gebhart/patrepeval huggingface dataset:
Generation of targeted nonpolar gene insertions and operon fusions in Pasteurella haemolytica and creation of a strain that produces and secretes inactive leukotoxin (1997)

An efficient method for targeted gene inactivation and generation of chromosomal gene fusions in Pasteurella haemolytica has been devised and used to create an lktC::cat operon fusion by allelic exchange at the leukotoxin gene cluster (lktCABD). A copy of the lktC gene was insertionally inactivated by using a nonpolar, promoterless cat cassette and then delivered into P. haemolytica on a shuttle vector. Plasmid incompatibility was used to detect clones where double recombination events had occurred at the chromosomal locus. The insertion in lktC did not affect expression of the downstream genes, and the mutant strain secreted an antigenic proleukotoxin that was neither leukotoxic nor hemolytic. Expression of the lktC gene in trans restored the wild-type phenotype, confirming that LktC is required for activation of the proleukotoxin to the mature leukotoxin. Construction of the lktC::cat operon fusion allowed us to quantitate leukotoxin promoter activity in P. haemolytica and to demonstrate that transcription was maximal during early logarithmic growth phase but was reduced following entry into late logarithmic phase. This allelic exchange system should be useful for future genetic studies in P. haemolytica and could potentially be applied to other members of Haemophilus-Actinobacillus-Pasteurella family, where genetic manipulation is limited.
Fresnel–Arago laws for interference in polarized light: A demonstration experiment (1981)

The author makes a experimental investigation of the influence of polarization of light on interference patterns. (AIP)
Systematic errors in digital image correlation caused by intensity interpolation (2000)

Recently, digital image correlation as a tool for surface defor- mation measurements has found widespread use and acceptance in the field of experimental mechanics. The method is known to reconstruct displacements with subpixel accuracy that depends on various factors such as image quality, noise, and the correlation algorithm chosen. How- ever, the systematic errors of the method have not been studied in detail. We address the systematic errors of the iterative spatial domain cross- correlation algorithm caused by gray-value interpolation. We investigate the position-dependent bias in a numerical study and show that it can lead to apparent strains of the order of 40% of the actual strain level. Furthermore, we present methods to reduce this bias to acceptable lev- els. © 2000 Society of Photo-Optical Instrumentation Engineers. (S0091-3286(00)00911-9)
Jasmonates and Na‐orthovanadate promote resveratrol production in Vitis vinifera cv. Barbera cell cultures (2005)

Here the effect of jasmonic acid, methyljasmonate and Na-orthovanadate on the production of resveratrol was studied in Vitis vinifera cv. Barbera cell suspension cultures. Na-orthovanadate at 0.1 mm and 1 mm concentration was efficient in promoting the production and/or accumulation and release in the culture medium of cis-resveratrol while trans-resveratrol levels were not affected by this treatment. Methyljasmonate was highly effective in stimulating both trans- and cis-resveratrol endogenous accumulation, as well as their release into the culture medium. Cis-resveratrol was absent or detected in very low amounts in the controls. Jasmonic acid was less efficient than methyljasmonate in promoting endogenous resveratrol accumulation, but it stimulated the release in the culture medium especially of cis-resveratrol. Gel analysis was performed on control and 10 microm MeJA treated cell suspensions. Results showed an up-regulation of the stilbene synthase demonstrating that MeJA stimulated the synthesis ex-novo of this protein.
Kinetic and Catalytic Mechanisms of Protein Kinases (2001)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTKinetic and Catalytic Mechanisms of Protein KinasesJoseph A. AdamsView Author Information Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0506 Cite this: Chem. Rev. 2001, 101, 8, 2271–2290Publication Date (Web):July 7, 2001Publication History Received21 December 2000Published online7 July 2001Published inissue 1 August 2001https://pubs.acs.org/doi/10.1021/cr000230whttps://doi.org/10.1021/cr000230wresearch-articleACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views11375Altmetric-Citations489LEARN 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:Cell and molecular biology,Equilibrium constant,Monomers,Peptides and proteins,Post-translational modification Get e-Alerts
“In situ-like” mantle cell lymphoma: a report of two cases: Figure 1 (2006)

