gebhart/patrepeval huggingface dataset:
Migration of Plasmodium Sporozoites Through Cells Before Infection (2001)

Intracellular bacteria and parasites typically invade host cells through the formation of an internalization vacuole around the invading pathogen. Plasmodium sporozoites, the infective stage of the malaria parasite transmitted by mosquitoes, have an alternative mechanism to enter cells. We observed breaching of the plasma membrane of the host cell followed by rapid repair. This mode of entry did not result in the formation of a vacuole around the sporozoite, and was followed by exit of the parasite from the host cell. Sporozoites traversed the cytosol of several cells before invading a hepatocyte by formation of a parasitophorous vacuole, in which they developed into the next infective stage. Sporozoite migration through several cells in the mammalian host appears to be essential for the completion of the life cycle.
Generation of in situ sequencing based OncoMaps to spatially resolve gene expression profiles of diagnostic and prognostic markers in breast cancer (2019)

ISS generated OncoMaps represent useful tools to extend our general understanding of the biological processes behind tumor progression and can further support the identification of novel therapeutical targets as well as refine tumor diagnostics. FUND: Swedish Cancerfonden, UCAN, Vetenskapsrådet, Cancer Genomics Netherlands, Iris, Stig och Gerry Castenbäcks Stiftelse, BRECT, PCM Program, King Gustaf V Jubilee Fund, BRO, KI and Stockholm County Council, Alice Wallenberg Foundation.
Equilibrium Thermodynamic Properties of the Mixture of Hard Spheres (1971)

An equation of state is proposed for the mixture of hard spheres based on an averaging process over the two results of the solution of the Percus–Yevick integral equation for the mixture of hard spheres. Compressibility and other equilibrium properties of the binary mixtures of hard spheres are calculated and they are compared with the related machine-calculated (Monte Carlo and molecular dynamics) data. The comparison shows excellent agreement between the proposed equation of state and the machine-calculated data.
Cardiotonic steroids. 5. A synthesis of bufadienolides and cardenolides from 3.beta.-acetoxy-5-androsten-17-one via common intermediates (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCardiotonic steroids. 5. A synthesis of bufadienolides and cardenolides from 3.beta.-acetoxy-5-androsten-17-one via common intermediatesMarek M. Kabat, Alicja Kurek, and Jerzy WichaCite this: J. Org. Chem. 1983, 48, 23, 4248–4251Publication Date (Print):November 1, 1983Publication History Published online1 May 2002Published inissue 1 November 1983https://pubs.acs.org/doi/10.1021/jo00171a018https://doi.org/10.1021/jo00171a018research-articleACS PublicationsRequest reuse permissionsArticle Views290Altmetric-Citations15LEARN 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 Get e-Alerts
Optical intensity modulator based on a novel electrooptic polymer incorporating high /spl mu//spl beta/ chromophore (2000)

We have synthesized a novel electrooptic (EO) polymer based on a high /spl mu//spl beta/ chromophore incorporating tricyanobutadiene acceptors. A crosslinked polyurethane network was also adopted to enhance its thermal stability. In order to find the optimum poling condition for the polymer, the influence of the electric poling profile on optical characteristics such as the EO effect, thermal stability, and damage was investigated. Then a high-speed intensity modulator using the EO polymer was designed and fabricated. The measured half-wave voltage V/sub /spl pi// was 4.5 V at the wavelength of 1.31 /spl mu/m. Accordingly, the achieved EO coefficient r/sub 33/ was as high as 25 pm/V, and the thermal stability of the poled polymer was as high as 95/spl deg/C. Finally, the modulator was successfully operated up to 40 GHz.
The Lightweight Directory Access Protocol: X.500 Lite (1995)

This paper describes the Lightweight Directory Access Protocol (LDAP), which provides low-overhead access to the X.500 directory. LDAP includes a subset of full X.500 functionality. It runs directly over TCP and uses a simplified data representation for many protocol elements. These simplifications make LDAP clients smaller, faster, and easier to implement than full X.500 clients. Our freely available implementation of the protocol is also described. It includes an LDAP server and a client library that makes writing LDAP programs much easier.
A fluorescence-based centrifugal microfluidic system for parallel detection of multiple allergens (2010)

