gebhart/patrepeval huggingface dataset:
TIM-3 Does Not Act as a Receptor for Galectin-9 (2013)

T cell immunoglobulin and mucin protein 3 (TIM-3) is a type I cell surface protein that was originally identified as a marker for murine T helper type 1 cells. TIM-3 was found to negatively regulate murine T cell responses and galectin-9 was described as a binding partner that mediates T cell inhibitory effects of TIM-3. Moreover, it was reported that like PD-1 the classical exhaustion marker, TIM-3 is up-regulated in exhausted murine and human T cells and TIM-3 blockade was described to restore the function of these T cells. Here we show that the activation of human T cells is not affected by the presence of galectin-9 or antibodies to TIM-3. Furthermore, extensive studies on the interaction of galectin-9 with human and murine TIM-3 did not yield evidence for specific binding between these molecules. Moreover, profound differences were observed when analysing the expression of TIM-3 and PD-1 on T cells of HIV-1-infected individuals: TIM-3 was expressed on fewer cells and also at much lower levels. Furthermore, whereas PD-1 was preferentially expressed on CD45RA(-)CD8 T cells, the majority of TIM-3-expressing CD8 T cells were CD45RA(+). Importantly, we found that TIM-3 antibodies were ineffective in increasing anti-HIV-1 T cell responses in vitro, whereas PD-L antibodies potently reverted the dysfunctional state of exhausted CD8 T cells. Taken together, our results are not in support of an interaction between TIM-3 and galectin-9 and yield no evidence for a functional role of TIM-3 in human T cell activation. Moreover, our data indicate that PD-1, but not TIM-3, is a promising target to ameliorate T cell exhaustion.
The CrP operon of Chlamydia psittaci and Chlamydia pneumoniae (1995)

One of the critical developmental events during the unique intracellular life cycle of Chlamydiae is their differentiation from a metabolically active, replicative form or reticulate body (RB) to an infectious extracellular form of the organism (elementary body or EB). This process is characterized by the expression of two extraordinarily cysteine-rich envelope proteins of molecular masses 9 kDa and 60 kDa. We describe the molecular cloning and sequence determination of the 9 kDa cysteine-rich proteins (CrPs) of C. pneumoniae and C. psittaci. Comparison of these 9 kDa CrP amino acid sequences with those of C. trachomatis showed regions of structural variation and conservation. Transcription of the 9 kDa CrP genes occurred as both a monocistronic message and as a bicistronic message which included the 60 kDa CrP gene. Transcription of the 9 kDa and 60 kDa CrP genes was tightly linked to the chlamydial growth cycle with synthesis of their mRNAs and consequent translation of the 60 kDa CrPs occurring as RBs differentiated to form EBs. The maximal rate of transcription occurred late in the growth cycle from a single but highly conserved promoter which had close similarity with the Escherichia coli consensus promoter sequences. A stem and loop structure which could be involved in regulating translation of mRNA occurred in all three species between the transcriptional start point and the ribosome binding site. Although transcription is initiated from a single promoter in all three chlamydial species, transcriptional termination points for the monocistronic and bicistronic mRNAs differ in both number and position.
Respiratory Syncytial Virus Infection of Human Airway Epithelial Cells Is Polarized, Specific to Ciliated Cells, and without Obvious Cytopathology (2002)

