subtilis</i> 30VD-1) has been conducted. The production of cellulase, xylanase, pectinase, and chitinase in functional assays was studied, followed by <i>in silico</i> gene analysis of the PGP-related and biocontrol-associated genes. Of all the bacilli included in this study, <i>B. subtilis</i> 30VD-1 (30VD-1) demonstrated the most effective antagonism against <i>Fusarium</i> spp. under <i>in vitro</i> conditions. Additionally, 100 μg/ml of the crude 1-butanol extract of 30VD-1's cell-free culture filtrate caused about 40% inhibition in radial growth of <i>Fusarium</i> spp. Pea seed bacterization with 30VD-1 led to considerable reduction in wilt severity in plants with about 35% increase in dry plant biomass over uninoculated plants growing in <i>Fusarium</i>-infested soil. Phase contrast microscopy demonstrated distortions and abnormal swellings in <i>F. oxysporum</i> hyphae on co-culturing with 30VD-1. The results suggest a multivariate mode of antagonism of 30VD-1 against phytopathogenic <i>Fusarium</i> spp., by producing chitinase, volatiles, and other antifungal molecules, the characterization of which is underway.
Human fibroblast stromelysin catalytic domain: expression, purification, and characterization of a C-terminally truncated form (1991)

Stromelysin-1 is a member of a tissue metalloproteinase family whose members are all capable of degrading extracellular matrix components. A truncated form of human fibroblast prostromelysin 1 lacking the C-terminal, hemopexin-like domain has been expressed in Escherichia coli and purified to homogeneity. Treatment of this short form of prostromelysin with (aminophenyl)mercuric acetate resulted in activation and loss of the propeptide in a manner identical with the wild-type, full-length protein. Kinetic comparisons using Nle11-substance P as a substrate showed that the wild-type stromelysin and the truncated form of the enzyme had similar kcat and Km values. Likewise, both enzymes displayed similar Ki values for a hydroxamate-containing peptide inhibitor. Taken together, these results indicate that the C-terminal portion of stromelysin is not required for proper folding of the catalytic domain, maintenance of the enzyme in a latent form, activation with an organomercurial, cleavage of a peptide substrate, or interaction with an inhibitor. Moreover, the active short form of stromelysin displayed a reduction in the C-terminal heterogeneity, a characteristic degradation of the full-length stromelysin, and thereby provides a more suitable protein for future structural studies.
Crohn's disease (2003)

This comprehensive review promotes the novel concept that a defensin deficiency, i.e. lack of mucosal peptide antibiotics, may play a pivotal role in the aetiopathogenesis of Crohn's disease. Such an impaired function of this chemical barrier is consistent with the epidemiological relationship of good domestic hygiene with the incidence of inflammatory bowel diseases. The disregulated adaptive immune system, formerly believed to be the major cause in the development of Crohn's disease, may reflect only the primary break of the mucosal defence since the immune response is mostly directed against lumenal bacteria. Recent work has identified five different defensins expressed in colonic mucosa. In contrast to ulcerative colitis, Crohn's disease is characterised by an impaired induction of human beta defensins 2 and 3. This deficient induction may be due to changes in the intracellular transcription by NFkappaB and the intracellular peptidoglycan receptor NOD2, mutated in Crohn's disease. These findings are consistent with the mucosal attachment of lumenal bacteria in inflammatory bowel diseases and the frequent occurrence of other infectious agents. The hypothesis of an impaired mucosal antibacterial activity is also consistent with the benefit from antibiotic or probiotic treatment in certain inflammatory bowel disease states.
Holographic equalisation using active arrayed waveguide gratings (1999)

We have described a novel holographic technique which is capable of achieving a variety of WDM functions by using a phase-modulation active arrayed waveguide grating (AWG). Simulations have demonstrated EDFA equalisation of 12dB for 8x 100 GHz spaced WDM channels, with inter-channel ASE suppressed by greater than 20 dB. The holographic designs are robust to individual phase-modulator failures and fabrication phase errors.
INFECTIOUS PANCREATIC NECROSIS VIRUS — TEMPERATURE AND AGE FACTORS IN MORTALITY (1971)

Infectious pancreatic necrosis virus was present in brook trout in two Ontario salmonid hatcheries but did not appear to cause high mortality. Experiments and field observations showed that a number of factors were responsible for the low mortality, in particular, low water temperatures during the age of highest susceptibility of the fry and a lack of, or low level of transmission of virus during these periods of cold water temperatures.
Protein engineering to create biologically active peptides: recombinant human rhinoviruses that display peptide sequences. (1997)