This paper reports a robust polymer based centrifugal microfluidic analysis system that can provide parallel detection of multiple allergens in vitro. Many commercial food products (milk, bean, pollen, etc.) may introduce allergy to people. A low-cost device for rapid detection of allergens is highly desirable. With this as the objective, we have studied the feasibility of using a rotating disk device incorporating centrifugal microfluidics for performing actuationfree and multi-analyte detection of different allergen species with minimum sample usage and fast response time. Degranulation in basophils or mast cells is an indicator to demonstrate allergic reaction. In this connection, we used acridine orange (AO) to demonstrate degranulation in KU812 human basophils. It was found that the AO was released from granules when cells were stimulated by ionomycin, thus signifying the release of histamine which accounts for allergy symptoms <sup>[1-2]</sup>. Within this rotating optical platform, major microfluidic components including sample reservoirs, reaction chambers, microchannel and flow-control compartments are integrated into a single bio-compatible polydimethylsiloxane (PDMS) substrate. The flow sequence and reaction time can be controlled precisely. Sequentially through varying the spinning speed, the disk may perform a variety of steps on sample loading, reaction and detection. Our work demonstrates the feasibility of using centrifugation as a possible immunoassay system in the future.
Gene expression profiling of clear cell renal cell carcinoma: Gene identification and prognostic classification (2001)

To better understand the molecular mechanisms that underlie the tumorigenesis and progression of clear cell renal cell carcinoma (ccRCC), we studied the gene expression profiles of 29 ccRCC tumors obtained from patients with diverse clinical outcomes by using 21,632 cDNA microarrays. We identified gene expression alterations that were both common to most of the ccRCC studied and unique to clinical subsets. There was a significant distinction in gene expression profile between patients with a relatively nonaggressive form of the disease [100% survival after 5 years with the majority (15/17 or 88%) having no clinical evidence of metastasis] versus patients with a relatively aggressive form of the disease (average survival time 25.4 months with a 0% 5-year survival rate). Approximately 40 genes most accurately make this distinction, some of which have previously been implicated in tumorigenesis and metastasis. To test the robustness and potential clinical usefulness of this molecular distinction, we simulated its use as a prognostic tool in the clinical setting. In 96% of the ccRCC cases tested, the prediction was compatible with the clinical outcome, exceeding the accuracy of prediction by staging. These results suggest that two molecularly distinct forms of ccRCC exist and that the integration of expression profile data with clinical parameters could serve to enhance the diagnosis and prognosis of ccRCC. Moreover, the identified genes provide insight into the molecular mechanisms of aggressive ccRCC and suggest intervention strategies.
Inhibition of human immunodeficiency virus (HIV-1/HTLV-IIIBa-L) replication in fresh and cultured human peripheral blood monocytes/macrophages by azidothymidine and related 2',3'-dideoxynucleosides. (1988)

Because of the probable role of HIV-infected monocyte/macrophages in the pathogenesis and progression of AIDS, it is essential that antiretroviral therapy address viral replication in cells of this lineage. Several dideoxynucleosides have been shown to have potent in vitro and, in the case of 3'-azido-2',3'-dideoxythymidine (AZT) and 2',3'-dideoxycytidine (ddC), in vivo activity against HIV. However, because these compounds must be phosphorylated (activated) in target cells, and because monocyte/macrophages may have levels of kinases that differ from those in lymphocytes, we investigated the capacity of these drugs to suppress HIV replication in monocyte/macrophages using HIV-1/HTLV-IIIBa-L (a monocytotropic isolate). In the present study, we observed that HTLV-IIIBa-L replication in fresh human peripheral blood monocyte/macrophages was suppressed by each of three dideoxynucleosides: 3'-azido-2',3'-dideoxythymidine (AZT), 2',3'-dideoxycytidine (ddC), and 2',3'-dideoxyadenosine (ddA). Similar results were observed in 5-d-cultured monocyte/macrophages, although higher concentrations of the drugs were required. We then studied the metabolism of AZT and ddC in such cells. The phosphorylation of ddC to a triphosphate moiety was somewhat decreased in monocyte/macrophages as compared with H9 T cells. On the other hand, the phosphorylation of AZT in monocyte/macrophages was markedly decreased to 25% or less of the level in T cells. However, when we examined the level of the normal endogenous 2'-deoxynucleoside triphosphate pools, which compete with 2',3'-dideoxynucleoside triphosphate for viral reverse transcriptase, we found that the level of 2'-deoxycytidine-triphosphate (dCTP) was six- to eightfold reduced, and that of 2'-deoxythymidine-triphosphate (dTTP) was only a small fraction of that found in T cell lines. These results suggest that the ratio of dideoxynucleoside triphosphate to normal deoxynucleoside triphosphate is a crucial factor in determining the antiviral activity of dideoxynucleosides in HIV target cells, and that the lower levels of dTTP may account for the antiretroviral activity of AZT in the face of inefficient phosphorylation of this compound.
Lymphocyte recruitment and homing to the liver in primary biliary cirrhosis and primary sclerosing cholangitis (2009)

