gebhart/patrepeval huggingface dataset:
BORIS Binding to the Promoters of Cancer Testis Antigens, <i>MAGEA2</i>, <i>MAGEA3</i>, and <i>MAGEA4</i>, Is Associated with Their Transcriptional Activation in Lung Cancer (2011)

These data suggest that BORIS positively regulates these CTAs by binding and inducing a shift to a more open chromatin conformation with promoter demethylation for MAGEA3 or independent of promoter demethylation in case of MAGEA2 and MAGEA4 and may be a key effector involved in their derepression in lung cancer.
At the Nexus of Food Security and Safety: Opportunities for Nanoscience and Nanotechnology (2016)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTAt the Nexus of Food Security and Safety: Opportunities for Nanoscience and NanotechnologyCherie R. KaganCite this: ACS Nano 2016, 10, 3, 2985–2986Publication Date (Web):March 22, 2016Publication History Published online22 March 2016Published inissue 22 March 2016https://pubs.acs.org/doi/10.1021/acsnano.6b01483https://doi.org/10.1021/acsnano.6b01483editorialACS PublicationsCopyright © 2016 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views3981Altmetric-Citations45LEARN 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 PDF (143 KB) Get e-AlertscloseSUBJECTS:Food,Immunology,Nanoscale,Safety,Sensors Get e-Alerts
On the feasibility and utility of exploiting real time database search to improve adaptive peak selection (2012)

Rationale: In a shotgun proteomics experiment with data-dependent acquisition, real-time analysis of a precursor scan results in selection of a handful of peaks for subsequent isolation, fragmentation and secondary scanning. This peak selection protocol typically focuses on the most abundant peaks in the precursor scan, while attempting to avoid re-sampling the same m/z values in rapid succession. The protocol does not, however, incorporate analysis of previous fragmentation scans into the peak selection procedure. Methods: In this work, we investigate the feasibility and utility of incorporating analysis of previous fragmentation scans into the peak selection protocol. We demonstrate that real-time identification of fragmentation spectra is feasible in principle, and we investigate, via simulations, several strategies to make use of the resulting peptide identifications during peak selection. Results: Our simulations fail to provide evidence that peptide identifications can provide a large improvement in the total number of peptides identified by a shotgun proteomics experiment. Conclusions: These results are significant because they point out the feasibility of using peptide identifications during peak selection, and because our experiments may provide a starting point for others working in this direction.
A new validation methodology combining test and formal verification for PowerPC/sup TM/ microprocessor arrays (2002)

Test and validation of embedded array blocks remain as a major challenge in today's processor design environment. The difficulty comes from two folds. First, the sizes of the arrays are too large to be handled by the most sophisticated sequential ATPG tools. On the other hand, the complex timing and control make it hard to model these arrays as well-defined transparent blocks which combinational ATPG tools can understand. This paper describes a novel methodology for test and validation of complex array blocks in PowerPC RISC microprocessors. Unlike traditional ATPG methods, our methodology uses formal techniques to functionally verify the arrays and then derive tests from the verification results. The superiority of these tests over the traditional ATPG tests will be discussed and shown at the transistor level through experiments on various recent PowerPC array designs.
Improved Growth of Human Urothelial Carcinoma Cell Cultures (1986)

From January, 1981 through June, 1982 specimens from 21 patients with bladder (urothelial) cancer were placed in tissue culture, and one long term cell line was established (5%). From July, 1982 through February, 1984, using an improved culture medium, seven long term cell cultures were established from 21 patients (33%). In addition, one long term culture from a patient with a bladder melanoma was established using the standard culture medium. The nine cell cultures were derived from the following types of tumors: transitional cell carcinoma (6), adenocarcinoma (1), squamous cell carcinoma (1) and melanoma (1). All of the cell lines have produced tumors in athymic nude mice except for one transitional cell carcinoma. All of the cultures demonstrate aneuploidy. Homogeneously staining regions have been seen in some cell cultures. A common marker chromosome has not been identified.
Revisiting the role of COX-2 inhibitor for non-small cell lung cancer. (2015)

