gebhart/patrepeval huggingface dataset:
Searching and browsing collections of structural information (2002)

This paper proposes a new approach to querying collections of structured textual information such as SGML/XML documents. Knowledge about the structure of documents is an additional resource that should be exploited during retrieval since the semantics of the different textual objects can be used to specify an information need much more precisely. However the traditional probabilistic retrieval model lacks the ability to handle structural information. We define a new retrieval function based on the probabilistic model which overcomes this drawback. The presented query language allows the assignment of structural roles to individual terms. The efficient evaluation of queries in this framework requires appropriate index structures. We design text and structure indexes and show how their information is combined during evaluation. The implementation supports additional functionalities such as a table of contents for browsing. First evaluation results show the feasibility of the approach on collections of unstructured documents.
Diet, anaerobic bacterial metabolism, and colon cancer: a review of the literature. (2005)

Epidemiologic studies have demonstrated variations in the incidence of colon cancer between populations and socioeconomic groups. Differences in dietary habits have been implicated in the risk of developing colon cancer. Diet appears to influence our colonic microflora. Such variations may allow for future utilization of the fecal flora as markers for screening and diagnosis of colon cancer. The composition of the diet not only dictates the available substrates for the flora but also helps to establish predictable and competitive relationships between intestinal bacteria. To appreciate the significance of populations deemed high and low risk based on host flora, an understanding of several dynamic microbial relationships and metabolites produced is necessary. In this review, we explore the critical relationships between bile acid 7 alpha-dehydroxylation, sulfidogenesis, methanogenesis, and how they relate to carbohydrate and bile acid metabolism. We summarize the chemopreventative, anticarcinogenic, and detoxifying activity of probiotics and prebiotics, as well as potential mechanisms for protection against colon cancer.
Separation of a Breast Cancer Cell Line from Human Blood Using a Quadrupole Magnetic Flow Sorter (2001)

We have developed a quadrupole magnetic flow sorter (QMS) to facilitate high-throughput binary cell separation. Optimized QMS operation requires the adjustment of three flow parameters based on the immunomagnetic characteristics of the target cell sample. To overcome the inefficiency of semiempirical operation/optimization of QMS flow parameters, a theoretical model of the QMS sorting process was developed. Application of this model requires measurement of the magnetophoretic mobility distribution of the cell sample by the cell tracking velocimetry (CTV) technique developed in our laboratory. In this work, the theoretical model was experimentally tested using breast carcinoma cells (HCC1954) overexpressing the HER-2/neu gene, and peripheral blood leukocytes (PBLs). The magnetophoretic mobility distribution of immunomagnetically labeled HCC1954 cells was measured using the CTV technique, and then theoretical predictions of sorting recoveries were calculated. Mean magnetophoretic mobilities of (1-3) x 10(-4) mm(3)/(T A s) were obtained depending on the labeling conditions. Labeled HCC1954 cells were mixed with unlabeled PBLs to form a "spiked" sample to be separated by the QMS. Fractional recoveries of cells for different flow parameters were examined and compared with theoretical predictions. Experimental results showed that the theoretical model accurately predicted fractional recoveries of HCC1954 cells. High-throughput (3.29 x 10(5) cells/s) separations with high recovery (0.89) of HCC1954 cells were achieved.
Ecology and characterization of polyhydroxyalkanoate-producing microorganisms on and in plants (2009)

Polyhydroxyalkanoates are energy reserve polymers produced by bacteria to survive periods of starvation in natural habitats. Little is known about the ecology of polyhydroxyalkanoate-producing bacteria. To analyse the occurrence of this specific group on/in seven different plant species, a combined strategy containing culture-dependent and -independent methods was applied. Using microbial fingerprint techniques (single-strand conformation polymorphism analysis with specific primers for phaC gene encoding the key enzyme of the polyhydroxyalkanoate synthesis), a high number of bands were especially found for the rhizosphere. Furthermore, cluster analysis revealed plant species-specific communities. Isolation of bacteria, recognition of brightly refractile cytoplasmatic inclusions, lipophilic stainings and a PCR strategy targeted on the phaC gene were used as a culture-dependent strategy for the detection of polyhydroxyalkanoate-producing bacteria. Results again represent a high degree of plant specificity: the rhizosphere of sugar beet contained the highest number of positive strains. This was confirmed by quantitative PCR: the relative copy number of phaC was statistically and significantly enhanced in all rhizospheres in comparison with bulk soil. New polyhydroxyalkanoate-producing bacterial species were detected: for example, Burkholderia terricola, Lysobacter gummosus, Pseudomonas extremaustralis, Pseudomonas brassicacearum and Pseudomonas orientalis. Our results confirm the hypothesis that the rhizosphere is an interesting hidden reservoir for polyhydroxyalkanoate producers.
Handbook of Sugars (1980)

