gebhart/patrepeval huggingface dataset:
The Suppressive Tumor Microenvironment: A Challenge in Cancer Immunotherapy (2011)

In this review, we introduce the changing public perception of vaccines and immunotherapy in cancer treatments. We discuss the roles that different immunosuppressive cells play in the tumor microenvironment. Tumor associated macrophages (TAMs) and M1 and M2 macrophage phenotypes are discussed in depth. Additionally, the role that myeloid derived suppressor cells (MDSC) and T regulatory cells (Tregs) play in the tumor microenvironment is addressed. Highlighted are examples of therapies used against each suppressive cell type, which vary from the hypothetical to the ineffective; the inefficient to the successful. A variety of treatments have been tried to combat this fundamental problem, indeed the cause that allows cancerous mutated cells to survive, multiply and overtake the body. Efficient methods to disable each particular suppressive type of cell have been introduced; this review summarizes the discussion with a table to guide future development. We see gene therapy as the most innovative and flexible method to lead the charge to specifically modifying the tumor microenvironment.
AIDS and Zinc Deficiency (1984)

<h3>To the Editor.—</h3> Acquired immune deficiency syndrome (AIDS) is a complex disease. A multifactorial model is receiving strong support from investigators suggesting that the disease is a cumulative process following exposure to multiple injuries to the immune system. Furthermore, it is likely that all cases of AIDS are not from the same set of causes. I want to propose a new etiologic possibility for AIDS in homosexual men. In the past ten years, homosexuals have asserted a right to self-expression and there has been an outburst of pent-up feeling and an overactive sexuality. Many homosexuals have more than 60 partners per year,<sup>1</sup>a great preoccupation with sex, and an overactive use of masturbation, often with multiple ejaculations each day. The average volume of semen is 3 to 5 mL per ejaculation.<sup>2</sup>Semen is complex, with many proteins, enzymes, and prostaglandins, and is remarkable in the quantity of zinc
From negative factor to a critical role in virus pathogenesis: the changing fortunes of Nef (1996)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
The Numerous Microbial Species in Oral Biofilms (2012)

Hundreds of bacterial species inhabit the oral cavity. Many of these have never been cultivated and can be assessed only with DNA-based techniques. This new understanding has changed the paradigm of the etiology of oral disease from that associated with 'traditional pathogens' as being primarily responsible for all diseases. Increasingly, associations between oral bacteria and systemic diseases are being reported. The emergence of antibiotic resistance is alarming and calls for in-depth studies of biofilms, bacterial physiology, and a body-wide approach to infectious diseases. We propose that the borderline between commensal bacteria and pathogens is no longer discrete. In a field of science where so many of the established paradigms are being undermined, a thorough analysis of threats and opportunities is required. This article addresses some of the questions that can be raised and serves to identify research opportunities and needs to leverage the prevention of oral diseases through novel antimicrobial strategies.
Identification of PhoB binding sites of the yibD and ytfK promoter regions in Escherichia coli (2011)

By using a lacZ operon fusion genomic library of the Escherichia coli 0157:H7 Sakai, we identified phosphate-starvation-inducible (psi) promoters located upstream of the yibD and ytfK genes. They have been previously proposed to belong to the phosphate regulon (pho regulon) by Beak and Lee (2006), based on the DNA array and in vivo transcriptional experiments. However, the direct interaction of these promoters with the activator protein of the pho regulon, PhoB, has not been determined. We determined the binding regions of PhoB in these promoter regions by DNase I footprinting. Both regions contained two pho boxes similar to the consensus sequence for PhoB binding.
Fluorogenic click reaction (2009)

Fluorogenic Cu(I)-catalyzed alkyne-azide cycloaddition (CuAAC) reactions have emerged as a powerful tool for bioconjugation, materials science, organic synthesis and drug discovery. This review highlights the design of the recent development of fluorogenic CuAAC reactions as well as their applications.
<title>Interactive personalized newspaper on the WWW</title> (1996)

This paper discusses the personalization of online newspapers based on our experience with the Krakatoa Chronicle, an interactive, personalized, newspaper on the World Wide Web. The personalization of newspapers involves both social and technical issues. In social terms, it is important that users can control the extent of personalization, because newspapers are not only a means to get personally interesting articles but also a way to get information you are not explicitly looking for. In technical terms, the manner in which the user's interest is measured, and the strategy used to personalize the presentation are important. The Krakatoa Chronicle's approach to solving these problems is by sending over an interaction agent (in Java) from the web server side to the web-client, to manage the layout, interactions with the user, and provide feedback about user actions. In our system, the newspaper has a similar appearance to everyday printed ones, with multiple columns. The user has various interaction techniques to read articles, and has easy control over layout parameters including how personal the contents should be. The system can get the user's interest without requiring the user to do anything other than just read articles. The Krakatoa Chronicle will serve as a good testbed to learn how people would like to have their newspapers personalized.
Function of a human cyclin gene as an oncogene. (1994)