Mantle cell lymphoma (MCL) is a B cell neoplasm that most often shows a diffuse growth pattern. Two cases of MCL are reported here, both with a previous diagnosis of lymphoid hyperplasia. Morphologically, germinal centres are hyperplasic with a normal or discretely enlarged mantle zone, where foci of irregularly shaped small lymphocytes are seen. These are positive for CD20, CD5 and cyclin D1, confirming a diagnosis of in situ-like MCL. This type differs from the mantle zone pattern in that the neoplastic mantle zone is very thin and there is very little or no spread of tumour cells into interfollicular areas. To the best of our knowledge, this is the first report on such a pattern of MCL, which is important to recognise, as it can be confused with lymphoid hyperplasia.
Psoriatic skin-derived dendritic cell function is inhibited by exogenous IL-10. Differential modulation of B7-1 (CD80) and B7-2 (CD86) expression. (1995)

Regulation of immune responses depends on interactions between APCs and T cells. Such cellular interactions are mediated by surface molecules including MHC class II Ags (DR) and CD28 ligands B7-1 (CD80) and B7-2 (CD86). Recent evidence indicates that the presence or absence of costimulatory molecules on APCs significantly influences the qualitative and quantitative nature of an immune response. In this report, we analyze two relevant cytokines in skin immunobiology, granulocyte-macrophage (GM)-CSF and IL-10, and demonstrate their effects on cultured dendritic cells obtained from dermis (DDCs) of normal skin and psoriatic lesions. For comparison, the effects on these professional APCs were contrasted with cultured blood-derived monocytes. Normal and psoriatic skin-derived DDCs express high levels of CD86 over CD80, and the overall hierarchy is DR > CD86 > CD80, whereas cultured monocytes express low and equivalent levels of CD80 and CD86. If Ab is added to GM-CSF at the initial period of cultivation, DDCs that emigrate have lower levels of CD86 without any detectable effect on CD80 or DR expression and display a reduced capacity to stimulate either superantigen-driven or alloantigen-responsive T cells. Conversely, by adding GM-CSF to monocytes, CD86 levels are enhanced. When IL-10 was added at the beginning of culture, DDCs had significantly lower levels of CD86, without any effect on CD80 or DR expression, and like anti-GM-CSF-treated cells, these DDCs had approximately a 50% reduction in their T cell-stimulating capacity. In contrast, when monocytes were treated identically with exogenously added IL-10, they retained their relatively low levels of CD80 and CD86 with no detectable change in APC function. Blocking studies of DDC:T cell interaction indicated that CD86 was more important than CD80. Thus, differential expression patterns and functional cytokine responses involving these APC populations may be relevant to skin disorders such as psoriasis, in which discordant patterns of CD28 ligand expression and disordered cytokine networks are present.
CD4 + CD25 + T regulatory cells control anti-islet CD8 + T cells through TGF-β–TGF-β receptor interactions in type 1 diabetes (2003)

Pancreatic lymph node-derived CD4+CD25+ T regulatory (Treg) cells inhibit in situ differentiation of islet-reactive CD8+ T cells into cytotoxic T lymphocytes, thereby preventing diabetes progression. The mechanism by which these Treg cells suppress anti-islet CD8+ T cells is unknown. Here, we show by using a CD8+ T cell-mediated model of type 1 diabetes that transforming growth factor (TGF)-beta-TGF-beta receptor signals are critical for CD4+CD25+ Treg cell regulation of autoreactive islet-specific cytotoxic T lymphocytes. Transgenic expression of tumor necrosis factor alpha from birth to 25 days of age in the islets of B6 mice that constitutively express CD80 on their beta cells results in accumulation of CD4+CD25+TGF-beta+ cells exclusively in the islets and pancreatic lymph nodes, which delays diabetes progression. In contrast, expression of tumor necrosis factor alpha until 28 days of age prevents islet accumulation of CD4+CD25+TGF-beta+ Treg cells, resulting in acceleration to diabetes. Furthermore, adoptive transfer experiments demonstrated that CD4+CD25+ Treg cells could not control naïve or activated islet-reactive CD8+ T cells bearing a dominant negative TGF-beta receptor type II. Our data demonstrate that, in vivo, TGF-beta signaling in CD8+ T cells is critical for CD4+CD25+ Treg cell suppression of islet-reactive CD8+ T cells in type 1 diabetes.
Novel autoantigens in type 1 diabetes. (2013)