Information on sugars used in commercial food processing is presented in recognition of the increasing importance of nutritive sweeteners in the food manufacturing industry. The physical properties of sucrose, invert syrups, corn syrups and sugars, lactose, fructose, dextrose, and blends are described to provide food processors with the necessary technological data to make food formulations or determine plant production. The amount and type of sugars used (granulated, liquid or specialty sugar products) have various effects in foods. Bulk handling of sucrose and handling and storage methods for corn syrups are discussed. The variety and complexity of products derived from starch hydrolysis are explained, especially the development and commercialization of high fructose corn syrups. Food applications of these commercial sugars in processed products are examined. Appendices provide analytical procedures for preparing sugars according to industrial standards
Allergy to Anacardiaceae: description of cashew and pistachio nut allergens. (2000)

Some members of the Anacardiaceae family, such as cashew nut, pistachio nut and mango, have been reported to cause immediate allergic reactions. We report three cases of anaphylaxis to cashew nuts. With the aim of describing the allergens existing in cashew and pistachio nuts, patients were prick tested with cashew and pistachio extracts. Specific IgE against both nuts was studied by CAP and SDS-PAGE/immunoblotting. It was found that skin tests and specific IgE to cashew and pistachio nuts were positive in the three patients. Both nuts showed several protein bands in SDS-PAGE. The strongest IgE-binding bands had similar molecular weights (15, 30 and 60 kDa) in cashew and pistachio nuts. These main bands were found to be sensitive to reducing agents. It was concluded that these three patients suffered immediate reactions to cashew nut due to an IgE-mediated mechanism.
A single-shot light probe (2012)

We demonstrate a novel light probe which can estimate the full dynamic range of a scene with multiple bright light sources. It places diffuse strips between mirrored spherical quadrants, effectively co-locating diffuse and mirrored probes to record the full dynamic range of illumination in a single exposure. From this image, we estimate the intensity of multiple saturated light sources by solving a linear system.
Coiled-Coil Structure of Murein Lipoprotein (1978)

Conference Article| December 01 1978 Coiled-Coil Structure of Murein Lipoprotein ANDREW D. McLACHLAN ANDREW D. McLACHLAN 1M.R.C. Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, U.K. Search for other works by this author on: This Site PubMed Google Scholar Author and article information Publisher: Portland Press Ltd Online ISSN: 1470-8752 Print ISSN: 0300-5127 © 1978 Biochemical Society1978 Biochem Soc Trans (1978) 6 (6): 1353–1354. https://doi.org/10.1042/bst0061353 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation ANDREW D. McLACHLAN; Coiled-Coil Structure of Murein Lipoprotein. Biochem Soc Trans 1 December 1978; 6 (6): 1353–1354. doi: https://doi.org/10.1042/bst0061353 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 1978 Biochemical Society1978 Article PDF first page preview Close Modal You do not currently have access to this content.
The effect of sodium nucleinate on allergic and immunological reactions. (1990)

Experiments on immunized rabbits and guinea pigs indicated that sodium nucleinate (SN) was capable of weakening or entirely eliminating anaphylactic and skin reactions of delayed type hypersensitivity to repeated administration of staphyloanatoxin, APDT vaccine. The findings on patients with the infectious form of bronchial asthma and chronic rheumatism showed that sodium nucleinate attenuated reactions to the subcutaneous administration of staphylococcal and streptococcal allergens. The treatment of patients suffering from infectious-allergic bronchial asthma and rheumatism with SN resulted in the recovery of deficient T cells, T-suppressors, normalization of immunoglobulin concentrations. In children with acute glomerulonephritis sodium nucleinate normalized decreased T-suppressor cells and increased IgG and circulating immune complexes (CIC), resulting in a pronounced remission of disease. The mechanism of desensitization and elimination of CIC by SN has not been explored, however, the parameters of SN-induced immunomodulation are known rather completely. It is suggested that SN brings about accumulation in the cell of cyclic AMP which diminished membrane permeability, activates monoaminooxidase resulting in the degradation of histamine and other biogenic amines, enhances the synthesis of endogenous corticosteroids with their desensitizing properties. All these effects contribute to the elimination of delayed type hypersensitivity. The role of SN in the inhibition of delayed type hypersensitivity remains obscure.
Th17-related cytokines: new players in the control of chronic intestinal inflammation (2011)

Crohn's disease (CD) and ulcerative colitis (UC), the main forms of inflammatory bowel diseases (IBD) in man, are thought to be caused by an excessive and poorly controlled immune response that is directed against components of the normal microflora. The exact sequence of events by which this pathological process is triggered and maintained is not fully understood, but studies in experimental models of IBD and data emerging from recent clinical trials indicate that T cell-derived cytokines are crucial mediators of the tissue damage. Although CD and UC have been traditionally considered two typical examples of T helper (Th)1 or Th2-associated disease respectively, it is now known that CD- and UC-related inflammation is also marked by enhanced production of cytokines made by a distinct subset of Th cells, termed Th17 cells. Th17 cytokines can have both tissue-protective and inflammatory effects in the gut and there is evidence that Th17 cells can alter their cytokine program according to the stimuli received and convert into Th1-producing cells. These novel findings have contributed to advancing our understanding of mechanisms of gut tissue damage and open new avenues for development of therapeutic strategies in IBD.
Optimizing combination treatment in the management of type 2 diabetes. (2007)