Accumulating preclinical and clinical studies have shown that cyclooxygenase-2 (COX-2) inhibitor has some efficacy for non-small cell lung cancer (NSCLC). However, two phase III clinical trials using COX-2 inhibitor in combination with platinum-based chemotherapy showed no survival benefit for "unselected" patients with advanced NSCLC. Thus, exploratory analyses of the association between biomarker and clinical outcome of NSCLC patients treated with COX-2 inhibitors have been warranted. A report by Edelman recently published in the Journal of Clinical Oncology demonstrated the results of a prospective randomized trial using a combination of chemotherapy (docetaxel or pemetrexed) and either COX-2 inhibitor or a placebo for patients with advanced NSCLC. The remarkable point of this study was that it adopted the eligible criteria requiring decreased urinary levels of prostaglandin E metabolite (PGE-M) after administration of COX-2 inhibitor in a run-in period, as a possible predictive marker for the COX-2 inhibitor. The primary endpoint was progression-free survival (PFS). However, no improvement in PFS was observed between the patients treated with COX-2 inhibitor and those with placebo. A number of efforts from various investigators, including this report, have failed to demonstrate the meaningful clinical effect of COX-2 inhibitor for NSCLC. Is COX-2 inhibitor useless anymore? Here, we address the "difficult" character of this COX-2 inhibitor from various viewpoints and discuss potential future strategy using this drug.
Clavibacter: a New Genus Containing Some Phytopathogenic Coryneform Bacteria, Including Clavibacter xyli subsp. xyli sp. nov., subsp. nov. and Clavibacter xyli subsp. cynodontis subsp. nov., Pathogens That Cause Ratoon Stunting Disease of Sugarcane and Bermudagrass Stunting Disease (1984)

A total of 23 strains of coryneform bacteria that cause ratoon stunting disease of sugarcane and Bermudagrass stunting disease were examined. These included 17 sugarcane strains from Florida, Louisiana, South Africa, Brazil, and Japan and six Bermudagrass strains from Florida and Taiwan. The sugarcane and Bermudagrass strains contained 2,4-diaminobutyric acid, rhamnose, and fucose in their cell walls, suggesting a relationship to some other phytopathogenic coryneform bacteria and related organisms with similar cell wall compositions. The cellular protein patterns of the sugarcane and Bermudagrass strains after polyacrylamide gel electrophoresis resembled the patterns of Corynebacterium michiganense subspecies more than the patterns of some other diaminobutyric acid-containing taxa. The protein patterns of the sugarcane strains were distinct from the patterns of the Bermudagrass strains examined. The guanine-plus-cytosine contents of the deoxyribonucleic acids of two sugarcane strains and one Bermudagrass strain were 66 mol%. The sugarcane and Bermudagrass strains formed a homogeneous group based on morphological characteristics and most biochemical characteristics. All of the sugarcane strains were nonpigmented (white) and grew more slowly in culture than the yellow-pigmented Bermudagrass strains. The Bermudagrass strains, unlike the sugarcane strains, hydrolyzed starch and utilized citrate and malate. Although the phytopathogenic coryneform bacteria with 2,4-diaminobutyric acid in the peptidoglycans of their cell walls are presently classified in the genus Corynebacterium, recent studies have indicated that these phytopathogens should be reclassified. These bacteria form a distinct group with characteristics different from those of all existing genera as presently circumscribed; therefore, we propose that a new genus, Clavibacter, be established for these and similar bacteria. We propose reclassification of Corynebacterium michiganense (including Corynebacterium michiganense subsp. michiganense, Corynebacterium michiganense subsp. insidiosum, Corynebacterium michiganense subsp. sepedonicum, Corynebacterium michiganense subsp. nebraskense, and Corynebacterium michiganense subsp. tessellarius), Corynebacterium iranicum, Corynebacterium tritici, and Corynebacterium rathayi in the new genus Clavibacter. We further propose that Clavibacter xyli be recognized as a new species with the following subspecies: Clavibacter xyli subsp. xyli sp. nov., subsp. nov., the species and subspecies type strain of which is sugarcane strain L1A (= ATCC 33974 = NCPPB 3152 = PDDC 7127), and Clavibacter xyli subsp. cynodontis subsp. nov., the subspecies type strain of which is Bermudagrass strain TB1A (= ATCC 33973).
A haptic digital tool to assist the design, planning and manufacture of micro- and nanostructures (2014)

This work addresses the engineering demands for precise interactive process planning for the manufacture of high precision in the manufacturing of 3D micro- and nanoproducts. It outlines the development of a digital tool based on a haptics-based human–machine interface. This interface is underpinned using an empirical model derived from a series of experimental results obtained from a focused ion beam machine through a series of experiments, which produced the surface topographies of a number of micro- and nanograting arrays; these were systemically analysed to provide an underpinning empirical database, which could be accessed via the haptic process planning system. On accessing these data, highly accurate geometrical models are then input into a haptics human machine interface to emulate the focused ion beam machining process as defined by the customised fabrication parameters. The haptic planning system predicts and simulates the shape and form of the finished product profiles as the haptic device is passed across a virtual substrate. Once the simulation is complete and the outputs verified by the user, the system then automatically outputs a stream file to drive the focused ion beam process to produce the surface topographies required. The simulation results reveal that compared with trial and error method, the haptics-based simulation method is a reliable way to plan and optimise the fabrication parameters in design and manufacture of micro- and nanogratings by focused ion beam machining cost-effectively. This could potentially provide substantial lead time and cost reductions associated with these currently inherently expensive unit cost products as well as demonstrate a novel tool not only for the planning of nanomachining cutting sequences but also for the interactive design of such products. This work also highlights the benefits of an empirical model as a means of underpinning and supporting real-time haptics interaction, something not possible using more numerical-based techniques.
Effect of acrylonitrile content of styrene‐<i>co</i>‐acrylonitrile (SAN) on morphology and electrooptical properties of polymer/liquid crystal composite films (1993)

Abstract Effects of copolymer composition on morphology and electrooptical properties of polymer/liquid crystal (LC) (40/60 w/w) composite films were studied with styrene‐ co ‐acrylonitrile (SAN) of varying acrylonitrile (AN) content (6.3–35 wt %) and a cyanobiphenyl‐type liquid crystal (E8). The dimension of the LC domain in the composite film decreased with increase of AN content of SAN up to 30 and increased at 35 wt %. The contact angle of the film with an LC drop showed a similar trend; however, its minimum was obtained at 24% AN. Threshold voltage ( V th ) and rise time (τ R ) increased, and decay time (τ D ) decreased with AN content up to 30%, and the tendency is reversed at 35%. The results were interpreted in terms of, possibly, a solubility parameter matching between SAN and LC. © 1993 John Wiley & Sons, Inc.
Tolerogenic dendritic cells and negative vaccination in transplantation: from rodents to clinical trials (2012)

The use of immunosuppressive (IS) drugs to treat transplant recipients has markedly reduced the incidence of acute rejection and early graft loss. However, such treatments have numerous adverse side effects and fail to prevent chronic allograft dysfunction. In this context, therapies based on the adoptive transfer of regulatory cells are promising strategies to induce indefinite transplant survival. The use of tolerogenic dendritic cells (DC) has shown great potential, as preliminary experiments in rodents have demonstrated that administration of tolerogenic DC prolongs graft survival. Recipient DC, Donor DC, or Donor Ag-pulsed recipient DC have been used in preclinical studies and administration of these cells with suboptimal immunosuppression increases their tolerogenic potential. We have demonstrated that autologous unpulsed tolerogenic DC injected in the presence of suboptimal immunosuppression are able to induce Ag-specific allograft tolerance. We derived similar tolerogenic DC in different animal models (mice and non-human primates) and confirmed their protective abilities in vitro and in vivo. The mechanisms involved in the tolerance induced by autologous tolerogenic DC were also investigated. With the aim of using autologous DC in kidney transplant patients, we have developed and characterized tolerogenic monocyte-derived DC in humans. In this review, we will discuss the preclinical studies and describe our recent results from the generation and characterization of tolerogenic monocyte-derived DC in humans for a clinical application. We will also discuss the limits and difficulties in translating preclinical experiments to theclinic.
Nanoemulsions: A Review on the Conceptualization of Treatment for Psoriasis Using a ‘Green’ Surfactant with Low-Energy Emulsification Method (2021)

Psoriasis is a skin disease that is not lethal and does not spread through bodily contact. However, this seemingly harmless condition can lead to a loss of confidence and social stigmatization due to a persons' flawed appearance. The conventional methods of psoriasis treatment include taking in systemic drugs to inhibit immunoresponses within the body or applying topical drugs onto the surface of the skin to inhibit cell proliferation. Topical methods are favored as they pose lesser side effects compared to the systemic methods. However, the side effects from systemic drugs and low bioavailability of topical drugs are the limitations to the treatment. The use of nanotechnology in this field has enhanced drug loading capacity and reduced dosage size. In this review, biosurfactants were introduced as a 'greener' alternative to their synthetic counterparts. Glycolipid biosurfactants are specifically suited for anti-psoriatic application due to their characteristic skin-enhancing qualities. The selection of a suitable oil phase can also contribute to the anti-psoriatic effect as some oils have skin-healing properties. The review covers the pathogenic pathway of psoriasis, conventional treatments, and prospective ingredients to be used as components in the nanoemulsion formulation. Furthermore, an insight into the state-of-the-art methods used in formulating nanoemulsions and their progression to low-energy methods are also elaborated in detail.
Substrate-like inhibition of the transgalactosylation reaction catalyzed by β-galactosidase from<i>Aspergillus oryzae</i> (2013)

The influence of key parameters in the kinetics of the transglycosylation system catalyzed by Aspergillus oryzae β-galactosidase when applied to the synthesis of galactosyl-ethylene glycol and galactosyl-glycerol has been studied. It was found that both acceptors were inhibitors of the enzyme, causing a decrease of 9 and 68 fold in enzyme catalytic efficiency in the presence of 4.0 M ethylene glycol and glycerol, respectively. The effect was characterized as “substrate-like inhibition”, suggesting the formation of a nonproductive enzyme-acceptor complex. Inhibition constants for both acceptors were determined as 618 mM for ethylene glycol and 244 mM for glycerol.
Highlights I. Global Environmental Governance, II. Climate Change and International Burden Sharing, III. Food Supplies and Global Warming (1991)

I. While our knowledge of environmental problems has grown immensely in the last few decades our ability to take rational and effective decisions and implement them has not kept pace with our accumulated information. II. A major contribution to the discussions concerning the carbon dioxide problem and its effects on our environment. III. The possible impact of climate warming is starvation and malnutrition in many parts of the world.
Helicobacter pylori cytotoxin: importance of native conformation for induction of neutralizing antibodies (1995)

We have attempted to express the Helicobacter pylori vacuolating cytotoxin in Escherichia coli. Although the 95-kDa VacA polypeptide was expressed abundantly, it completely lacked any biological activity. In addition, this material failed to induce neutralizing antibodies after immunization of rabbits. In contrast, highly purified high-molecular-mass cytotoxin from the supernatant of H. pylori cultures was active in a HeLa cell assay and effectively induced a neutralizing response in rabbits. Neutralizing sera were shown to contain a high proportion of antibodies which recognized conformational epitopes found only on the native toxin. The data indicate that toxin-neutralizing epitopes are conformational and that potential vaccines based on the cytotoxin may benefit from the use of the intact molecule.
Flavonoids in Inflammatory Bowel Disease: A Review (2016)

Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the intestine that compromises the patients' life quality and requires sustained pharmacological and surgical treatments. Since their etiology is not completely understood, non-fully-efficient drugs have been developed and those that have shown effectiveness are not devoid of quite important adverse effects that impair their long-term use. In this regard, a growing body of evidence confirms the health benefits of flavonoids. Flavonoids are compounds with low molecular weight that are widely distributed throughout the vegetable kingdom, including in edible plants. They may be of great utility in conditions of acute or chronic intestinal inflammation through different mechanisms including protection against oxidative stress, and preservation of epithelial barrier function and immunomodulatory properties in the gut. In this review we have revised the main flavonoid classes that have been assessed in different experimental models of colitis as well as the proposed mechanisms that support their beneficial effects.
Sampling-Based Motion Planning (2006)

There are two main philosophies for addressing the motion planning problem, in Formulation 4.1 from Section 4.3.1. This chapter presents one of the philosophies, sampling-based motion planning, which is outlined in Figure 5.1. The main idea is to avoid the explicit construction of Cobs as described in Section 4.3, and instead conduct a search that probes the C-space with a sampling scheme. This probingis enabled by a collision detection module, which the motion planning algorithm considers as a “black box.” This enables the development of planning algorithms that are independent of the particular geometric models. The collision detection module handles concerns such as whether the models are semi-algebraic sets, 3D triangles, nonconvex polyhedra, and so on. This general philosophy has been very successful in recent years for solving problems from robotics, manufacturing, and biological applications that involve thousands and even millions of geometric primitives. Such problems would be practically impossible to solve using techniques that explicitly represent Cobs.
A comparison of seed-and-extend techniques in modern DNA read alignment algorithms (2016)

DNA read alignment is a major step in genome analysis. However, as DNA reads continue to become longer, new approaches need to be developed to effectively use these longer reads in the alignment process. Modern aligners commonly use a two-step approach for read alignment: 1. seeding, 2. extension. In this paper, we have investigated various seeding and extension techniques used in modern DNA read alignment algorithms to find the best seeding and extension combinations. We developed an open source generic DNA read aligner that can be used to compare the alignment accuracy and total execution time of different combinations of seeding and extension algorithms. For extension, our results show that local alignment is the best extension approach, achieving up to 3.6× more accuracy than other extension techniques, for longer reads. For seeding, if BLAST-like seed extension is used, the best seeding approach is identifying all SMEMs in the DNA read (e.g., approach used by BWA-MEM). This combination is up to 6× more accurate than other seeding techniques, for longer reads. With local alignment, we observed that the seeding technique does not impact the alignment accuracy. Furthermore, we showed that an optimized implementation of local alignment using vector instructions, enabling 4.5× speedup, makes it the fastest of all extension techniques. Overall, we show that using local alignment with non-overlapping maximal exact matching seeds is the best seeding-extension combination due to its high accuracy and higher potential for optimization/acceleration for future DNA reads.