The cyclin D1 (PRAD1, CCND1) gene is affected by translocations and amplification in the genomes of a number of human tumors, suggesting that these changes confer growth advantage on developing tumor cell clones. We show here that in cultured cells, a cDNA clone of the cyclin D1 gene can contribute to cell transformation by complementing a defective adenovirus E1A oncogene. In such cells, this candidate oncogene indeed functions like an oncogene, suggesting a similar role in tumor progression in vivo.
Population Dynamics of Immune Responses to Persistent Viruses (1996)

Mathematical models, which are based on a firm understanding of biological interactions, can provide nonintuitive insights into the dynamics of host responses to infectious agents and can suggest new avenues for experimentation. Here, a simple mathematical approach is developed to explore the relation between antiviral immune responses, virus load, and virus diversity. The model results are compared to data on cytotoxic T cell responses and viral diversity in infections with the human T cell leukemia virus (HTLV-1) and the human immunodeficiency virus (HIV-1).
Advances in lecture recognition: the ISL RT-06s evaluation system (2006)

This paper describes the 2006 lecture recognition system developed at the Interactive Systems Laboratories (ISL), for individual head-microphone (IHM), single distant microphone (SDM), and multiple distant microphones (MDM) conditions.It was evaluated in RT-06S rich transcription meeting evaluation sponsored by the US National Institute of Standards and Technologies (NIST).We describe the principal differences between our current system and those submitted in previous years, namely, improved acoustic and language models, cross adaptation between systems with different front-ends and phoneme sets, and the use of various automatic speech segmentation algorithms.Our system achieved word error rates of 38.5% (53.4%) and 22.9% (32.2%), respectively, on the MDM and IHM conditions of the RT-05S (RT-06S) lecture evaluation set.
TBCRC 001: Randomized Phase II Study of Cetuximab in Combination With Carboplatin in Stage IV Triple-Negative Breast Cancer (2012)

Despite strong preclinical data, combination cetuximab plus carboplatin in metastatic TNBC produced responses in fewer than 20% of patients. EGFR pathway analysis showed that most TNBCs involved activation. However, cetuximab blocked expression of the EGFR pathway in only a minority, suggesting that most had alternate mechanisms for pathway activation.
ras gene Amplification and malignant transformation. (1985)

Morphologic transformation of NIH 3T3 mouse cells occurs upon transfection of these cells with large amounts (greater than or equal to 10 micrograms) of recombinant DNA molecules carrying the normal human H-ras-1 proto-oncogene. We provide experimental evidence indicating that transformation of these NIH 3T3 cells results from the combined effect of multiple copies of the H-ras-1 proto-oncogene rather than from spontaneous mutation of one of the transfected H-ras-1 clones (E. Santos, E.P. Reddy, S. Pulciani, R.J. Feldman, and M. Barbacid, Proc. Natl. Acad. Sci. USA 80:4679-4683, 1983). Levels of H-ras-1 RNA and p21 expression are highly elevated in the NIH 3T3 transformants, and in those cases examined, these levels correlate with the malignant properties of these cells. We have also investigated the presence of amplified ras genes in a variety of human carcinomas. In 75 tumor biopsies, we found amplification of the human K-ras-2 locus in one carcinoma of the lung. These results indicate that ras gene amplification is an alternative pathway by which ras genes may participate in the development of human neoplasia.
Aberrant expression of sialidase and cancer progression (2008)

Aberrant sialylation is closely associated with the malignant phenotype of cancer cells including metastatic potential and invasiveness. However, its biological significance and molecular mechanisms have yet to be fully elucidated. To determine causes and consequences, we have focused attention on mammalian sialidases, which cleave sialic acids from gangliosides and glycoproteins. The four types of human sialidases identified to date behave in different manners during carcinogenesis. One, found in the lysosomes, shows down-regulation in cancers, promoting anchorage-independent growth and contributing to metastatic ability, while another, found in the plasma membranes, exhibits marked up-regulation, resulting in suppression of apoptosis. The present review summarizes mostly our results on aberrant expression of sialidases and their possible roles in cancer progression.
New Compounds. Some Mono- and Disubstituted Guanidines (1942)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNew Compounds. Some Mono- and Disubstituted GuanidinesRichard Baltzly and Clayton FerryCite this: J. Am. Chem. Soc. 1942, 64, 9, 2231–2232Publication Date (Print):September 1, 1942Publication History Published online13 November 2002Published inissue 1 September 1942https://pubs.acs.org/doi/10.1021/ja01261a602https://doi.org/10.1021/ja01261a602research-articleACS PublicationsRequest reuse permissionsArticle Views88Altmetric-Citations4LEARN 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
Formation and Stability of Complex Membrane−Mimetic Monolayers on Solid Supports (1999)