Type 1 diabetes mellitus (T1DM) is characterized by recognition of beta cell proteins as self-antigens, called autoantigens (AAgs), by patients' own CD4+ and CD8+ T cells and/or the products of self-reactive B cells, called autoantibodies. These AAgs are divided into two categories on the basis of beta-cell-specificity. The list of the targets associated with beta cell-specific AAgs is continuously growing. Many T1DM-associated AAgs are well characterized and have important clinical applications for disease prediction, diagnosis, and antigen-specific tolerance immunotherapy. Identification of T1DM-associated AAgs provides insight into the pathogenesis of T1DM and to understanding the clinical aspects of the disease. Since many excellent reviews have covered the previously identified T1DM-associated AAgs exhaustedly, here we only focus on several recently discovered T1DM-AAgs (PDX1, ZnT8, CHGA, and IAAP).
Phosphoramidate Derivatives of AZT as Inhibitors of HIV: Studies on the Carboxyl Terminus (1993)

Novel phosphoramidate derivatives of the anti-HIV nucleoside analogue AZT have been prepared by phosphorochloridate chemistry. These materials carry carboxy-protected, amino acids, and are designed to act as membrane-soluble prodrugs of the bio-active free nucleotides. In vitro evaluation revealed the compounds to have a pronounced, selective antiviral activity. In particular, variation in the carboxy terminus region is studied. For alkyl phosphates small changes in the structure of the amino ester lead to marked changes in biological activity. However, for analogous aryl phosphates there is little dependence on the structure of the ester. This suggests a different mechanism of action for these two categories of phosphate prodrug.
First Experiments on Module Assembly Line Using Back-Contact Solar Cells (2008)

There is a great need for cost-effective high-throughput equipment to assemble thin and high-efficiency solar cells into modules. Single-step assembly using back-contact cells (monolithic module assembly) provides substantial advantages in terms of performance and costs. Progress towards development of a commercial module and assembly process using back-contact cells and monolithic module assembly is described. A fully operational pilot line consisting of dedicated equipment to process back-contact cell modules with the focus on the production of 4 x 9 and up to 6 x 10 cells configuration was build by TTA/Eurotron and ECN. The emphasis is on the production of modules with ultra-thin back-contact cells of mc-Si (156 x 156 mm2) and only 130 μm in thickness. The design of the equipment is targeting for a throughput rate of 1 cell per second, or equivalently a module production capacity of 100 MWp per year. Processing of the first set of modules shows good results in terms of process reliability and yield. The overall yield for the first series of 23 modules (4 x 9 configuration) built with ECN-MWT cells was 100% while 9 of the 23 modules had a fill factor better than 74%. In addition, a series of 25 modules (6 x 10 configuration) with industrial back-contact cells was built and revealed excellent reproducibility. A standard deviation of the FF of only () 1.44 was observed.
Prevention of Adriamycin-Induced Full-Thickness Skin Loss Using Hyaluronidase Infiltration (1998)