The mechanisms operating in lymphocyte recruitment and homing to liver are reviewed. A literature review was performed on primary biliary cirrhosis (PBC), progressive sclerosing cholangitis (PSC), and homing mechanisms; a total of 130 papers were selected for discussion. Available data suggest that in addition to a specific role for CCL25 in PSC, the CC chemokines CCL21 and CCL28 and the CXC chemokines CXCL9 and CXCL10 are involved in the recruitment of T lymphocytes into the portal tract in PBC and PSC. Once entering the liver, lymphocytes localize to bile duct and retain by the combinatorial or sequential action of CXCL12, CXCL16, CX3CL1, and CCL28 and possibly CXCL9 and CXCL10. The relative importance of these chemokines in the recruitment or the retention of lymphocytes around the bile ducts remains unclear. The available data remain limited but underscore the importance of recruitment and homing.
<title>Solubility properties of siloxane polymers for chemical sensors</title> (1995)

Many chemical sensors rely on a sorbent material to collect and concentrate analyte molecules at the sensor's surface where they can be detected. Ideally, this sorbent material will impart the chemical sensor with both sensitivity and selectivity for the target species. If the sensor is to be reversible, then the species must also desorb from the material or be actively removed by some process such as catalytic destruction. Polymer materials offer many attractive features for chemical sensing. Organic compounds are readily sorbed in a reversible fashion, selectivity can be altered by varying the chemical structure, and polymer materials can be processed into thin films. In this paper, we discuss the factors that govern the sorption of vapors by organic polymers. The approach described has been applied in the past for the design and selection of polymers for acoustic wave sensors. However, the principles apply equally well to the sorption of vapors by polymers used on optical chemical sensors. For example, the polymer could be applied as a thin film to a planar waveguide as the cladding along the length of an optical fiber, or to the end of an optical fiber. Species sorbed into the polymer could then be detected by a change in an optical signal.
Members of the HRT family of basic helix–loop–helix proteins act as transcriptional repressors downstream of Notch signaling (2000)

The Hairy-related transcription-factor (HRT) genes encode three related basic helix-loop-helix transcription factors that show sequence similarity to the Hairy and Enhancer of split family of transcriptional repressors. HRT proteins are expressed in specific regions of the developing heart, vasculature, pharyngeal arches and somites, and the periodicity of their expression in somitic precursors mirrors that of Notch signaling-related molecules. In the present study, we show that the intracellular domain of the Notch1 receptor (Notch1 IC), which is constitutively active, up-regulates HRT2 expression in 10T(1/2) fibroblasts. Luciferase reporter assays using the regulatory regions of the mouse HRT genes revealed that transcription of all three genes is stimulated by Notch1 IC. The promoters of the HRT genes share homology in a binding site for Suppressor of Hairless [Su(H)], a transcriptional mediator of Notch signaling. A dominant-negative Su(H) mutant abolished Notch-activated HRT2 expression, and mutation of the conserved Su(H) consensus site in the HRT2 promoter attenuated transcriptional activation by Notch. Ectopic expression of HRT proteins also blocked activation of HRT2 expression by Notch1 IC through a mechanism requiring the basic region, but not the conserved carboxyl-terminal YQPW-TEVGAF motif of HRT2. These findings identify HRT genes as downstream targets for Notch signaling and reveal a negative autoregulatory loop whereby HRT proteins repress their own expression through interference with Notch signaling.
Isolation of a Cytomegalovirus from African Green Monkey (1963)