This paper describes the use of human rhinovirus to display peptides corresponding to biologically active sequences. While this system can be used to reconstruct essentially any biologically active sequence for which there is a corresponding ligand that can be used for its selection, we have focused on using this system to display immunogens from dangerous pathogens as a means to develop vaccines. Five mutagenesis approaches are illustrated as ways to generate functionally active moieties. The mutagenesis approaches illustrated can be employed with any of a large number of possible display vectors; however, human rhinovirus might be especially useful in cases where it will be important to derive the benefits of delivery by a live-virus approach. Examples are shown in which reconstruction of immunogens corresponding to the V3 loop of the gp120 glycoprotein of the human immunodeficiency virus type 1 (HIV-1) on the surface of rhinovirus has yielded apparently effective mimics of the HIV-1 immunogens (as measured by their ability to be neutralized by anti-HIV-1 antibodies as well as their ability to elicit the production of antibodies capable of neutralizing HIV-1 in cell culture). This system offers the opportunity to reconstruct functionally important moieties that derive from proteins or pathogens that are either too dangerous or difficult to isolate for use as vaccine preparations themselves.
Isolation and characterization of PKC-L, a new member of the protein kinase C-related gene family specifically expressed in lung, skin, and heart. (1991)

We have isolated and characterized a new human cDNA, coding for a protein kinase, related to the protein kinase C (PKC) gene family. Although this protein kinase shares some homologous sequences and structural features with the four members of the PKC family initially isolated (alpha, beta I, beta II, and gamma), it shows more homology with the recently described PKC-related subfamily, encoded by the cDNAs delta, epsilon, and zeta. The transcript for this gene product, termed PKC-L, is most abundant in lung tissue, less expressed in heart and skin tissue, and exhibited very low expression in brain tissue. Thus, its tissue distribution is different from that described for other mammalian members of the PKC gene family, their expression being enriched in brain tissues. PKC-L is also expressed in several human cell lines, including the human epidermoid carcinoma line A431. The ability of phorbol esters to bind to and stimulate the kinase activity of PKC-L was revealed by introducing the cDNA into COS cells.
Prediction of lipoprotein signal peptides in Gram‐negative bacteria (2003)

A method to predict lipoprotein signal peptides in Gram-negative Eubacteria, LipoP, has been developed. The hidden Markov model (HMM) was able to distinguish between lipoproteins (SPaseII-cleaved proteins), SPaseI-cleaved proteins, cytoplasmic proteins, and transmembrane proteins. This predictor was able to predict 96.8% of the lipoproteins correctly with only 0.3% false positives in a set of SPaseI-cleaved, cytoplasmic, and transmembrane proteins. The results obtained were significantly better than those of previously developed methods. Even though Gram-positive lipoprotein signal peptides differ from Gram-negatives, the HMM was able to identify 92.9% of the lipoproteins included in a Gram-positive test set. A genome search was carried out for 12 Gram-negative genomes and one Gram-positive genome. The results for Escherichia coli K12 were compared with new experimental data, and the predictions by the HMM agree well with the experimentally verified lipoproteins. A neural network-based predictor was developed for comparison, and it gave very similar results. LipoP is available as a Web server at www.cbs.dtu.dk/services/LipoP/.
A Novel Preclinical Method to Quantitatively Evaluate Early-Stage Metastatic Events at the Murine Blood–Brain Barrier (2014)

The observation that approximately 15% of women with disseminated breast cancer will develop symptomatic brain metastases combined with treatment guidelines discouraging single-agent chemotherapeutic strategies facilitates the desire for novel strategies aimed at outright brain metastasis prevention. Effective and robust preclinical methods to evaluate early-stage metastatic processes, brain metastases burden, and overall mean survival are lacking. Here, we develop a novel method to quantitate early metastatic events (arresting and extravasation) in addition to traditional end time-point parameters such as tumor burden and survival in an experimental mouse model of brain metastases of breast cancer. Using this method, a reduced number of viable brain-seeking metastatic cells (from 3,331 ± 263 cells/brain to 1,079 ± 495 cells/brain) were arrested in brain one week postinjection after TGFβ knockdown. Treatment with a TGFβ receptor inhibitor, galunisertib, reduced the number of arrested cells in brain to 808 ± 82 cells/brain. Furthermore, we observed a reduction in the percentage of extravasated cells (from 63% to 30%) compared with cells remaining intralumenal when TGFβ is knocked down or inhibited with galunisertib (40%). The observed reduction of extravasated metastatic cells in brain translated to smaller and fewer brain metastases and resulted in prolonged mean survival (from 36 days to 62 days). This method opens up potentially new avenues of metastases prevention research by providing critical data important to early brain metastasis of breast cancer events.
N-myristoyltransferase proteins in breast cancer: prognostic relevance and validation as a new drug target (2021)