Full-thickness skin ulceration after extravasation of the commonly used vesicant chemotherapeutic agent doxorubicin hydrochloride (Adriamycin) is a significant source of morbidity in cancer patients. Controversy exists regarding the appropriate management of this extravasation injury. Current therapy includes local hypothermia, local clysis with hyaluronidase, and surgical excision of the involved tissue. Experimental data supporting local clysis with hyaluronidase are limited despite its current use clinically. The purpose of this study was to determine the efficacy of local infiltration with heparin sodium, hyaluronidase, and saline in the prevention of extravasation ulcers in a rat model. One hundred fifty male Sprague-Dawley rats (Upjohn, Milan, Italy) weighing 240 to 260 g, anesthetized with sodium pentobarbital, were used in this study. One hundred thirty rats received a 0.3-ml subcutaneous flank injection of doxorubicin (1.5 mg/ml) followed 15 minutes later by local infiltration with saline (n = 10), 25 to 100 units of heparin (n = 30), or 2.5 to 10.0 units of hyaluronidase (n = 90). Control animals received either subcutaneous doxorubicin (n = 10) or subcutaneous saline alone (n = 10). Volumes of the infiltration solution were less than 1 ml in all groups. All animals were sacrificed at 4 weeks; presence and size of ulcers at the injection site were quantified. Statistical analysis was performed using the two-sided Fisher's exact test and Student's t test. Control rats injected with saline alone did not develop ulceration in any case. All rats injected with doxorubicin alone developed ulcers with an average size of 33 mm2. Heparin infiltration decreased ulcer rate by 20 to 40 percent and decreased ulcer size by up to 67 percent. Local infiltration with hyaluronidase decreased ulcer rate by 50 to 60 percent (p < 0.05, two-sided Fisher's exact test) and decreased ulcer size by up to 50 percent ( p < 0.05, Student's t test). In this rat extravasation injury model, local infiltration with saline, heparin, or hyaluronidase decreased ulcer size after doxorubicin extravasation. This effect may be secondary to dilution of the extravasant. Additionally, local infiltration with hyaluronidase decreased ulcer rate by at least 50 percent. The mechanism of this phenomenon presumably relates to the ability of hyaluronidase to temporarily decrease the viscosity of the hyaluronic acid component of ground substance, thus allowing greater diffusion of doxorubicin into the surrounding tissue and therefore decreasing its local concentration.
ICAM-2: regulator of leukocyte migration and angiogenesis (2005)

Comment on Huang et al, page [1636][1] 

In this issue of Blood, Huang and colleagues show that the endothelial adhesion molecule ICAM-2, a well-known ligand of leukocyte integrins, can mediate homophilic binding and regulate angiogenesis in various cellular assays in vitro and in vivo. 

Leukocyte
A Quote-Driven Automated Market (2001)

This paper reports on preliminary research into a new type of automated market, namely a quote-driven market. The research aims to develop the necessary market protocols and infrastructure, and to investigate the impact of pre-set parameters on the effectiveness of the market in terms of liquidity, price volatility, throughput and profitability for the market participants. Quote-driven trading is well-suited to products such as financial instruments, bandwidth, electricity—any product that requires real-time trading. In particular, we discuss how this form of regulated but decentralised marketplace may offer advantages over more traditional automated market mechanisms such as auction protocols. 1
On the influence of surfactants in electrowetting systems (2007)

Buffer liquids currently used in biotechnology contain surfactants. These surfactants modify the wetting properties of the liquid and affect the behavior of droplets in electrowetting on dielectric (EWOD) microsystems. An analysis of the effect of surfactants in EWOD-based microsystems, at equilibrium and in a non-equilibrium state, is given here. First, a reference for the value of the surface tension and its time variation is obtained by the use of the pendant drop method, showing that the time variation of the surface tension follows a decreasing exponential law. Next, equilibrium experiments have been performed on a specially designed EWOD experimental microsystem. It has been observed that the Lippmann–Young theoretical equation for electrowetting is satisfied at equilibrium, even in the presence of surfactants. However, at the CMC, equilibrium surface tension values are different from those obtained by the pendant drop method. This difference is explained by an internal convective motion that remixes the surfactants. This internal motion is observed by following the motion of fluorophores. Consequently, surfactant concentrations about ten times the CMC are required to obtain the same values of the surface tension in the pendant drop method and by EWOD measurements. In a second section, it is shown that the behavior of surfactant-loaded droplets in EWOD-based microsystems can be explained by considering that the surface tension relaxes with time according to the exponential law found in the first section.
The structure of cytomegalovirus immune modulator UL141 highlights structural Ig-fold versatility for receptor binding (2014)