Membrane−mimetic phospholipid films with or without cholesterol and varying concentrations of one or more synthetic lipopeptide conjugates were formed on an alkylsilane self-assembled monolayer on glass by a process of lipid vesicle fusion. Using a combination of radiochemical titration with 125I-labeled lipopeptides and atomic force microscopy imaging in an aqueous environment, we have characterized the kinetics of multicomponent monolayer formation and film stability as a function of temperature, lipid alkyl chain length, cholesterol content, and the concentration of solution phase bovine serum albumin. These data confirm that multicomponent membrane−mimetic monolayers can be produced in a predictable fashion by vesicle fusion to an alkylated glass substrate. The stability of these systems, however, is compromised when operating above the phase transition temperature of the lipid component, as well as in the presence of albumin.
Controlled outgrowth of dissociated neurons on patterned substrates (1988)

The cytoarchitecture of nervous tissue is lost during the dissociation procedures used to form primary cell cultures. As a first step toward reestablishing an ordered arrangement of these cells in vitro, we developed a set of procedures for patterning the outgrowth of cells cultured on 2-dimensional substrates. These procedures used a combination of surface chemistry and photolithographic techniques. The adhesive properties of either silicon or silicon dioxide (quartz) surfaces were controlled by covalently binding small organic molecules to the surface with silane coupling agents. The attachment and growth of either embryonic mouse spinal cells or perinatal rat cerebellar cells were found to be promoted by binding certain amine derivatives to the surface. In particular, cells grown on surfaces bound with diamines and triamines, but not with monoamines, formed cultures whose morphology was similar to that of cells cultured on conventional substrates, i.e., glass coated with poly(D-lysine). The attachment of cells to a substrate was inhibited by binding alkane chains (e.g., n-tetradecane) to the surface and plating the cells in media containing 5-10% (vol/vol) serum. Patterns of selected adhesivity were formed using photochemical resist materials and lithographic masking techniques compatible with the silane chemistry. Cultures of either spinal cord cells or cerebellar cells could be confined to square regions on the scale of 50 micron. Cerebellar cells could be confined to grow on lines with widths less than 10 micron. This width is comparable to the diameter of granule cell somata. The patterned growth of cerebellar cells was maintained up to 12 d in vitro. Over this time period the granule cells were observed to develop electrical excitability and immunoreactivity for neuron-specific enolase. Purkinje neurons also developed electrical excitability when grown on the chemically modified surfaces. Immunochemical reactivity of the patterned cultures for glial fibrillary acid protein (GFAP) showed that glia are patterned along with the associated granule cells. Interestingly, the GFAP-positive glia that proliferated on surfaces bound with amine derivatives attained primarily a tile-shaped, fibroblast-like morphology, while those proliferating on glass coated with poly(D-lysine) developed primarily a spindle-shaped, process-bearing morphology. Granule cells preferentially associated with the spindle-shaped glia.
Ultimate Computing: Biomolecular Consciousness and NanoTechnology (1987)

Toward Ultimate Computing. Brain/Mind/Computer. Origin and Evolution of Life. From Brain to Cytoskeleton. Cytoskeleton/Cytocomputer. Protein Conformational Dynamics. Anesthesia: Another Side of Consciousness. Models of Cytoskeletal Computing. Viruses/Ambiguous Life Forms. NanoTechnology. The Future of Consciousness. Bibliography. Appendices. Index.
Methylation of Discrete Regions of the O 6 -Methylguanine DNA Methyltransferase (MGMT) CpG Island Is Associated with Heterochromatinization of the MGMT Transcription Start Site and Silencing of the Gene (1997)

O6-Methylguanine DNA methyltransferase (MGMT) repairs the mutagenic and cytotoxic O6-alkylguanine lesions produced by environmental carcinogens and the chemotherapeutic nitrosoureas. As such, MGMT-mediated repair of O6-alkylguanine lesions constitutes a major form of resistance to nitrosourea chemotherapy and makes control of MGMT expression of clinical interest. The variability of expression in cell lines and tissues, along with the ease with which the MGMT phenotype reverts under various conditions, suggests that MGMT is under epigenetic control. One such epigenetic mechanism, 5-methylation of cytosines, has been linked to MGMT expression. We have used an isogenic human multiple myeloma tumor cell line model composed of an MGMT-positive parent cell line, RPMI 8226/S, and its MGMT-negative variant, termed 8226/V, to study the control of MGMT expression. The loss of MGMT activity in 8226/V was found to be due to the loss of detectable MGMT gene expression. Bisulfite sequencing of the MGMT CpG island promoter revealed large increases in the levels of CpG methylation within discrete regions of the 8226/V MGMT CpG island compared to those in 8226/S. These changes in CpG methylation are associated with local heterochromatinization of the 8226/V MGMT transcription start site and provide a likely mechanism for the loss of MGMT transcription in 8226/V.
LSU Expands Distance Learning Program through Online Learning Solution. (Applications) (2002)

Louisiana State University (LSU) and its Ourso College of Business, like many leading universities, had the challenge of providing the highest quality of education to as many students as possible with limited physical space and resources. The implementation of an online learning program is alleviating the need for more classrooms by providing instructors, like myself, with the means to publish lecture material online, as well as giving students an alternative for accessing the information from a lab or residence instead of physically coming to a lecture hall. Students had been accessing online resources through two campuswide learning management systems -- CourseInfo by Blackboard and SemesterBook, developed by LSU's division of computing services -- which provided a navigational framework for content and communication with instructors. I was eager to add streaming audio and video to make online offerings more engaging than sitting in a lecture hall, but the experts at LSU told me my desires were problematic and unachievable due to technical problems. Realizing I had no multimedia production experience, limited Internet bandwidth connections and minimal university support staff, there appeared to be no way to employ streaming video to my PowerPoint slides. Integrating Streaming Media In spring 2000, Tegrity Inc. was invited to demonstrate their WebLearner platform to the technical systems administrators at LSU. The technical problem was trying to integrate streaming video with the PowerPoint slides so students could see a lecture that referred directly to slides on their computer, with the added challenge that most of the students have 28.8K modems. The Tegrity platform solved this problem in two ways. First, it dramatically reduced the time and effort required to record audio and video in sync with the classroom PowerPoint presentations. Second, it delivered high-quality, indexed modules at connection speeds as low as 28.8K, which is essential for practical, inexpensive viewing by all students. Frankly, the demonstration impressed me because I could use the portable WebLearner Studio by simply rolling it into any free classroom with a standard whiteboard and record my lecture using my PowerPoint slides. And since I had already used the standard Microsoft PowerPoint, the learning curve was minimal. Tegrity software is integrated into Microsoft Office and uses Windows Media as its audio/video delivery format. LSU was impressed enough to buy the WebLearner system. Immediately after the system arrived, I placed all of my lectures on CourseInfo using streaming video for my courses. To do so, I produced more than 100 online modules in less than half a semester without any production assistance or technical support from the university, except for their assistance in placing the files on a special server. My recording studio became any available classroom with a whiteboard, PowerPoint and the Tegrity mobile WebLearner Studio I brought in. …
Potent cytotoxicity of the phosphatase inhibitor microcystin LR and microcystin analogues in OATP1B1- and OATP1B3-expressing HeLa cells (2007)

Microcystins are a family of cyclic peptides that are potent inhibitors of the protein phosphatase families PP1 and PP2A. Only three human proteins are thought to be able to mediate the hepatic uptake of microcystins (the organic anion-transporting polypeptides OATP1B1, OATP1B3, and OATP1A2), and the predominant hepatic expression of these transporters accounts for the liver-specific toxicity of microcystins. A significant obstacle in the study of microcystins as anticancer drugs is the requirement of specific transport proteins for cellular uptake. We report that OATP1B3 mRNA is up-regulated in non-small cell lung cancer tumors in comparison with normal control tissues. This finding led to the exploration of microcystins as potential anticancer agents. We have developed a HeLa cell model with functional OATP1B1 and OATP1B3 activity. Transiently transfected HeLa cells are over 1,000-fold more sensitive to microcystin LR than the vector-transfected control cells, showing that transporter expression imparts marked selectivity for microcystin cytotoxicity. In addition, microcystin analogues showed variable cytotoxicities in the OATP1B1- and OATP1B3-transfected cells, including two analogues with IC(50) values <1 nmol/L. Cytotoxicity of microcystin analogues seems to correlate to the inhibition of PP2A in these cells and induces rapid cell death as seen by chromatin condensation and cell fragmentation. These studies show that microcystin-induced phosphatase inhibition results in potent cytotoxicity when microcystin compounds can gain intracellular access and are a potent novel class of therapeutic agents for tumors expressing these uptake proteins.
Combination therapy with T cell engager and PD-L1 blockade enhances the antitumor potency of T cells as predicted by a QSP model (2020)

Individual biomarkers for TCE monotherapy, anti-PD-L1 monotherapy and their combination have been determined based on the QSP model. Best treatment options for specific patients could be suggested based on their own characteristics to improve clinical trial efficiency. The model can be further used to assess plausible combination strategies for different TCEs and immune checkpoint inhibitors in different types of cancer.