gebhart/patrepeval huggingface dataset:
Concise Review: Roles of Polycomb Group Proteins in Development and Disease: A Stem Cell Perspective (2007)

The acquisition and maintenance of cell fate are essential for metazoan growth and development. A strict coordination between genetic and epigenetic programs regulates cell fate determination and maintenance. Polycomb group (PcG) genes are identified as essential in these epigenetic developmental processes. These genes encode components of multimeric transcriptional repressor complexes that are crucial in maintaining cell fate. PcG proteins have also been shown to play a central role in stem cell maintenance and lineage specification. PcG proteins, together with a battery of components including sequence-specific DNA binding/accessory factors, chromatin remodeling factors, signaling pathway intermediates, noncoding small RNAs, and RNA interference machinery, generally define a dynamic cellular identity through tight regulation of specific gene expression patterns. Epigenetic modification of chromatin structure that results in expression silencing of specific genes is now emerging as an important molecular mechanism in this process. In embryonic stem (ES) cells and adult stem cells, such specific genes represent those associated with differentiation and development, and silencing of these genes in a PcG protein-dependent manner confers stemness. ES cells also contain novel chromatin motifs enriched in epigenetic modifications associated with both activation and repression of genes, suggesting that certain genes are poised for activation or repression. Interestingly, these chromatin domains are highly coincident with the promoters of developmental regulators, which are also found to be occupied by PcG proteins. The epigenetic integrity is compromised, however, by mutations or other alterations that affect the function of PcG proteins in stem cells leading to aberrant cell proliferation and tissue transformation, a hallmark of cancer. Disclosure of potential conflicts of interest is found at the end of this article.
De novo expression of endothelial sialyl Lewis(a) and sialyl Lewis(x) during cardiac transplant rejection: superior capacity of a tetravalent sialyl Lewis(x) oligosaccharide in inhibiting L-selectin-dependent lymphocyte adhesion. (1995)

Acute organ transplant rejection is characterized by a heavy lymphocyte infiltration. We have previously shown that alterations in the graft endothelium lead to increased lymphocyte traffic into the graft. Here, we demonstrate that lymphocytes adhere to the endothelium of rejecting cardiac transplants, but not to the endothelium of syngeneic grafts or normal hearts analyzed with the in vitro Stamper-Woodruff binding assay. Concomitant with the enhanced lymphocyte adhesion, the cardiac endothelium begins to de novo express sialyl Lewis(a) and sialyl Lewis(x) (sLea and sLex) epitopes, which have been shown to be sequences of L-selectin counterreceptors. The endothelium of allografts, but not that of syngeneic grafts or normal controls, also reacted with the L-selectin-immunoglobulin G fusion protein, giving further proof of inducible L-selectin counterreceptors. The lymphocyte adhesion to endothelium could be significantly decreased either by treating the lymphocytes with anti-L-selectin antibody HRL-1, or by treating the tissue sections with sialidase or anti-sLea or anti-sLex monoclonal antibodies. Finally, we synthetized enzymatically several members of the sLex family oligosaccharides and analyzed their ability to block lymphocyte adhesion to cardiac endothelium. The monovalent sLex (a tetramer), divalent sLex (a decamer), and tetravalent sLex (a 22-mer) could all significantly reduce lymphocyte binding, but the inhibition by the tetravalent sLex-construct was clearly superior to other members of the sLex family. The crucial control oligosaccharides, sialyl lactosamines lacking fucose but being otherwise similar to the members of sLex family, had no effect on lymphocyte binding.
Automatic recognition of emotion evoked by general sound events (2012)

Without a doubt there is emotion in sound. So far, however, research efforts have focused on emotion in speech and music despite many applications in emotion-sensitive sound retrieval. This paper is an attempt at automatic emotion recognition of general sounds. We selected sound clips from different areas of the daily human environment and model them using the increasingly popular dimensional approach in the emotional arousal and valence space. To establish a reliable ground truth, we compare mean and median of four annotators with their evaluator weighted estimator. We discuss human labelers' consistency, feature relevance, and automatic regression. Results reach correlation coefficients of .61 (arousal) and .49 (valence).
A new method for improving camera calibration precision (2010)