Natural killer (NK) cells are critical components of the innate immune system as they rapidly detect and destroy infected cells. To avoid immune recognition and to allow long-term persistence in the host, Human cytomegalovirus (HCMV) has evolved a number of genes to evade or inhibit immune effector pathways. In particular, UL141 can inhibit cell-surface expression of both the NK cell-activating ligand CD155 as well as the TRAIL death receptors (TRAIL-R1 and TRAIL-R2). The crystal structure of unliganded HCMV UL141 refined to 3.25 Å resolution allowed analysis of its head-to-tail dimerization interface. A `dimerization-deficient' mutant of UL141 (ddUL141) was further designed, which retained the ability to bind to TRAIL-R2 or CD155 while losing the ability to cross-link two receptor monomers. Structural comparison of unliganded UL141 with UL141 bound to TRAIL-R2 further identified a mobile loop that makes intimate contacts with TRAIL-R2 upon receptor engagement. Superposition of the Ig-like domain of UL141 on the CD155 ligand T-cell immunoreceptor with Ig and ITIM domains (TIGIT) revealed that UL141 can potentially engage CD155 similar to TIGIT by using the C'C'' and GF loops. Further mutations in the TIGIT binding site of CD155 (Q63R and F128R) abrogated UL141 binding, suggesting that the Ig-like domain of UL141 is a viral mimic of TIGIT, as it targets the same binding site on CD155 using similar `lock-and-key' interactions. Sequence alignment of the UL141 gene and its orthologues also showed conservation in this highly hydrophobic (L/A)X6G `lock' motif for CD155 binding as well as conservation of the TRAIL-R2 binding patches, suggesting that these host-receptor interactions are evolutionary conserved.
ST-segment elevation in the electrocardiogram: a sign of myocardial ischemia (2000)

In 1972 Kjekshus et al. published the seminal article 'Distribution of myocardial injury and its relations to epicardial ST-segment changes after coronary occlusion in the dog' in Cardiovascular Research. In this article it was shown that the ST-segment elevation occurring early after occlusion of the left descending coronary artery was closely related to the depletion of the necrotic cells from creatine kinase and to flow reduction at a later stage (24 h). This correlation was especially prominent if the infarction was transmural. Starting from these phenomenological relationships, this article briefly describes and summarizes the experimental research which was carried out in other laboratories after the publication of Kjekshus et al. Special emphasis is laid on the discussion of the main basic mechanisms which underly the clinically observed ST-segment elevation and its evolution after the acute stage of ischemia, i.e. the changes in the transmembrane action potential and the alteration in electrical cell-to-cell coupling.
Applications 2000 [computer graphics] (2000)

Applications have driven the development of computer graphics from the beginning. With so many original technical objectives achieved, the coming decades will likely see a greater emphasis on graphics applications, both taking advantage of these technologies and motivating new ones. The problem with predicting the future in this fast-moving area is that most "predictions" are already true. That said, this article explores a selected set of application domains and speculates on what the next few years may bring. The application domains considered are: science (astronomy, chemistry, biology, heath and medicine, physics, and mathematics); the environment (meteorology, geology, oceanography, and agriculture and land use); entertainment and the arts (movies, television, games and amusements, sports, fine arts, and archaeology); and other industries (publishing, manufacturing, transportation, the military, and business).
Fluorescent Cocaine Probes:  A Tool for the Selection and Engineering of Therapeutic Antibodies (2005)

Cocaine is a highly addictive drug, and despite intensive efforts, effective therapies for cocaine craving and addiction remain elusive. In recent years, we and others have reported advances in anti-cocaine immunopharmacotherapy based on specific antibodies capable of sequestering the drug before it reaches the brain. In an effort to obtain high affinity therapeutic anti-cocaine antibodies, either whole IgGs or other antibody constructs, fluorescence spectroscopic techniques could provide a means of assisting selection and engineering strategies. We report the synthesis of a series of cocaine-fluorophore conjugates (GNC-F1, GNC-F2, GNC-I) and the functional evaluation of these compounds against single-chain Fv antibodies obtained via crystallographic analysis/engineering and against commercially available anti-cocaine monoclonal antibodies with a wide range of cocaine-binding affinities. From these studies, we determined that the GNC-F2 fluorophore reproduced affinity constants obtained using [(3)H]-labeled cocaine. We anticipate that the readily synthesized and nonradioactive GNC-F2 will find use both as a tool for bioimaging and in the high-throughput selection and engineering of potential therapeutic antibodies against cocaine.