Gene therapy for cystic fibrosis (CF) lung disease requires efficient gene transfer to airway epithelial cells after intralumenal delivery. Most gene transfer vectors so far tested have not provided the efficiency required. Although human respiratory syncytial virus (RSV), a common respiratory virus, is known to infect the respiratory epithelium, the mechanism of infection and the epithelial cell type targeted by RSV have not been determined. We have utilized human primary airway epithelial cell cultures that generate a well-differentiated pseudostratified mucociliary epithelium to investigate whether RSV infects airway epithelium via the lumenal (apical) surface. A recombinant RSV expressing green fluorescent protein (rgRSV) infected epithelial cell cultures with high gene transfer efficiency when applied to the apical surface but not after basolateral inoculation. Analyses of the cell types infected by RSV revealed that lumenal columnar cells, specifically ciliated epithelial cells, were targeted by RSV and that cultures became susceptible to infection as they differentiated into a ciliated phenotype. In addition to infection of ciliated cells via the apical membrane, RSV was shed exclusively from the apical surface and spread to neighboring ciliated cells by the motion of the cilial beat. Gross histological examination of cultures infected with RSV revealed no evidence of obvious cytopathology, suggesting that RSV infection in the absence of an immune response can be tolerated for >3 months. Therefore, rgRSV efficiently transduced the airway epithelium via the lumenal surface and specifically targeted ciliated airway epithelial cells. Since rgRSV appears to breach the lumenal barriers encountered by other gene transfer vectors in the airway, this virus may be a good candidate for the development of a gene transfer vector for CF lung disease.
Low-Temperature Catalytic Gasification of Lignin and Cellulose with a Ruthenium Catalyst in Supercritical Water (2003)

Lignin and cellulose were gasified at 400 °C with gas yields of 30% and 70%, respectively, in supercritical water with a ruthenium catalyst. In both cases, the main gas product was CH4 and no solid product was formed. Without water or catalyst, lignin and cellulose were gasified slightly and a brown solid product was formed. The decomposition of formaldehyde was also demonstrated in supercritical water. Formaldehyde was rapidly decomposed to gases such as CH4, CO2, and H2 with ruthenium, whereas formaldehyde was converted into methanol and CO2 without catalyst. The catalytic conversion of biomass with ruthenium in supercritical water is an efficient method for biomass gasification at temperatures of ∼400 °C.
Volume rendering of 3D medical ultrasound data using direct feature mapping (1994)

The authors explore the application of volume rendering in medical ultrasonic imaging. Several volume rendering methods have been developed for X-ray computed tomography (X-CT), magnetic resonance imaging (MRI) and positron emission tomography (PET). Limited research has been done on applications of volume rendering techniques in medical ultrasound imaging because of a general lack of adequate equipment for 3D acquisitions. Severe noise sources and other limitations in the imaging system make volume rendering of ultrasonic data a challenge compared to rendering of MRI and X-CT data. Rendering algorithms that rely on an initial classification of the data into different tissue categories have been developed for high quality X-CT and MR-data. So far, there is a lack of general and reliable methods for tissue classification in ultrasonic imaging. The authors focus on volume rendering methods which are not dependent on any classification into different tissue categories. Instead, features are extracted from the original 3D data-set, and projected onto the view plane. The authors found that some of these methods may give clinically useful information which is very difficult to get from ordinary 2D ultrasonic images, and in some cases renderings with very fine structural details. The authors have applied the methods to 3D ultrasound images from fetal examinations. The methods are now in use as clinical tools at the National Center of Fetal Medicine in Trondheim, Norway.
MHC class II‐independent CD25+ CD4+ CD8α β+ α β T cells attenuate CD4+ T cell‐induced transfer colitis (2004)

CD4+ alpha beta T cell populations that develop in mice deficient in MHC class II (through 'knockout' of either the Aalpha, or the Abeta chain of the I-A(b) molecule) comprise a major 'single-positive' (SP) CD4+ CD8- subset (60-90%) and a minor 'double-positive' (DP) CD4+ CD8alpha beta+ subset (10-40%). Many DP T cells found in spleen, mesenteric lymph nodes (MLN) and colonic lamina propria (cLP) express CD25, CD103 and Foxp3. Adoptive transfer of SP but not DP T cells from Aalpha(-/-) or Abeta(-/-) B6 mice into congenic RAG(-/-) hosts induces colitis. Transfer of SP T cells repopulates the host with only SP T cells; transfer of DP T cells repopulates the host with DP and SP T cells. Anti-CD25 antibody treatment of mice transplanted with DP T cells induces severe, lethal colitis; anti-CD25 antibody treatment of mice transplanted with SP T cells further aggravates the course of severe colitis. Hence, regulatory CD25+ T cells within (or developing from) the DP T cell population of MHC class II-deficient mice control the colitogenic potential of CD25- CD4+ T cells.
Immune Modulation in Cancer Patients After Adoptive Transfer of Anti-CD3/Anti-CD28–Costimulated T Cells—Phase I Clinical Trial (2001)