The camera calibration precision directly affects the computer vision application. A method for improving camera calibration precision is proposed in this paper, which follows in details: Firstly, a new iterative sub-pixel detection approach based on the Forstner operator is proposed. Secondly, instead of print plane, this paper uses LCD (completely flat Liquid Crystal Display) for camera calibration. Finally, a new distortion correction method using image corners is proposed, which is based on the fact that the straight line is still straight in projective transformation. This method could be used to compute the radial distortion coefficients, and correct the corners location. Both simulation and real experiments show the effectiveness of the proposed method.
A Model to Study Viral and Cytokine Involvement in Sjogren's Syndrome (1994)

To investigate mechanisms that may be important in the pathogenesis of Sjögren's syndrome (SS) we developed a protocol for the growth of salivary gland epithelial cells in culture. We examined the effect that viral infection has on the cellular location of the autoantigen La. Autoantibodies to La are common in SS and it has been proposed that viral infection may result in cell membrane expression of La. Co-expression of MHC class II molecules in infected cells could lead to the presentation of La peptides to the immune system. Advenovirus infection of salivary gland epithelial cells resulted in an altered nuclear staining of La. Treatment with interferon-gamma resulted in the expression of La in the cell cytoplasm and HLA-DR molecules at the cell surface. These findings suggest that a cytokine-driven mechanism may generate an autoimmune response to La in SS. Using the polymerase chain reaction (PCR) we tested salivary gland epithelial cell cultures for the presence of human herpesvirus-6 (HHV-6) and Epstein-Barr virus (EBV). Only HHV-6 was detected in 2 of 10 salivary gland epithelial cell cultures although the presence of HHV-6 was not associated with SS. Primary salivary gland cultures may prove useful as an in vitro model to study mechanisms of autoimmunity in SS.
Factors influencing the type, timing and severity of symptomatic responses to dietary gluten in patients with biopsy-proven coeliac disease. (2013)

Patients with consistent GFD adherence experience a SRDG faster and more severe in comparison to prior gluten exposure possibly demonstrating an adept immunological response. Anxiety and depression also enhance the speed of symptom onset and co-existing visceral hypersensitivity is a risk factor for severe reactions to dietary gluten.
Anti–neuropilin‐1 peptide inhibition of synoviocyte survival, angiogenesis, and experimental arthritis (2009)

Anti-NP-1 peptide suppressed VEGF(165)-induced increases in synoviocyte survival and angiogenesis, and thereby blocked experimental arthritis. Our findings suggest that anti-NP-1 peptide could be useful in alleviating chronic arthritis.
Fibrin targeting of tissue plasminogen activator-loaded echogenic liposomes (2007)

We recently reported entrapment of tissue-plasminogen activator (tPA) into echogenic liposomes (ELIP) with retention of echogenicity and thrombolytic effect. Integral to the potential of this agent for ultrasound-detectable local drug delivery is the specific binding of tPA-ELIP to clots. tPA contains fibrin-binding sites; we hypothesized that tPA when associated with ELIP, will maintain fibrin binding properties, rendering further manipulation for targeting of the tPA-ELIP unnecessary. We demonstrated strong fibrin binding of the ELIP-associated tPA. Fibrin binding for ELIP-associated tPA was twice that of free tPA. This strong affinity for fibrin was confirmed using echogenicity analysis of porcine clots in vitro. Both objective (mean gray scale analysis) and subjective (visual estimation by two experienced echocardiographers) evaluation of the clots showed enhanced highlighting of clots treated with tPA-ELIP when compared to control. The findings in this study represent new approaches for fibrin-targeted, ultrasound-directed and enhanced local delivery of a thrombolytic agent.
Up-Regulation of MicroRNA-21 Correlates with Lower Kidney Cancer Survival (2012)

The current study shows a clear correlation between miR-21 expression and clinical characteristics of renal cancer. Thus we believe that miR-21 can be used as a tumor marker and its inhibition may prove to be useful in controlling cancers with up-regulated miR-21.
Bacillus cereus and related species (1993)