SummaryTwo similar strains of virus were recovered from Cercopithecus monkey salivary gland tissue and kidney tissue culture. The agents possessed the biological characteristics of cytomegaloviruses, and shared CF antigens with a human cytomegalovirus. They are unique among cytomegaloviruses in their ability to grow in heterologous (human) tissue cultures. Antibodies were common in Cercopithecus held in captivity but were not found in freshly captured rhesus monkeys.
Commutative algebra with a view toward algebraic geometry (1996)

Introduction.- Elementary Definitions.- I Basic Constructions.- II Dimension Theory.- III Homological Methods.- Appendices.- Hints and Solutions for Selected Exercises.- References.- Index of Notation.- Index.
Ligase chain reaction assay for human mutations: the Sickle Cell by LCR assay (1997)

We can detect the beta-globin gene sickle cell mutation by using an assay based on the ligase chain reaction. The simultaneous amplification of the human growth hormone gene in the same reaction serves as a control for the amount of template DNA or amplification efficiency. Ligation products, which are biotinylated at one end and tagged with an arbitrary "tail" sequence at the other, are captured by hybridization to "tail"-complementary oligonucleotides immobilized on polystyrene microwells. The captured ligation products are detected colorimetrically by use of streptavidin-alkaline phosphatase conjugate. In a study of 24 subjects, the assay unequivocally discriminated among normal, carrier, and sickle cell genotypes.
The I Domain Is Required for Efficient Plasma Membrane Binding of Human Immunodeficiency Virus Type 1 Pr55 Gag (1998)

The interaction of the human immunodeficiency virus type 1 (HIV-1) Pr55Gag molecule with the plasma membrane of an infected cell is an essential step of the viral life cycle. Myristic acid and positively charged residues within the N-terminal portion of MA constitute the membrane-binding domain of Pr55Gag. A separate assembly domain, termed the interaction (I) domain, is located nearer the C-terminal end of the molecule. The I domain is required for production of dense retroviral particles, but has not previously been described to influence the efficiency of membrane binding or the subcellular distribution of Gag. This study used a series of Gag-green fluorescent protein fusion constructs to define a region outside of MA which determines efficient plasma membrane interaction. This function was mapped to the nucleocapsid (NC) region of Gag. The minimal region in a series of C-terminally truncated Gag proteins conferring plasma membrane fluorescence was identified as the N-terminal 14 amino acids of NC. This same region was sufficient to create a density shift in released retrovirus-like particles from 1.13 to 1.17 g/ml. The functional assembly domain previously termed the I domain is thus required for the efficient plasma membrane binding of Gag, in addition to its role in determining the density of released particles. We propose a model in which the I domain facilitates the interaction of the N-terminal membrane-binding domain of Pr55Gag with the plasma membrane.
Fresnel incoherent correlation holography (FINCH): a review of research (2012)

Abstract In this review, we describe our method for creating holograms of incoherent objects, dubbed Fresnel incoherent correlation holography (FINCH). FINCH creates holograms by a single-channel on-axis incoherent interferometer process. Like any Fresnel hologram, the object is correlated with quadratic phase functions, but the correlation is carried out without any movement. Generally, in the FINCH system, light is reflected, or emitted, from a three-dimensional (3D) object, propagates through a spatial light modulator (SLM), and is recorded by a digital camera. The SLM is used as a beam-splitter of the single-channel incoherent interferometer, such that each spherical beam originated from each object point is split into two spherical beams with two different curve radiuses. Incoherent summing of the entire interferences between all the couples of the spherical beams creates the Fresnel hologram of the observed 3D object. When this hologram is reconstructed in the computer, the 3D properties of the object are revealed. In this review, we describe various aspects of FINCH which have been described recently, including FINCH of reflected white light, FINCH of fluorescence objects, a FINCH-based holographic fluorescence microscope, a FINCH configuration which capitalizes on the polarization sensitivity of the SLM and finally FINCH is analyzed in view of linear system theory.
Strong localization of photons in certain disordered dielectric superlattices (1987)