Anti-CD3/anti-CD28 monoclonal antibody-coactivated T cells (COACTs) proliferate, secrete tumoricidal cytokines, and mediate non-major histocompatibility complex (MHC)-restricted cytotoxicity. This phase I study was done to determine the safety, maximum tolerated dose, technical limits of expansion, and modulation of immune functions in cancer patients given COACTs. Coactivated T cells were produced by stimulating peripheral blood mononuclear cells (PBMCs) with OKT3 anti-CD3 and 9.3 (anti-CD28)-coated beads in the presence of 100 IU interleukin (IL)-2 per milliliter for 14 days. The beads were removed after 4 days of culture. Ten courses of COACTs were given to eight patients with renal cell (1), ovarian (2), breast (1), and colorectal (4) carcinomas; two patients received two courses of COACTs. Patients were given up to 10 x 10 9 COACTs twice a week for 3 weeks without dose-limiting toxicities. Patients at the first and second dose levels received a mean total of 17.6 and 42.4 x 10 9 COACTs, respectively. After 14 days of culture, the COACTs contained a mean of 57.5% CD4+ cells and 42.5% CD8+ cells, exhibited non-MHC-restricted cytotoxicity, and produced significant amounts of interferon (IFN)-gamma, tumor necrosis factor (TNF)-alpha, and granulocyte macrophage colony-stimulating factor (GM-CSF). Infusions were safe and induced measurable serum levels of IFNgamma, TNFalpha, and IL-4 in two patients. Peripheral blood mononuclear cells from patients who received COACTs secreted higher amounts of IFNgamma and GM-CSF on in vitro anti-CD3/anti-CD28 restimulation than PBMCs obtained before immunotherapy. The detection of cytokines in patient sera and enhanced in vitro production of cytokines by anti-CD3/anti-CD28-stimulated patient PBMCs after COACT infusions suggest that COACTs were modulating immune responses in cancer patients.
USER fusion: a rapid and efficient method for simultaneous fusion and cloning of multiple PCR products (2007)

We present a method that allows simultaneous fusion and cloning of multiple PCR products in a rapid and efficient manner. The procedure is based on the use of PCR primers that contain a single deoxyuridine residue near their 5' end. Treatment of the PCR products with a commercial deoxyuridine-excision reagent generates long 3' overhangs designed to specifically complement each other. The combination of this principle with the improved USER cloning technique provides a simple, fast and very efficient method to simultaneously fuse and clone multiple PCR fragments into a vector of interest. Around 90% positive clones were obtained when three different PCR products were fused and cloned into a USER-compatible vector in a simple procedure that, apart from the single PCR amplification step and the bacterial transformation, took approximately one hour. We expect this method to replace overlapping PCR and the use of type IIS restriction enzymes in many of their applications.
Feature sets for interactive images (1991)

article Free Access Share on Feature sets for interactive images Author: Andrew Lippman Massachusetts Institute of Technology, Cambridge, MA Massachusetts Institute of Technology, Cambridge, MAView Profile Authors Info & Claims Communications of the ACMVolume 34Issue 4April 1991pp 92–102https://doi.org/10.1145/103085.103094Published:01 April 1991Publication History 26citation443DownloadsMetricsTotal Citations26Total Downloads443Last 12 Months14Last 6 weeks4 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
Antibodies against Early Proteins of Human Papillomaviruses as Diagnostic Markers for Invasive Cervical Cancer (1998)