Bacillus cereus is a gram-positive aerobic or facultatively anaerobic spore-forming rod. It is a cause of food poisoning, which is frequently associated with the consumption of rice-based dishes. The organism produces an emetic or diarrheal syndrome induced by an emetic toxin and enterotoxin, respectively. Other toxins are produced during growth, including phospholipases, proteases, and hemolysins, one of which, cereolysin, is a thiol-activated hemolysin. These toxins may contribute to the pathogenicity of B. cereus in nongastrointestinal disease. B. cereus isolated from clinical material other than feces or vomitus was commonly dismissed as a contaminant, but increasingly it is being recognized as a species with pathogenic potential. It is now recognized as an infrequent cause of serious nongastrointestinal infection, particularly in drug addicts, the immunosuppressed, neonates, and postsurgical patients, especially when prosthetic implants such as ventricular shunts are inserted. Ocular infections are the commonest types of severe infection, including endophthalmitis, panophthalmitis, and keratitis, usually with the characteristic formation of corneal ring abscesses. Even with prompt surgical and antimicrobial agent treatment, enucleation of the eye and blindness are common sequelae. Septicemia, meningitis, endocarditis, osteomyelitis, and surgical and traumatic wound infections are other manifestations of severe disease. B. cereus produces beta-lactamases, unlike Bacillus anthracis, and so is resistant to beta-lactam antibiotics; it is usually susceptible to treatment with clindamycin, vancomycin, gentamicin, chloramphenicol, and erythromycin. Simultaneous therapy via multiple routes may be required.
Itinerário terapêutico, escolha e avaliação de tratamento para problemas de saúde (2016)

Individuos encontram diferentes maneiras de resolver os seus problemas de saude. Isso implica em levar em consideracao que a escolha de um tratamento, e os caminhos que levam para a cura, seja ele biomedico ou nao, e influenciada pelo contexto sociocultural em que ocorre. A nocao de itinerario terapeutico mostra-se eficaz quando identifica a dinâmica contextual, com base na qual se desenvolvem os projetos individuais e coletivos de tratamentos. Se as alternativas que o mundo social oferece estao fora de controle dos individuos, e sao todas igualmente possiveis, o itinerario terapeutico esta em forma de projeto individual como um campo de possibilidades dentro do controle do individuo. Acima de tudo e preciso entender que inexiste uma logica orientando a escolha e a sequencia do itinerario terapeutico, pois doenca e procura de tratamento sao processos imersos e mediados por contextos culturais especificos4. O itinerario terapeutico demonstra tambem os limites dos modelos biomedicos de tratamento, pois o social e integral da experiencia da doenca, e o sistema biomedico e, muitas vezes, a forma para reger um modelo moral no tratamento da doenca. A percepcao do paciente sobre o sintoma e seu significado e parte de sua experiencia de enfermidade, e o itinerario terapeutico e a construcao social da doenca; assim o significado atribuido nao e dado a priori, mas emerge neste processo.
Simple maximum power point tracker for photovoltaicarrays (2000)

A new technique is presented for tracking the maximum power point (MPP) of solar arrays. Although the control circuit is extremely simple and robust, its dynamics are complex. The MPP becomes inherently the global attractor of the system, thus ensuring optimum operation under transient and steady-state conditions. Experimental results confirm excellent tracking effectiveness and rapid dynamic response.
Complete In Vitro Reconstitution of Adeno-Associated Virus DNA Replication Requires the Minichromosome Maintenance Complex Proteins (2007)

Adeno-associated virus (AAV) replicates its DNA exclusively by a leading-strand DNA replication mechanism and requires coinfection with a helper virus, such as adenovirus, to achieve a productive infection. In previous work, we described an in vitro AAV replication assay that required the AAV terminal repeats (the origins for DNA replication), the AAV Rep protein (the origin binding protein), and an adenovirus-infected crude extract. Fractionation of these crude extracts identified replication factor C (RFC), proliferating cell nuclear antigen (PCNA), and polymerase delta as cellular enzymes that were essential for AAV DNA replication in vitro. Here we identify the remaining factor that is necessary as the minichromosome maintenance (MCM) complex, a cellular helicase complex that is believed to be the replicative helicase for eukaryotic chromosomes. Thus, polymerase delta, RFC, PCNA, and the MCM complex, along with the virally encoded Rep protein, constitute the minimal protein complexes required to reconstitute efficient AAV DNA replication in vitro. Interfering RNAs targeted to MCM and polymerase delta inhibited AAV DNA replication in vivo, suggesting that one or more components of the MCM complex and polymerase delta play an essential role in AAV DNA replication in vivo as well as in vitro. Our reconstituted in vitro DNA replication system is consistent with the current genetic information about AAV DNA replication. The use of highly conserved cellular replication enzymes may explain why AAV is capable of productive infection in a wide variety of species with several different families of helper viruses.
Using cache memory to reduce processor-memory traffic (1998)