These results support further evaluation of NMT immunohistochemistry for patient selection and clinical trials of NMT inhibition in breast cancer patients.
Processing of cyclin E differs between normal and tumor breast cells. (2000)

Cyclin E is a G1 cyclin essential for G1 to S-phase transition of the cell cycle with a profound role in oncogenesis. In tumor cells and tissues, cyclin E is overexpressed and present in its lower molecular weight (LMW) isoforms, and it can be used as a prognosticator for poor patient outcome. In this study, we have examined differences in the processing of cyclin E between normal mammary epithelial and breast cancer cell lines. Five NH2-terminally deleted epitope-tagged (FLAG) cyclin E vectors were constructed spanning the range of LMW forms observed in tumor cells. These constructs were transfected into normal and tumor cells and analyzed for the production of cyclin E-FLAG protein products by Western blot analysis with FLAG and cyclin E antibodies. Our results show that only tumor cells had the machinery to process these cyclin E-FLAG constructs to their LMW forms, whereas normal cells mainly expressed the full-length unprocessed form of each protein. Tumor and normal cells always process the cyclin E-FLAG protein in the same way as endogenously expressed cyclin E. This phenomenon is consistent with all of the cell lines used, regardless of transfection efficiency, time of processing posttransfection, or method of transfection. Furthermore, measurement of FLAG-associated kinase activity in the transfectants revealed that the protein products of the cyclin E-FLAG constructs are 10 times more active in tumor cells than in normal cells. These studies suggest that the LMW forms of cyclin E detected at a much higher level in tumor cells arise from posttranslational action of a protease.
HDAC inhibitor PCI-24781 decreases RAD51 expression and inhibits homologous recombination (2007)

Histone deacetylase (HDAC) inhibitors such as the phenyl hydroxamic acid PCI-24781 have emerged recently as a class of therapeutic agents for the treatment of cancer. Recent data showing synergy of HDAC inhibitors with ionizing radiation and other DNA-damaging agents have suggested that HDAC inhibitors may act, in part, by inhibiting DNA repair. Here we present evidence that HDAC enzymes are important for homologous recombinational repair of DNA double-strand breaks. Combination studies of PCI-24781 with the poly(ADP-ribose) polymerase inhibitor PJ34, an agent thought to produce lesions repaired by homologous recombination (HR), resulted in a synergistic effect on apoptosis. Immunofluorescence analysis demonstrated that HDAC inhibition caused a complete inhibition of subnuclear repair foci in response to ionizing radiation. Mechanistic investigations revealed that inhibition of HDAC enzymes by PCI-24781 led to a significant reduction in the transcription of genes specifically associated with HR, including RAD51. RAD51 protein levels were significantly decreased after 24 h of drug exposure both in vitro and in vivo. Consistent with inhibition of HR, treatment with PCI-24781 resulted in a decreased ability to perform homology directed repair of I-SceI-induced chromosome breaks in transfected CHO cells. In addition, an enhancement of cell killing was observed in Ku mutant cells lacking functional nonhomologous end joining compared with WT cells. Together these results demonstrate that HDAC enzymes are critically important to enable functional HR by controlling the expression of HR-related genes and promoting the proper assembly of HR-directed subnuclear foci.
Regulation of retrotransposition in Saccharomyces cerevisiae (1991)

Retrotransposons are a widely distributed group of eukaryotic mobile genetic elements that transpose through an RNA intermediate. The element Ty (Transposon yeast), found in the yeast Saccharomyces cerevisiae, is a model system for the study of retrotransposons because of the experimental tools that exist to manipulate and detect transposition. Ty transposition can be elevated to levels exceeding one transposition event per cell when an element is expressed from an inducible yeast promoter. In addition, individual genomic Ty elements can be tagged with a retrotransposition indicator gene that allows transposition events occurring at a rate of 10(-5) to 10(-7) per element per cell division to be detected phenotypically. These systems are being used to elucidate the mechanism of Ty transposition and clarify how Ty transposition is controlled.
Adalimumab in the treatment of arthritis (2007)