Cervical cancer is the most prevalent tumor in developing countries and the second most frequent cancer among females worldwide. Specific human papillomaviruses (HPVs) and, most notably, HPV types 16 and 18 are recognized as being causally associated with this malignancy. Antibodies against early HPV proteins E6 and E7 have been found more often in patients with tumors than in controls. Existing peptide enzyme-linked immunosorbent assays (ELISAs) for the detection of anti-E6 and anti-E7 antibodies in human sera have low levels of sensitivity and specificity and thus are not suitable for use as diagnostic tools. Based on highly purified recombinant native proteins, we developed four sandwich ELISAs for the detection of antibodies against HPV type 16 and 18 E6 and E7 proteins. We demonstrate their sensitivities and high degrees of specificity for cervical cancer. Among a total of 501 serum specimens from unselected patients with invasive cervical cancer, 52.9% reacted positively in at least one of the four assays. In contrast, among 244 serum specimens from control subjects without cervical cancer, only 2 reactive serum specimens (0.8%) were found. For 19 of 19 antibody-positive patients, the HPV type indicated by seroreactivity was identical to the HPV DNA type found in the tumor, which also indicates a high degree of specificity for antibody detection with respect to HPV type. In a direct comparison of 72 serum specimens from patients with cervical cancer, 56% of the specimens reacted in at least one of the four protein ELISAs, whereas 40% reacted in at least one of seven peptide ELISAs covering the four antigens. These assays could be of value for the detection of invasive cervical cancer in settings in which cytology-based early tumor screening is not available, for the clinical management of patients diagnosed with cervical cancer, and for the immunological monitoring of E6 and E7 vaccination trials.
Serological and allergic reactions of ewes after simultaneous vaccinations with two living attenuated strains of Brucella and Salmonella. (1990)

Four groups of 50 4-6-month old ewe-lambs were vaccinated with 1 or 2 living attenuated vaccines administered simultaneously. One hundred ewe-lambs received B melitensis strain REV 1 vaccine subcutaneously and 100 others received Rev 1 vaccine conjunctivally. In each group, 50 ewe-lambs simultaneously received the S abortusovis strain Rv6 vaccine via a contralateral subcutaneous route. Reactions to Brucella antigens (estimated by allergic intrapalpebral reaction to brucellin, complement fixation test and Rose Bengal plate test) or to S abortusovis antigens (agglutination of O and H antigens) were recorded. Agglutinating titers against Salmonella antigens increased in all animals vaccinated with Abortusovis Rv6, whatever the route of the associated Rev1 vaccination. Rv6 vaccination did not interfere with serological or allergic responses to Rev 1 vaccination 1 month after vaccination. Six months after vaccination, no interference was observed with serological reactions to Rev 1 vaccination, which were still positive in about 10% of subcutaneously vaccinated ewes and negative in all conjunctivally vaccinated ewes. However, 6 months after vaccination, the frequencies of allergic responses to Rev 1 vaccine were significantly decreased by Rv6 vaccination in the Rev 1 subcutaneously vaccinated (45 versus 24%, P less than 0.05), but not in the Rev 1 conjunctivally vaccinated groups (12 versus 17%). According to these serological and allergic criteria, 1), association of the 2 vaccines does not appear to interfere with detection of Brucellosis more than by using a single anti-Brucella vaccination; 2), immunogenicity of each vaccinal valence was demonstrated after simultaneous vaccination; and 3), anti-Brucella serological and allergic responses remained in any case lower after conjunctival vaccination than after subcutaneous Rev 1 injection.
A SIMO Parallel-String Driver IC for Dimmable LED Backlighting With Local Bus Voltage Optimization and Single Time-Shared Regulation Loop (2011)

Traditional LED drivers with multiple converters for powering up multiple strings in parallel suffer from high system volume and cost. The reported literature with single converter and dynamic bus voltage offers compact designs. However, the performance on power consumption is degraded. Meanwhile, all the aforementioned approaches require multiple current regulation elements, which inflict current balance errors due to mismatches. A compact single-inductor multiple-output parallel-string LED driver with time-multiplexing control is, thus, proposed. It can independently optimize local bus voltages for power loss reduction. In addition, a single time-shared control loop is proposed for current regulation in multiple parallel strings, resulting in a dramatic reduction of current balance errors. A 0.35 μm CMOS prototype achieves 2.8 times loss reduction over the reported literature, with a current balance error well controlled below 1.7%. The control scheme also offers flexible dimming for advanced backlighting operations.
Molecular determinants of positive allosteric modulation of the human metabotropic glutamate receptor 2 (2015)