Article Free Access Share on Using cache memory to reduce processor-memory traffic Author: James R. Goodman Department of Computer Sciences, University of Wixconsm-Madison, Madison, WI Department of Computer Sciences, University of Wixconsm-Madison, Madison, WIView Profile Authors Info & Claims ISCA '98: 25 years of the international symposia on Computer architecture (selected papers)August 1998 Pages 255–262https://doi.org/10.1145/285930.285984Published:01 August 1998Publication History 12citation1,095DownloadsMetricsTotal Citations12Total Downloads1,095Last 12 Months42Last 6 weeks2 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
Energy Barriers for Alkaline Hydrolysis of Carboxylic Acid Esters in Aqueous Solution by Reaction Field Calculations (2000)

The hydrolysis of six representative alkyl esters in aqueous solution were evaluated by performing ab initio molecular orbital calculations using five different self-consistent reaction field (SCRF) procedures. Energy barriers were obtained for hydrolysis by bimolecular base-catalyzed acyl-oxygen cleavage (BAC2) and bimolecular base-catalyzed alkyl-oxygen cleavage (BAL2). Despite strong solute−solvent hydrogen bonding, the calculated solvent shifts of the energy barriers are dominated by electrostatic interactions between solute and solvent, and nonelectrostatic interactions largely cancel out. SCRF calculations that ignore volume polarization or use a charge renormalization scheme usually overestimate the solvent shifts of the energy barriers. A recently developed surface and volume polarization for electrostatic interaction (SVPE) procedure yields results comparable to experimental data when the solute cavity surface is defined as the 0.002 au electron charge isodensity contour. The differences between values from the SVPE calculations with this contour and the corresponding average experimental values for the examined esters are smaller than the range of experimental values reported by different laboratories. The SVPE calculations for the BAC2 hydrolysis predicted the lowest energy barrier for methyl formate and the highest for tert-butyl acetate, and the remaining four esters grouped closely. These results are consistent with the substituent shifts of the experimental activation energies. The energy barriers predicted for BAL2 hydrolysis are always considerably higher than those predicted for the BAC2, consistent with the observation that in aqueous solution BAL2 hydrolysis is negligible compared to BAC2 for alkyl esters.
Bacteriophage lambda cloning system for the construction of directional cDNA libraries. (1987)

We have developed a bacteriophage lambda cloning vector, lambda ORF8, that can be used for the construction of cDNA libraries. The wild-type lambda genome contains five BamHI, five EcoRI, and seven HindIII restriction sites that have all been removed from the genome of lambda ORF8. Sites for these endonucleases are present within the multiple cloning site of lambda ORF8. We report a method for preparing cDNAs that can be cloned in a single orientation in our phage vector. The method utilizes the synthesis of double-stranded cDNA, including priming of first-strand synthesis by oligo(dT). After completion of second-strand synthesis, a bifunctional oligodeoxynucleotide linker is ligated to the cDNA fragments. This linker, which contains a BamHI restriction site, will create a HindIII restriction site when ligated to the 3' end of cDNA fragments. Subsequent treatment of methylated cDNA with HindIII and BamHI endonucleases allows these fragments to be cloned directionally into lambda ORF8. To demonstrate the utility of this cloning system, we prepared a library from 5 micrograms of mRNA isolated from phytohemagglutinin-stimulated human peripheral blood lymphocytes. The primary library contained 2 X 10(8) plaque-forming phage, at least 80% of which contain inserts. A portion of the library was examined for the presence of gamma-interferon-related clones to verify the method had generated a library that was representative of phytohemagglutinin-stimulated peripheral blood lymphocytes. This simple and efficient cDNA cloning system significantly reduces the amount of RNA and effort required for the preparation of large directionally cloned libraries.
Molecular basis of antibiotic resistance and β-lactamase inhibition by mechanism-based inactivators: perspectives and future directions (2000)