A new mechanism for strong Anderson localization of photons in carefully prepared disordered dielectric superlattices with an everywhere real positive dielectric constant is described. In three dimensions, two photon mobility edges separate high- and low-frequency extended states from an intermediate-frequency pseudogap of localized states arising from remnant geometric Bragg resonances. Experimentally observable consequences are discussed.
Proteolytic interactions of factor IXa with human factor VIII and factor VIIIa (1992)

Factor IXa was shown to inactivate both factor VIII and factor VIIIa in a phospholipid-dependent reaction that could be blocked by an antifactor IX antibody. Factor IXa-catalyzed inactivation correlated with proteolytic cleavages within the A1 subunit of factor VIIIa and within the heavy chain (contiguous A1-A2-B domains) of factor VIII. Furthermore, a relatively slow conversion of factor VIII light chain to a 68-Kd fragment was observed after prolonged incubation. Sites of cleavage were identified within the A1 domain at Arg336-Met337 and within the factor VIII light chain at Arg1719-Asn1720. Factor IXa failed to cleave isolated factor VIII heavy chains, yet cleaved isolated factor VIII light chain. In addition, the purified A1/A3-C1-C2 dimer derived from factor VIIIa was a substrate for factor IXa; however, cleavage of the A1 subunit occurred at less than 30% the rate of cleavage of A1 in trimeric factor VIIIa. These data suggest that factor VIII light chain contributes to the binding site for factor IXa and also support a role for a heavy chain determinant located within the A2 subunit in the association of factor VIIIa with factor IXa. Furthermore, the capacity of factor IXa to proteolytically inactivate its cofactor, factor VIIIa, suggests a mode of regulation within the intrinsic tenase complex.
Rapid Detection of Group B Streptococci in Pregnant Women at Delivery (2000)

Colonization with group B streptococci can be identified rapidly and reliably by a PCR assay in pregnant women in labor both before and after the rupture of membranes.
[The structure of cellular vaults, their role in the normal cell and in the multidrug resistance of cancer]. (2011)

The cellular vaults have been described for the first time in 1986 as ribonucleoprotein complexes composed of three proteins, MVP, TEP1 and vPARP and several vRNA strains. Biochemical and structural studies revealed their ubiquitous existence in the cytoplasm of many eukaryotic cells and their barrel-like structure indicating their engagement in the intracellular transport. Furthermore, the high homology between MVP and LRP which was already known to be involved in multidrug resistance mechanism opened a discussion about the role of vaults in both normal and cancer cells. The histopathology research demonstrated an increased amount of MVP/LRP proteins in the cancer as well as showed translocation possibility between cytoplasm and nuclear envelope, which can be of crucial point in the prevention of nucleus against anticancer drugs.
Datawarehouse design for educational data mining (2016)

Business intelligence (BI) builds upon a set of tools and applications that enable the analysis of vast amounts of information (Big Data). Educational institutions handle large volumes of Big Data every year. There is a strong need for the use of BI in these institutions to improve their processes and support decision making. The core technology in a BI project is a datawarehouse (DW). This paper describes the design considerations for the implementation of the DW in an educational scenario. The DW will be used in a knowledge discovery process to handle the information for the analysis of key performance indicators using educational data mining (EDM) techniques. The DW along with an enterprise architecture (EA) repository are the key technological assets of a knowledge management framework (KMF). This framework was designed to put order in the creation, capture, transfer and digitalization of knowledge. This guide and the framework are two of the outcomes of a research project in a private university. Furthermore, a case study suggests how to choose the best methodology in higher institutions. In the case study the steps for the DW design are presented. This study can be useful for academics and practitioners that plan to design a DW to analyze information using EDM techniques.