This extensive study furthers our understanding of positive allosteric modulation of the mGlu2 receptor and can contribute to improved future design of mGlu2 PAMs.
Sex-Specific Expression of Gastrin-Releasing Peptide Receptor: Relationship to Smoking History and Risk of Lung Cancer (2000)

Our results suggest that the GRPR gene is expressed more frequently in women than in men in the absence of smoking and that expression of this gene is activated earlier in women in response to tobacco exposure. The presence of two expressed copies of the GRPR gene in females may be a factor in the increased susceptibility of women to tobacco-induced lung cancer.
Multicenter Phase II Trial of Immunotherapy With the Humanized Anti-CD22 Antibody, Epratuzumab, in Combination With Rituximab, in Refractory or Recurrent Non-Hodgkin's Lymphoma (2006)

Epratuzumab combined with rituximab was well tolerated, demonstrating promising antilymphoma activity that warrants additional study.
Complex protein-DNA dynamics at the latent origin of DNA replication of Epstein-Barr virus (2003)

The sequential binding of the origin recognition complex (ORC), Cdc6p and the minichromosome maintenance proteins (MCM2-7) mediates replication competence at eukaryotic origins of DNA replication. The latent origin of Epstein-Barr virus, oriP, is a viral origin known to recruit ORC. OriP also binds EBNA1, a virally encoded protein that lacks any activity predicted to be required for replication initiation. Here, we used chromatin immunoprecipitation and chromatin binding to compare the cell-cycle-dependent binding of pre-RC components and EBNA1 to oriP and to global cellular chromatin. Prereplicative-complex components such as the Mcm2p-Mcm7p proteins and HsOrc1p are regulated in a cell-cycle-dependent fashion, whereas other HsOrc subunits and EBNA1 remain constantly bound. In addition, HsOrc1p becomes sensitive to the 26S proteasome after release from DNA during S phase. These results show that the complex protein-DNA dynamics at the viral oriP are synchronized with the cell division cycle. Chromatin-binding and chromatin-immunoprecipitation experiments on G0 arrested cells indicated that the ORC core complex (ORC2-5) and EBNA1 remain bound to chromatin and oriP. HsOrc6p and the MCM2-7 complex are released in resting cells. HsOrc1p is partly liberated from chromatin. Our data suggest that origins remain marked in resting cells by the ORC core complex to ensure a rapid and regulated reentry into the cell cycle. These findings indicate that HsOrc is a dynamic complex and that its DNA binding activity is regulated differently in the various stages of the cell cycle.
The Clinicopathologic Characteristics and 5-year Survival Rate of Epithelial Ovarian Cancer in Yazd, Iran. (2015)

The survival of patients with epithelial ovarian cancer was significantly associated with disease stage. Serous adenocarcinoma also had the best prognosis among the pathologies studied. Therefore, early detection of ovarian cancer can substantially increase the survival rate.
Mechanistic Investigations of Porphyrin Syntheses. I. Preliminary Studies on ms-Tetraphenylporphin (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMechanistic Investigations of Porphyrin Syntheses. I. Preliminary Studies on ms-TetraphenylporphinAlan D. Adler, Frederick R. Longo, and William. ShergalisCite this: J. Am. Chem. Soc. 1964, 86, 15, 3145–3149Publication Date (Print):August 1, 1964Publication History Published online1 May 2002Published inissue 1 August 1964https://doi.org/10.1021/ja01069a035RIGHTS & PERMISSIONSArticle Views5125Altmetric-Citations302LEARN 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 InReddit PDF (656 KB) Get e-Alerts Get e-Alerts