Antibacterial chemotherapy is particularly striking in the family of penicillins and cephalosporins. Over 40 structurally different beta-lactam molecules are available in 73 formulations and the majority of them are currently prescribed for medical use in hospitals. beta-Lactams are well tolerated by humans with few side effects. They interact very specifically with their bacterial target, the D-alanyl-D-alanine carboxypeptidase-transpeptidase usually referred to as DD-peptidase. The outstanding number of beta-lactamases produced by bacteria represent a serious threat to the clinical utility of beta-lactams. The discovery of beta-lactamase inhibitors was thought to solve, in part, the problem of resistance. Unfortunately, bacteria have evolved new mechanisms of resistance to overcome the inhibitory effects of beta-lactamase inactivators. Here, we summarize the diversified mechanistic features of class A beta-lactamases interactions with mechanism-based inhibitors using available microbiological, kinetic and structural data for the prototype TEM beta-lactamases. A brief historical overview of the strategies developed to counteract beta-lactamases will be presented followed by a short description of the chemical events which lead to the inactivation of TEM beta-lactamase by inhibitors from different classes. Finally, an update on the clinical prevalence of natural and inhibitor-resistant enzyme mutants, the total chemical synthesis to design and synthesize a new structure and produced a broad spectrum beta-lactamase inhibitor that mimics the beta-lactam ring, but does not contain it is discussed.
West Nile Virus-Specific CD4 T Cells Exhibit Direct Antiviral Cytokine Secretion and Cytotoxicity and Are Sufficient for Antiviral Protection (2008)

CD4 T cells have been shown to be necessary for the prevention of encephalitis during West Nile virus (WNV) infection. However, the mechanisms used by Ag-specific CD4 T cells to protect mice from WNV encephalitis remain incompletely understood. Contrary to the belief that CD4 T cells are protective because they merely maintain the CD8 T cell response and improve Ab production, in this study we provide evidence for the direct antiviral activity of CD4 T cells that functions to protect the host from WNV encephalitis. In adoptive transfers, naive CD4 T cells protected a significant number of lethally infected RAG(-/-) mice, demonstrating the protective effect of CD4 T cells independent of B cells and CD8 T cells. To shed light on the mechanism of this protection, we defined the peptide specificities of the CD4 T cells responding to WNV infection in C57BL/6 (H-2(b)) mice, and used these peptides to characterize the in vivo function of antiviral CD4 T cells. WNV-specific CD4 T cells produced IFN-gamma and IL-2, but also showed potential for in vivo and ex vivo cytotoxicity. Furthermore, peptide vaccination using CD4 epitopes conferred protection against lethal WNV infection in immunocompetent mice. These results demonstrate the role of direct effector function of Ag-specific CD4 T cells in preventing severe WNV disease.
Cyanine-Labeling Reagents:  Sulfobenzindocyanine Succinimidyl Esters (1996)

A synthetic method for shifting the absorption and emission wavelengths of cyanine dye labels by 15-30 nm to the red has been developed. This step significantly increases the potential for preparing fluorescent probes for multiparameter analysis in cytometry and diagnostics. The new sulfobenzindocyanine dyes contain succinimidyl esters as reactive groups and can be readily conjugated to antibodies, avidin, modified DNA, and other amino group-containing materials. The labeling reagents are water soluble, and their fluorescence is not sensitive to pH. One of the reagents, Cy3.205, can be optimally excited with the 568 nm Kr laser line and is useful for confocal microscopy and flow cytometry. Another dye, Cy5.205, can be excited with the 633 He-Ne or 647 nm Kr laser lines available with many flow cytometers and laser-scanning microscopes. New laser diodes emitting near 660-690 nm should also be excellent excitation sources for Cy5.205.