gebhart/patrepeval huggingface dataset:
HrpB2 and HrpF from Xanthomonas are type III‐secreted proteins and essential for pathogenicity and recognition by the host plant (2000)

The interaction between the plant pathogen Xanthomonas campestris pv. vesicatoria and its host plants is controlled by hrp genes (hypersensitive reaction and pathogenicity), which encode a type III protein secretion system. Among type III-secreted proteins are avirulence proteins, effectors involved in the induction of plant defence reactions. Using non-polar mutants, we investigated the role of 12 hrp genes in the secretion of the avirulence protein AvrBs3 from X. c. pv. vesicatoria and a heterologous protein, YopE, from Yersinia pseudotuberculosis. Genes conserved among type III secretion systems (hrcQ, hrcR, hrcS and hrcT) as well as non-conserved genes (hrpB1, hrpB2, hrpB4, hrpB5, hrpD5 and hrpD6) were shown to be required for secretion. Protein localization studies using specific antibodies showed that HrpB1 and HrpB4, as well as the putative ATPase HrcN, were mainly found in the soluble fraction of the bacterial cell. In contrast, HrpB2 and HrpF, which is related to NolX of Rhizobium fredii, are secreted into the culture medium in an hrp-dependent manner. As HrpB2, but not HrpF, is essential for type III protein secretion, there might be a hierarchy in the secretion process. We propose that HrpF, which is dispensable for protein secretion but required for AvrBs3 recognition in planta, functions as a translocator of effector proteins into the host cell.
Expression of multiple epigenetically regulated cancer/germline genes in nonsmall cell lung cancer (2005)

Cancer/germline (CG) antigens represent promising targets for widely applicable mono- and multiantigen cancer vaccines for nonsmall cell lung cancer (NSCLC). Since little is known about their composite expression in this tumor type, we analyzed 7 CG genes (MAGE-A3, NY-ESO-1, LAGE-1, BRDT, HOM-TES-85, TPX-1 and LDHC) in 102 human NSCLC specimens. About 81% of NSCLC express at least 1 and half of the specimen at least 2 CG genes. Activation of most of these genes occurs more frequently in squamous cell cancer than in adenocarcinomas. Even though we found all genes but one to be regulated by genomic methylation, not all of them are co-expressed. In particular, combining CG genes not localized on the X-chromosome may provide effective treatment for an extended number of patients.
Electrochemistry in Hollow-Channel Paper Analytical Devices (2014)

In the present article we provide a detailed analysis of fundamental electrochemical processes in a new class of paper-based analytical devices (PADs) having hollow channels (HCs). Voltammetry and amperometry were applied under flow and no flow conditions yielding reproducible electrochemical signals that can be described by classical electrochemical theory as well as finite-element simulations. The results shown here provide new and quantitative insights into the flow within HC-PADs. The interesting new result is that despite their remarkable simplicity these HC-PADs exhibit electrochemical and hydrodynamic behavior similar to that of traditional microelectrochemical devices.
A semantic event-detection approach and its application to detecting hunts in wildlife video (2000)

We propose a three-level video-event detection methodology and apply it to animal-hunt detection in wildlife documentaries. The first level extracts color, texture, and motion features, and detects shot boundaries and moving object blobs. The mid-level employs a neural network to determine the object class of the moving object blobs. This level also generates shot descriptors that combine features from the first level and inferences from the mid-level. The shot descriptors are then used by the domain-specific inference process at the third level to detect video segments that match the user defined event model. The proposed approach has been applied to the detection of hunts in wildlife documentaries. Our method can be applied to different events by adapting the classifier at the intermediate level and by specifying a new event model at the highest level. Event-based video indexing, summarization, and browsing are among the applications of the proposed approach.
East/West Philosophical Synthesis in Transpersonal Theory (1991)