Tumor necrosis factor (TNF) has been implicated in a number of arthritic disease states, including rheumatoid arthritis, psoriatic arthritis, and ankylosing spondylitis. Adalimumab is the first fully human, high-affinity, recombinant immunoglobulin G(1) (IgG(1)) anti-TNF monoclonal antibody. Adalimumab in combination with methotrexate or standard antirheumatic therapies, or as monotherapy, is effective in the treatment of adults with active rheumatoid arthritis who have had an inadequate response to disease-modifying antirheumatic drugs. Adalimumab is also effective in the treatment of patients with moderately to severely active psoriatic arthritis, improving both joint and skin manifestations of the disease as well as disability due to joint damage. In the Adalimumab Trial Evaluating Long-term Efficacy and Safety in Ankylosing Spondylitis (ATLAS), adalimumab significantly reduced the signs and symptoms of active ankylosing spondylitis and established a sustained clinical response in patients who had an inadequate response or intolerance to nonsteroidal antiinflammatory drug therapy. Overall, across these indications, adalimumab demonstrated a rapid onset of action, sustained efficacy with long-term treatment, and was well-tolerated, with few patients discontinuing treatment because of adverse events. The safety profile was similar to other TNF antagonists. Inhibition of TNF activity by adalimumab also significantly improved physical functioning and quality of life measures.
Epitaxial Heterostructures:  Side-to-Side Si−ZnS, Si−ZnSe Biaxial Nanowires, and Sandwichlike ZnS−Si−ZnS Triaxial Nanowires (2003)

Epitaxial semiconducting heterostructures: side-to-side Si-ZnS, Si-ZnSe biaxial nanowires, and sandwichlike ZnS-Si-ZnS triaxial nanowires were grown via a simple two-stage thermal evaporation of mixed SiO and ZnS or SiO and ZnSe powders under a precise temperature control. Each nanowire had a uniform diameter of 40-120 nm and length ranging from several to several tens of micrometers. Subnanowires of Si, ZnS, and ZnSe within them had a diameter of 20-50, 40-60, and 20-50 nm, respectively. The optical property (nanoscale cathodoluminescence) was also investigated from these new structures. It is proposed that the Si nanowires formed through disproportionation of SiO to Si in the first evaporation stage and then served as one-dimensional nanoscale substrates (or templates) for an epitaxial growth of ZnS or ZnSe nanowires in the following thermal evaporation of ZnS or ZnSe powders. The present results suggest that the simple method might be useful for the synthesis of many other heterostructures containing Si and II-VI or III-V semiconducting composite nanowires to meet the growing demands of nanoscale science and technology.
Identification of CD4 and major histocompatibility complex functional peptide sites and their homology with oligopeptides from human immunodeficiency virus type 1 glycoprotein gp120: role in AIDS pathogenesis. (1993)

CD4 molecules interact with class II major histocompatibility complex molecules as a critical costimulatory signal in CD4+ cell immune activation. CD4 also recognizes a specific region of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein gp120 forming a binding site for early stages of HIV-1 infection. We designed two software packages, AUTOMAT and CRITIC, which allowed us to identify similarities between regions of HIV-1 proteins and immunoregulatory protein sequences stored in data banks. In this report we have characterized (i) a pentapeptide, SLWDQ, found in both CD4 and HIV-1 gp120, which surprisingly had remained undetected in these two well-studied molecules until now, and (ii) an HLA sequence corresponding to the putative functional site of H2 I-A. We found that a region of gp120 (residues 254-263) known to be similar to a sequence in HLA class II beta chain overlaps this functional region. We showed experimentally that these two CD4 and HLA peptide segments inhibit CD4+ cell immune activation. There is strong inhibition (50% up to 80%) of immune activation by SLWDQ-containing gp120 segments and a lesser inhibition by the gp120 HLA-homologous segment. In addition, we found that SLWDQ induced in HIV-1-infected individuals a humoral (antibody) and cellular (cytotoxic T lymphocyte) immune reaction. We propose that these HIV-1 gp120 segments, together with the known CD4-binding region, may contribute to the HIV-1-induced immunosuppression by two mechanisms affecting CD4-HLA interaction during T-cell immune activation: autoimmune reaction toward CD4 and direct interference with the CD4-HLA costimulatory signal inducing CD4+ cell anergy with, as a consequence, generation of immunosuppression.
Navigating in hyperspace (1994)

article Free Access Share on Navigating in hyperspace: designing a structure-based toolbox Authors: Ehud Rivlin Dept. of Computer Science, University of Maryland, College Park, MD Dept. of Computer Science, University of Maryland, College Park, MDView Profile , Rodrigo Botafogo Dept. of Computer Science, University of Maryland, College Park, MD Dept. of Computer Science, University of Maryland, College Park, MDView Profile , Ben Shneiderman Dept. of Computer Science, University of Maryland, College Park, MD Dept. of Computer Science, University of Maryland, College Park, MDView Profile Authors Info & Claims Communications of the ACMVolume 37Issue 2Feb. 1994pp 87–96https://doi.org/10.1145/175235.175242Published:01 February 1994Publication History 72citation661DownloadsMetricsTotal Citations72Total Downloads661Last 12 Months23Last 6 weeks3 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF