gebhart/patrepeval huggingface dataset:
Circulating free DNA in the era of precision oncology: Pre‐ and post‐analytical concerns (2016)

Cancer treatment has entered the era of precision medicine, where knowledge of a patient's genetic profile is used to facilitate early diagnosis, drug selection, prognosis, prediction of drug responsiveness, the onset of secondary resistance, and relapse. Circulating free DNA (cfDNA) has emerged as an ideal source of genetic information for cancer patients, and numerous studies have explored its validity in various clinical applications. However, clinical implementation of cfDNA-based tests has been slow. In this review, we addressed some of the pre- and post-analytical issues regarding cfDNA tests. First, we summarized the characteristics of cfDNA and reviewed the methods used to identify tumor-derived cfDNA from the pool of total cfDNA. Second, we described the procedures used to extract cfDNA, which have a great impact on representativeness and yield. Finally, we discussed our thoughts on the validation of cfDNA-based tests and the reporting of test results amid drastic limitations.
Increased copy number at 20q13 in breast cancer: defining the critical region and exclusion of candidate genes. (1994)

Studies by comparative genomic hybridization have indicated that a major new locus for DNA amplification in breast cancer is 20q13 and suggested that this genetic event is associated with aggressive clinical behavior. We used interphase fluorescence in situ hybridization with anonymous cosmid probes and gene-specific P1 clones to determine the minimal common region of increased copy number and to study involvement of known genes at 20q13. Based on high-level copy number increases (3 to 10-fold) found with one or more probes in 5 of 14 (35%) breast cancer cell lines and in 3 of 36 (8%) primary tumors, the critical region was narrowed to approximately 1.5 megabases at 20q13.2 defined by fractional length pter values 0.81-0.84. Previously known genes were excluded as candidates, implying that this chromosomal region harbors a novel oncogene that contributes to the malignant progression of breast cancer.
Angiogenesis and melanoma - from basic science to clinical trials. (2011)

The effective management of malignant melanoma has remained centred around the surgeon. The arrival of anti-angiogenic agents as the 'fourth' cancer treatment joining the ranks of surgery, chemotherapy and radiotherapy has been a source of renewed hope. This article provides an up-to-date review of the focus, state and rationale of clinical trials of anti-angiogenic therapies in metastatic malignant melanoma. Vascular Endothelial Growth Factor (VEGF) is by no means the only target, although perhaps the most extensively studied following the successful introduction of the anti-VEGF Antibody bevacizumab. This has been combined with other established therapies to try and improve outcomes in metastatic disease, and is being trialled in the UK to prevent metastasis in high-risk patients. We describe the encouraging preclinical work that lead to great enthusiasm for these agents, assess the key trials and their outcomes, discuss why these therapies have not revolutionised melanoma care and explore how they might be better targeted in the future.
Oxidative stress and cognitive impairment in the elderly. (2002)

Cognitive impairment is a major component of age-related dementing diseases and it has been suggested that it could share the same pathological pathways with neurodegenerative processes and cerebrovascular lesions. The free radical theory of aging could be one of these pathways. Observational studies of relationships between cognitive impairment and antioxidant status are based on the evaluation of dietary intake or on the levels of carotenoids, selenium and vitamins A, C and E in plasma. More convincing results were obtained on vitamin C and carotenoids. Despite some limitations, the comparison between results obtained in various populations is becoming increasingly informative and these studies argue for a protective effect of antioxidants on cognitive performance.
Auto‐Tandem Catalysis with Frustrated Lewis Pairs for Reductive Etherification of Aldehydes and Ketones (2017)

Herein we report that a single frustrated Lewis pair (FLP) catalyst can promote the reductive etherification of aldehydes and ketones. The reaction does not require an exogenous acid catalyst, but the combined action of FLP on H<sub>2</sub> , R-OH or H<sub>2</sub> O generates the required Brønsted acid in a reversible, "turn on" manner. The method is not only a complementary metal-free reductive etherification, but also a niche procedure for ethers that would be either synthetically inconvenient or even intractable to access by alternative synthetic protocols.
Gremlin-1 Induces BMP-Independent Tumor Cell Proliferation, Migration, and Invasion (2012)

Gremlin-1, a bone morphogenetic protein (BMP) antagonist, is overexpressed in various cancerous tissues but its role in carcinogenesis has not been established. Here, we report that gremlin-1 binds various cancer cell lines and this interaction is inhibited by our newly developed gremlin-1 antibody, GRE1. Gremlin-1 binding to cancer cells was unaffected by the presence of BMP-2, BMP-4, and BMP-7. In addition, the binding was independent of vascular endothelial growth factor receptor-2 (VEGFR2) expression on the cell surface. Addition of gremlin-1 to A549 cells induced a fibroblast-like morphology and decreased E-cadherin expression. In a scratch wound healing assay, A549 cells incubated with gremlin-1 or transfected with gremlin-1 showed increased migration, which was inhibited in the presence of the GRE1 antibody. Gremlin-1 transfected A549 cells also exhibited increased invasiveness as well as an increased growth rate. These effects were also inhibited by the addition of the GRE1 antibody. In conclusion, this study demonstrates that gremlin-1 directly interacts with cancer cells in a BMP- and VEGFR2-independent manner and can induce cell migration, invasion, and proliferation.
Truncation of the μ heavy chain alters BCR signalling and allows recruitment of CD5+ B cells (2001)

Ig are multifunctional molecules with distinct properties assigned to individual domains. To assess the importance of IgM domain assembly in B cell development we generated two transgenic mouse lines with truncated muH chains by homologous integration of the neomycin resistance gene (neo(r)) into exons C(mu)1 and C(mu)2. Upon DNA rearrangement shortened muH chain transcripts, V(H)-D-J(H)-C(mu)3-C(mu)4, are produced independent of the transcriptional orientation and termination signals provided by neo(r). The truncated muH chain of approximately 52 kDa associates non-covalently with the L chain to form a monovalent HL heterodimer. Surface IgM is assembled into a defective BCR complex which has lost important signalling capacity. In immunizations with T-dependent and T-independent antigens, specific IgM antibodies cannot be detected, whilst IgG responses remain normal. B cell development in the bone marrow is characterized by an increase in early B cells, but a decrease of B220(+) cells from the stage when muH chain rearrangement is completed. The peritoneal lymphocyte population has elevated levels of CD5(+) B cells and their expansion may be the result of a negative feedback mechanism. The results show that antigenic stimulation is compromised by truncated monovalent IgM and that this deficit in stimulation leads to reduced levels of conventional B-2 lymphocytes, but dramatically increased levels of B-1 cells.
Respiratory disease and wasting in athymic mice infected with pneumonia virus of mice. (1988)

Although pneumonia virus of mice (PVM) is ubiquitous among rodent colonies in the United States, it has not been reported to cause clinically apparent disease in euthymic mice. However, PVM has been reported to cause respiratory disease and death in experimentally infected euthymic and athymic mice. A group of nu/nu mice, housed in quarantine in a Trexler-type isolator, had weight loss and dyspnea. Gross necropsy findings included cachexia and diffuse pulmonary edema or lobar consolidation. Histologically there was diffuse interstitial pneumonia. Electron microscopy revealed filamentous virions budding from plasma membranes, and immunohistochemical staining of lung tissue was positive for PVM antigen. PVM was isolated from affected lung tissue in BHK 21 cells and mouse antibody production tests resulted in seroconversion to PVM. Experimental inoculation of athymic mice with lung homogenate from spontaneously infected mice resulted in clinically apparent respiratory disease and histologic lung changes similar to those in naturally infected mice. Inoculation of athymic mice with infected BHK 21 cell culture fluid resulted in pneumonia which was qualitatively similar to, but less severe than, that observed in mice with spontaneous disease. These findings indicate that naturally occurring PVM infection in athymic mice may cause respiratory disease and wasting.
Inhibition of Immune Complex‐Induced Inflammation by A small Molecular Weight Selectin Antagonist (1994)

The anti-inflammatory effect of a small molecular weight antagonist of P- and E-selectin-dependent cell adhesion was examined. The glycolipid sulphatide was shown to block the adherence of thrombin-activated rat platelets to HL-60 cells. This interaction is known to be dependent on P-selectin. The rat dermal reverse passive Arthus reaction was used to assess the effect of sulphatide on a neutrophil dependent inflammatory response. Sulphatide dosedependently blocked both the vascular permeability increase and cell infiltration after intraperitoneal administration. These results show that a small molecular weight compound which blocks P- and E-selectin dependent adhesion in vitro can effectively block the inflammation due to immune complex deposition. A compound with this type of profile may have therapeutic potential in the treatment of immune complex mediated diseases.
Fat-Soluble Vitamins: Clinical Indications and Current Challenges for Chromatographic Measurement. (2016)

Fat-soluble vitamins, including vitamins A, D and E, are required for a wide variety of physiological functions. Over the past two decades, deficiencies of these vitamins have been associated with increased risk of cancer, type II diabetes mellitus and a number of immune system disorders. In addition, there is increasing evidence of interactions between these vitamins, especially between vitamins A and D. As a result of this enhanced clinical association with disease, translational clinical research and laboratory requests for vitamin measurements have significantly increased. These laboratory requests include measurement of 25-OHD (vitamin D), retinol (vitamin A) and α-tocopherol (vitamin E); the most accepted blood indicators for the assessment of body fat-soluble vitamin (FSV) status. There are significant obstacles to precise FSV measurement in blood. These obstacles include their physical and chemical properties, incomplete standardisation of measurement and limitations in the techniques that are currently used for quantification. The aim of this review is to briefly outline the metabolism and interactions of FSV as a prelude to identifying the current challenges for the quantification of blood vitamins A, D and E.
Image compression—from DCT to wavelets (2000)

article Free Access Share on Image compression—from DCT to wavelets: a review Author: Subhasis Saha View Profile Authors Info & Claims XRDS: Crossroads, The ACM Magazine for StudentsVolume 6Issue 3March 2000pp 12–21https://doi.org/10.1145/331624.331630Published:01 March 2000Publication History 60citation4,097DownloadsMetricsTotal Citations60Total Downloads4,097Last 12 Months1,142Last 6 weeks204 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 SiteView all FormatsPDF
Specific antibody response towards predicted epitopes of the epidermal growth factor receptor induced by a thermostable synthetic peptide adjuvant conjugate. (1989)

Applying computer-assisted epitope prediction to the amino-acid sequence of the epidermal growth factor receptor (EGFR), the extracytoplasmic domain EGFR(516-529) was selected as a putative antigenic region. EGFR(516-529) was synthesized on a solid-phase matrix and N-terminally linked to the low mol. wt adjuvant tripalmitoyl-S-glyceryl-cysteinyl-serine (Pam3 Cys-Ser). The conjugation to this B cell and macrophage-activating lipopeptide considerably enhanced the immunogenicity of the EGFR peptide. Using the conjugate Pam3 Cys-Ser-EGFR(516-529), a peptide-specific monoclonal antibody was produced. By flow cytometry and immunoprecipitation the antibody was demonstrated to recognize EGFR on A431 cells, expressing large numbers of EGFR. With this novel approach synthetic immunogens can be prepared which could serve as thermostable synthetic vaccines with great potential in countries where a functional cold chain cannot be maintained.
Evidence implicating the 5′ untranslated region ofListeria monocytogenes actAin the regulation of bacterial actin-based motility (2004)

The ActA protein of Listeria monocytogenes is a major virulence factor, essential for the recruitment and polymerization of host actin filaments that lead to intracellular motility and cell-to-cell spread of bacteria within the infected host. The expression of actA is tightly regulated and is strongly induced only when L. monocytogenes is within the host cytosol. Intracellular induction of actA expression is mediated through a single promoter element that directs the expression of a messenger RNA with a long (150 bp) 5' untranslated region (UTR). Deletion of the actA+3 to +130 upstream region was found to result in bacterial mutants that were no longer capable of intracellular actin recruitment or cell-to-cell spread, thus indicating that this region is important for actA expression. L. monocytogenes strains that contained smaller deletions (21-23 bp) within the actA upstream region demonstrated a range of actA expression levels that coincided with the amount of bacterial cell-to-cell spread observed within infected monolayers. A correlation appeared to exist between levels of actA expression and the ability of L. monocytogenes to transition from uniform actin accumulation surrounding individual bacteria (actin clouds) to directional assembly and the formation of actin tails. Bacterial mutants containing deletions that most significantly altered the predicted secondary structure of the actA mRNA 5' UTR had the largest reductions in actA expression. These results suggest that the actA 5' UTR is required for maximal ActA synthesis and that a threshold level of ActA synthesis must be achieved to promote the transition from bacteria-associated actin clouds to directional actin assembly and movement.
Hit-and-run programming of therapeutic cytoreagents using mRNA nanocarriers (2017)

Therapies based on immune cells have been applied for diseases ranging from cancer to diabetes. However, the viral and electroporation methods used to create cytoreagents are complex and expensive. Consequently, we develop targeted mRNA nanocarriers that are simply mixed with cells to reprogram them via transient expression. Here, we describe three examples to establish that the approach is simple and generalizable. First, we demonstrate that nanocarriers delivering mRNA encoding a genome-editing agent can efficiently knock-out selected genes in anti-cancer T-cells. Second, we imprint a long-lived phenotype exhibiting improved antitumor activities into T-cells by transfecting them with mRNAs that encode a key transcription factor of memory formation. Third, we show how mRNA nanocarriers can program hematopoietic stem cells with improved self-renewal properties. The simplicity of the approach contrasts with the complex protocols currently used to program therapeutic cells, so our methods will likely facilitate manufacturing of cytoreagents.Current widely used viral and electroporation methods for creating therapeutic cell-based products are complex and expensive. Here, the authors develop targeted mRNA nanocarriers that can transiently program gene expression by simply mixing them with cells, to improve their therapeutic potential.
Prothrombin complex concentrate (Beriplex® P/N) for emergency anticoagulation reversal: a prospective multinational clinical trial (2008)

PCC treatment serves as an effective rapid hemorrhage control resource in the emergency anticoagulant reversal setting. More widespread availability of PCC is warranted to ensure its benefits in appropriate patients.
Mutant E-cadherin breast cancer cells do not display constitutive Wnt signaling. (2001)

Participation of E-cadherin in the Wnt signaling pathway was suggested because of the dual role of beta-catenin in cell adhesion and the Wnt signaling cascade. Whereas beta-catenin interacts at the cell membrane with the cell adhesion protein E-cadherin, in the nucleus it activates Wnt target genes through formation of transcriptionally active complexes with members of the Tcf/Lef family of transcription factors. Here, we analyzed by PCR and direct cycle sequencing 26 human breast cancer cell lines for alterations in the E-cadherin gene. Genetic alterations were identified in eight cell lines. Five cell lines had truncating mutations, whereas three cell lines had in-frame deletions in the gene transcript and expressed mutant E-cadherin proteins at the cell membrane. Involvement of E-cadherin in the Wnt pathway was evaluated through determination of the activity of a Tcf reporter gene, which had been transiently transfected into 15 breast cancer cell lines. None of six E-cadherin mutant cell lines and four cell lines that exhibit transcriptional silencing of the E-cadherin gene showed Tcf-mediated transcriptional activation. E-cadherin wild-type cell line DU4475 exhibited constitutive Tcf-beta-catenin signaling activity and was found to express truncated APC proteins. These results indicate that if cellular transformation occurred through mutation of E-cadherin, it is not mediated via constitutive activation of the Wnt signaling pathway.
Hydrogen-bonded layers of hydrogentartrate anions: two-dimensional building blocks for crystal engineering (1993)

An investigation of hydrogen-bond patterns in a family of ionic crystals has established the use of hydrogen bonding as a potential design strategy for crystal engineering of ionic materials. In 11 out of 12 crystal structures of anhydrous hydrogentartrate salts (data extracted from the Cambridge Structural Database), the anions were found to generate infinite two-dimensional sheets created by relatively short O–H⋯O hydrogen bonds. The regular occurrence of the infinite layer, even in the presence of widely differing cations, demonstrates the selectivity, strength and directionality of hydrogen bonds between ions in the solid state. The two-dimensional sheet was subsequently employed as a building block (‘scaffolding’) in the synthesis of a material with a threedimensional hydrogen-bond network, 1H-imidazolium hydrogen L-tartrate (the X-ray single-crystal structure is reported), where the cation provides the anticipated cross-link between adjacent anionic layers. Each anionic network was also described using a notation based upon graph theory which simplifies the process of recognizing and communicating complex structural information.
Water-filling capacity and beamforming performance of MIMO systems with covariance feedback (2003)

The paper presents the exact moment generating function (MGF) of the water-filling capacity for the correlated MIMO Rayleigh fading channels with covariance feedback. This MGF result is then used to derive the capacity mean and variance as well as the outage capacity. We also derive the outage capacity and capacity mean as well as the outage probability and average bit error rate for the MIMO beamforming scheme with covariance feedback in a correlated Rayleigh fading environment.
Service specification in cloud environments based on extensions to open standards (2009)

Cloud computing technologies are changing the way in which services are deployed and operated nowadays, introducing advantages such as a great degree of flexibility (e.g. pay-peruse models, automatic scalability, etc.). However, existing offerings (Amazon EC2, GoGrid, etc.) are based on proprietary service definition mechanisms, thus introducing vendor lock-in to the customers who deploy their services on those clouds. On the other hand, there are open standards that address the problem of packaging and distributing virtual appliances (i.e. complete software stacks deployed in one or more virtual machines), but they have not been designed specifically for clouds. This paper proposes a service specification language for cloud computing platforms, based on the DMTF's Open Virtualization Format standard, extending it to address the specific requirements of these environments. In order to assess the feasibility of our proposal, we have implemented a prototype system able to deploy and scale service specifications using the proposed extensions. Additionally, practical results are presented based on an industrial case study that demonstrates using the software prototype how to automatically deploy and flexibly scale the Sun Grid Engine application.
A Distributed Problem Solving Approach to Cooperative Information Gathering (1995)

this paper, we present a model of information gathering designed specifically for such complex environments, a model of Cooperative Information Gathering (CIG). In addition to the complexity of query specification, control of the acquisition process may itself be complex and dynamic in IG systems. Traditional Information Retrieval (IR) is a limited sub-case of such information gathering systems in which queries generally map onto static, pre-specified retrieval plans. In this paper, we propose a cooperative agent-based solution for information gathering. Top level queries drive the creation of partially elaborated information gathering plans, resulting in the employment of multiple semi-autonomous, cooperative agents for the purpose of achieving goals and subgoals within those plans. Cooperation between agents implies management of interdependencies between their activities so as to integrate and evolve consistent clusters of high quality information from distributed heterogeneous sources. This paper draws upon a long history of thought in Distributed Problem Solving (DPS) to present a model of this type of cooperative information acquisition.
Human CD1d–glycolipid tetramers generated byin vitrooxidative refolding chromatography (2001)

CD1 molecules are specialized in presenting lipids to T lymphocytes, but identification and isolation of CD1-restricted lipid specific T cells has been hampered by the lack of reliable and sensitive techniques. We here report the construction of CD1d-glycolipid tetramers from fully denatured human CD1d molecules by using the technique of oxidative refolding chromatography. We demonstrate that chaperone- and foldase-assisted refolding of denatured CD1d molecules and beta(2)-microglobulin in the presence of synthetic lipids is a rapid method for the generation of functional and specific CD1d tetramers, which unlike previously published protocols ensures isolation of CD1d tetramers loaded with a single lipid species. The use of human CD1d-alpha-galactosylceramide tetramers for ex vivo staining of peripheral blood lymphocytes and intrahepatic T cells from patients with viral liver cirrhosis allowed for the first time simultaneous analysis of frequency and specificity of natural killer T cells in human clinical samples. Application of this protocol to other members of the CD1 family will provide powerful tools to investigate lipid-specific T cell immune responses in health and in disease.