Transpersonal theory is a perspective on human behavior and development that synthesizes philosophical and scientific insights from Eastern and Western traditions of thought. This article presents challenges from transpersonal theory to ethnocentric limitations of conventional developmental theories in social work. Three fundamental philosophical assumptions of conventional theories are critiqued: that linear, rational thinking is the standard for optimal cognitive development; that autonomy is the standard for psychosocial maturity; and that ordinary waking dualistic consciousness is the standard for normal mental operation. Limitations of transpersonal theory are also examined. Based on the challenges and insights of transpersonal theory, suggestions for innovation in teaching and philosophizing about human behavior in social work are offered.
Ultrastructural Alterations of Myelinated Fibers and Oligodendrocytes in the Prefrontal Cortex in Schizophrenia: A Postmortem Morphometric Study (2011)

Schizophrenia is believed to result from altered neuronal connectivity and impaired myelination. However, there are few direct evidence for myelin abnormalities in schizophrenia. We performed electron microscopic study of myelinated fibers and oligodendrocytes and morphometric study of myelinated fibers in the prefrontal cortex in gray and white matters in schizophrenia and normal controls. Six types of abnormal fibers and ultrastructural alterations of oligodendrocytes were found in schizophrenia. No significant group differences in area density of myelinated fibers were found. Frequency of pathological fibers was increased significantly in gray matter in young and elderly schizophrenia patients and in patients with predominantly positive symptoms. In contrast, in white matter, frequency of altered fibers was increased significantly in elderly patients, in patients with predominantly negative symptoms, and correlated with illness duration. Progressive alterations of myelinated fibers in white matter might be followed by alterations of myelinated fibers in gray matter in schizophrenia.
CREB activity in the nucleus accumbens shell controls gating of behavioral responses to emotional stimuli (2002)

The transcription factor cAMP response element (CRE)-binding protein (CREB) has been shown to regulate neural plasticity. Drugs of abuse activate CREB in the nucleus accumbens, an important part of the brain's reward pathways, and local manipulations of CREB activity have been shown to affect cocaine reward, suggesting an active role of CREB in adaptive processes that follow exposure to drugs of abuse. Using CRE-LacZ reporter mice, we show that not only rewarding stimuli such as morphine, but also aversive stimuli such as stress, activate CRE-mediated transcription in the nucleus accumbens shell. Using viral-mediated gene transfer to locally alter the activity of CREB, we show that this manipulation affects morphine reward, as well as the preference for sucrose, a more natural reward. We then show that local changes in CREB activity induce a more general syndrome, by altering reactions to anxiogenic, aversive, and nociceptive stimuli as well. Increased CREB activity in the nucleus accumbens shell decreases an animal's responses to each of these stimuli, whereas decreased CREB activity induces an opposite phenotype. These results show that environmental stimuli regulate CRE-mediated transcription within the nucleus accumbens shell, and that changes in CREB activity within this brain area subsequently alter gating between emotional stimuli and their behavioral responses. This control appears to be independent of the intrinsic appetitive or aversive value of the stimulus. The potential relevance of these data to addiction and mood disorders is discussed.
PD-1 Pathway Inhibitors: Changing the Landscape of Cancer Immunotherapy (2014)

The PD-1/PD-L1 pathway in cancer is implicated in tumors escaping immune destruction and is a promising therapeutic target. The development of anti-PD-1 and anti-PD-L1 agents marks a new era in the treatment of cancer with immunotherapies. Early clinical experience has shown encouraging activity of these agents in a variety of tumors, and further results are eagerly awaited from completed and ongoing studies.
Correlation of Two-Hybrid Affinity Data with In Vitro Measurements (1995)

Since their introduction, the interaction trap and other two-hybrid systems have been used to study protein-protein interactions. Despite their general use, little is known about the extent to which the degree of protein interaction determined by two-hybrid approaches parallels the degree of interaction determined by biochemical techniques. In this study, we used a set of lexAop-LEU2 and lexAop-lacZ reporters to calibrate the interaction trap. For the calibration, we used two sets of proteins, the Myc-Max-Mxi1 helix-loop-helix proteins, and wild-type and dimerization-defective versions of the lambda cI repressor. Our results indicate that the strength of interaction as predicted by the two-hybrid approach generally correlates with that determined in vitro, permitting discrimination of high-, intermediate-, and low-affinity interactions, but there was no single reporter for which the amount of gene expression linearly reflected affinity measured in vitro. However, some reporters showed thresholds and only responded to stronger interactions. Finally, some interactions were subject to directionality, and their apparent strength depended on the reporter used. Taken together, our results provide a cautionary framework for interpreting affinities from two-hybrid experiments.
Detecting and counting people in surveillance applications (2006)

A number of surveillance scenarios require the detection and tracking of people. Although person detection and counting systems are commercially available today, there is need for further research to address the challenges of real world scenarios. The focus of this work is the segmentation of groups of people into individuals. One relevant application of this algorithm is people counting. Experiments document that the presented approach leads to robust people counts.
Anti‐Interleukin‐6 Antibodies in Normal Human Serum (1991)

High-avidity IgG antibodies to the cytokine interleukin-6 (IL-6) were found in sera of apparently healthy adult individuals. These antibodies specifically interfered with an ELISA (enzyme-linked immunosorbent assay) for IL-6 in which specific polyclonal rabbit antibodies to human recombinant IL-6 (rIL-6) were used. Furthermore, using precipitation of 125I-rIL-6 with rabbit antibodies to human immunoglobulins (Ig), the sera of 7 out of 68 Danish blood donors were found to contain specific antibodies in substantial amounts. Judged by ELISA interference, gel filtration of sera incubated with 125I-rIL-6 and second antibody precipitation of 125I-rIL-6, IgG seemed to be the dominant IL-6 binding protein in these normal sera. Using specific antibodies to human Ig light chains, it was found that the anti-IL-6 antibodies were of polyclonal origin. Moreover, there are at least two epitopes on the IL-6 molecule, because more than one IgG bound to some IL-6 molecules at the same time. The anti-IL-6 antibodies did not cross-react with a number of other human recombinant-derived and native cytokines. The antibodies recognized native as well as rIL-6, but preferentially monomeric IL-6.
ABFs, a Family of ABA-responsive Element Binding Factors (2000)

Abscisic acid (ABA) plays an important role in environmental stress responses of higher plants during vegetative growth. One of the ABA-mediated responses is the induced expression of a large number of genes, which is mediated by cis-regulatory elements known as abscisic acid-responsive elements (ABREs). Although a number of ABRE binding transcription factors have been known, they are not specifically from vegetative tissues under induced conditions. Considering the tissue specificity of ABA signaling pathways, factors mediating ABA-dependent stress responses during vegetative growth phase may thus have been unidentified so far. Here, we report a family of ABRE binding factors isolated from young Arabidopsis plants under stress conditions. The factors, isolated by a yeast one-hybrid system using a prototypical ABRE and named as ABFs (ABRE binding factors) belong to a distinct subfamily of bZIP proteins. Binding site selection assay performed with one ABF showed that its preferred binding site is the strong ABRE, CACGTGGC. ABFs can transactivate an ABRE-containing reporter gene in yeast. Expression of ABFs is induced by ABA and various stress treatments, whereas their induction patterns are different from one another. Thus, a new family of ABRE binding factors indeed exists that have the potential to activate a large number of ABA/stress-responsive genes in Arabidopsis.
Exploiting Data Deduplication to Accelerate Live Virtual Machine Migration (2010)

As one of the key characteristics of virtualization, live virtual machine (VM) migration provides great benefits for load balancing, power management, fault tolerance and other system maintenance issues in modern clusters and data centers. Although Pre-Copy is a widespread used migration algorithm, it does transfer a lot of duplicated memory image data from source to destination, which results in longer migration time and downtime. This paper proposes a novel VM migration approach, named Migration with Data Deduplication (MDD), which introduces data deduplication into migration. MDD utilizes the self-similarity of run-time memory image, uses hash based fingerprints to find identical and similar memory pages, and employs Run Length Encode (RLE) to eliminate redundant memory data during migration. Experiment demonstrates that compared with Xen's default Pre-Copy migration algorithm, MDD can reduce 56.60% of total data transferred during migration, 34.93% of total migration time, and 26.16% of downtime on average.
Different positively charged amino acids have similar effects on the topology of a polytopic transmembrane protein in Escherichia coli. (1992)

Integral membrane proteins from a wide variety of sources conform to a "positive-inside rule," with many more positively charged amino acids in their cytoplasmic as compared to extracytoplasmic domains. A growing body of experimental work also points to positively charged residues in regions flanking the apolar transmembrane segments as being the main topological determinants. In this paper, we report a systematic comparison of the effects of positively (Arg, Lys, His) as well as negatively (Asp, Glu) charged residues on the membrane topology of a model Escherichia coli inner membrane protein. Our results show that positive charge is indeed the major factor determining the transmembrane topology, with Arg and Lys being of nearly equal efficiency. His, although normally a very weak topological determinant, can be potentiated by a lowering of the cytoplasmic pH. Asp and Glu affect the topology to similar extents and only when present in very high numbers.
In-vivo measurement of swine myocardial resistivity (2002)

We used a four-terminal plunge probe to measure myocardial resistivity in two directions at three sites from the epicardial surface of eight open-chest pigs in-vivo at eight frequencies ranging from 1 Hz to 1 MHz. We calibrated the plunge probe to minimize the error due to stray capacitance between the measured subject and ground. We calibrated the probe in saline solutions contained in a metal cup situated near the heart that had an electrical connection to the pig's heart. The mean of the measured myocardial resistivity was 319 ohm x cm at 1 Hz down to 166 ohm x cm at 1 MHz. Statistical analysis showed the measured myocardial resistivity of two out of eight pigs was significantly different from that of other pigs. The myocardial resistivity measured with the resistivity probe oriented along and across the epicardial fiber direction was significantly different at only one out of the eight frequencies. There was no significant difference in the myocardial resistivity measured at different sites.
Prevention of exercised induced cardiomyopathy following Pip-PMO treatment in dystrophic mdx mice (2015)

Duchenne muscular dystrophy (DMD) is a fatal neuromuscular disorder caused by mutations in the Dmd gene. In addition to skeletal muscle wasting, DMD patients develop cardiomyopathy, which significantly contributes to mortality. Antisense oligonucleotides (AOs) are a promising DMD therapy, restoring functional dystrophin protein by exon skipping. However, a major limitation with current AOs is the absence of dystrophin correction in heart. Pip peptide-AOs demonstrate high activity in cardiac muscle. To determine their therapeutic value, dystrophic mdx mice were subject to forced exercise to model the DMD cardiac phenotype. Repeated peptide-AO treatments resulted in high levels of cardiac dystrophin protein, which prevented the exercised induced progression of cardiomyopathy, normalising heart size as well as stabilising other cardiac parameters. Treated mice also exhibited significantly reduced cardiac fibrosis and improved sarcolemmal integrity. This work demonstrates that high levels of cardiac dystrophin restored by Pip peptide-AOs prevents further deterioration of cardiomyopathy and pathology following exercise in dystrophic DMD mice.
Validation of four candidate pancreatic cancer serological biomarkers that improve the performance of CA19.9 (2013)

Additional serum biomarkers, particularly SYCN and REG1B, when combined with CA19.9, show promise as improved diagnostic indicators of pancreatic cancer, which therefore warrants further validation.
Glycerol prevents loss of immunoreactive follicle-stimulating hormone and luteinizing hormone from frozen urine (1983)

First morning urine samples were collected from both menstruant and post-menopausal women and stored at -25 degrees C. Immunoreactive FSH disappeared from these samples (t1/2 = 30 days), ultimately stabilizing at about 20% of the initial value. The loss was more rapid at -20 degrees C and less rapid at -55 degrees C and +4 degrees C. Immunoreactive LH was also lost from frozen urine, but more slowly than FSH. The addition of glycerol to urine (0.52 mol/l) stored at -25 degrees C prevented loss of immunoreactive FSH and LH for at least 105 days.
Xist RNA and the Mechanism of X Chromosome Inactivation (2002)

Dosage compensation in mammals is achieved by the transcriptional inactivation of one X chromosome in female cells. From the time X chromosome inactivation was initially described, it was clear that several mechanisms must be precisely integrated to achieve correct regulation of this complex process. X-inactivation appears to be triggered upon differentiation, suggesting its regulation by developmental cues. Whereas any number of X chromosomes greater than one is silenced, only one X chromosome remains active. Silencing on the inactive X chromosome coincides with the acquisition of a multitude of chromatin modifications, resulting in the formation of extraordinarily stable facultative heterochromatin that is faithfully propagated through subsequent cell divisions. The integration of all these processes requires a region of the X chromosome known as the X-inactivation center, which contains the Xist gene and its cis-regulatory elements. Xist encodes an RNA molecule that plays critical roles in the choice of which X chromosome remains active, and in the initial spread and establishment of silencing on the inactive X chromosome. We are now on the threshold of discovering the factors that regulate and interact with Xist to control X-inactivation, and closer to an understanding of the molecular mechanisms that underlie this complex process.
Polymer Synthesis by In Vitro Enzyme Catalysis (2001)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolymer Synthesis by In Vitro Enzyme CatalysisRichard A. Gross, Ajay Kumar, and Bhanu KalraView Author Information NSF IUCRC for Biocatalysis and BioProcessing of Macromolecules, Department of Chemistry and Chemical Engineering, Polytechnic University, Six Metrotech Center, Brooklyn, New York 11201 Cite this: Chem. Rev. 2001, 101, 7, 2097–2124Publication Date (Web):June 9, 2001Publication History Received12 January 2001Published online9 June 2001Published inissue 1 July 2001https://pubs.acs.org/doi/10.1021/cr0002590https://doi.org/10.1021/cr0002590research-articleACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views5271Altmetric-Citations643LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Monomers,Peptides and proteins,Polymerization,Polymers,Solvents Get e-Alerts
Identification of Multiple Novel Epididymis-Specific β-Defensin Isoforms in Humans and Mice (2002)

Defensins comprise a family of cationic antimicrobial peptides that are characterized by the presence of six conserved cysteine residues. We identified two novel human beta-defensin (hBD) isoforms by mining the public human genomic sequences. The predicted peptides conserve the six-cysteine motif identical with hBD-4, termed hBD-5 and hBD-6. We also evaluated the characteristics of the mouse homologs of hBD-5, hBD-6, and HE2beta1, termed mouse beta-defensin (mBD)-12, mBD-11, and mouse EP2e (mEP2e). The mBD-12 synthetic peptide showed salt-dependent antimicrobial activity. We demonstrate the epididymis-specific expression pattern of hBD-5, hBD-6, mBD-11, mBD-12, and mEP2e. In situ hybridization revealed mBD-11, mBD-12, and mEP2e expression in the columnar epithelium of the caput epididymis, contrasting with the predominant expression of mBD-3 in the capsule or septum of the whole epididymis. In addition, the regional specificity of mBD-11, mBD-12, and mEP2e was somewhat overlapping, but not identical, in the caput epididymis, suggesting that specific regulation may work for each member of the beta-defensin family. Our findings indicated that multiple beta-defensin isoforms specifically and cooperatively contribute to the innate immunity of the urogenital system.