Obtaining the suggested glycemic control is the most important achievement in order to prevent cardiovascular complications in patients with type 2 diabetes. Monotherapy often fails after a period of treatment, so that multiple drugs are needed to achieve effective glycemic control. A number of oral glucose lowering drugs is now available such as metformin, sulfonylureas, non-sulfonylureas secretagogues (metiglinides derivatives), alpha-glucosidases inhibitors, and the newest agent: thiazolidinediones (TZD). The possible associations of oral glucose lowering drugs for optimal treatment of type 2 diabetes are briefly reviewed. In particular, the effects of different classes of drugs on cardiovascular risk factors (and particular hypertension and dyslipidemia) and well recognized cardiovascular disease markers in type 2 diabetes are analyzed: in this context TZD appear the more innovative drugs and have been shown to play a key role in the management of hypertension, dyslipidemia, inflammation and endothelial disfunction in diabetic patients. The possible adverse effects derived from the association of different drug classes are also considered.
A tumour‐associated DEAD‐box protein, rck/p54 exhibits RNA unwinding activity toward c‐myc RNAs in vitro (2003)

These findings strongly suggest that rck/p54 may play an important role in translation initiation by restructuring mRNAs even in the cell and contribute to carcinogenesis.
Design of Selective, ATP-Competitive Inhibitors of Akt (2010)

This paper describes the design and synthesis of novel, ATP-competitive Akt inhibitors from an elaborated 3-aminopyrrolidine scaffold. Key findings include the discovery of an initial lead that was modestly selective and medicinal chemistry optimization of that lead to provide more selective analogues. Analysis of the data suggested that highly lipophilic analogues would likely suffer from poor overall properties. Central to the discussion is the concept of optimization of lipophilic efficiency and the ability to balance overall druglike propeties with the careful control of lipophilicity in the lead series. Discovery of the nonracemic amide series and subsequent modification produced an advanced analogue that performed well in advanced preclinical assays, including xenograft tumor growth inhibition studies, and this analogue was nominated for clinical development.
hGPR87 contributes to viability of human tumor cells (2008)

Emerging in vitro and in vivo data underline the crucial role of G-protein-coupled receptors (GPCRs) in tumorigenesis. Here, we report the contribution of hGPR87, a predicted member of the P2Y subfamily of GPCRs, to proliferation and survival of human tumor cell lines. hGPR87 mRNA transcript was found to be preferentially overexpressed in squamous cell carcinomas (SCCs) of different locations and in their lymph node metastases. Up-regulation of both, transcript and protein, was detected in samples of SCC of the lung, cervix, skin and head and neck (pharynx, larynx and epiglottis). In addition to the expression of hGPR87 in tumors which originate from stratified epithelia, we identified other hGPR87-positive tumor types including subsets of large cell and adenocarcinomas of the lung and transitional cell carcinomas of the urinary bladder. Loss of function studies using siRNA in human cancer cell lines lead to antiproliferative effects and induction of apoptosis. Like other known P2Y receptors, hGPR87 was found to be mainly located on the cell surface. The overexpression of hGPR87 preferentially in SCCs together with our functional data suggests a common molecular mechanism for SCC tumorigenesis and may provide a novel intervention site for mechanism-based antitumor therapies.
5-Methylcytosine in Eukaryotic DNA (1981)

A small portion of the cytosine residues in the DNA of higher eukaryotes as well as in that of many lowe eukaryotes if methylated. The resulting 5-methylcytosine residues occur in specific in the DNA, usually adjacent to guanine residues on the 3' side. This methylation of eukaryotic DNA has been proposed to function in many ways, including control of transcription, maintenance of chromosome structure, repair of DNA, establishment of preferred sites for mutation, oncogenic transformation, and, in certain systems, protection of DNA against enzymatic degradation.
Tumor-Induced Suppression of CTL Expansion and Subjugation by gp96-Ig Vaccination (2009)

Established tumors suppress antitumor immune responses and induce tolerance by incompletely characterized mechanisms, and this phenomenon is an important barrier to tumor immunotherapy. Single vaccination with tumor cells expressing gp96-Ig stimulates robust expansion of tumor-specific CTLs in tumor-naïve mice and this expansion is inhibited by established tumors. Interestingly, frequent vaccinations restore antitumor immune responses in the presence of established tumors. Syngeneic EG7 tumor-bearing mice have heterogeneous responses to frequent vaccination with EG7-gp96-Ig, with 32% complete responders and 68% partial responders. Comparison of responders to nonresponders revealed an inverse correlation between tumor-specific CTL expansion in the peripheral blood and tumor size. To identify immune cells and molecules associated with effective antitumor immune responses, reverse transcription-PCR arrays were performed using cells isolated from the vaccination site. ELISAs, cellular phenotyping, and tumor immunohistochemistry were also performed comparing vaccine responders to nonresponders. These data show that up-regulation of T-bet, RORgammat, IFNgamma, CCL8, CXCL9, and CXCL10 at the vaccination site are associated with vaccine-induced antitumor immunity. These data correlate with increased CTL expansion in the peripheral blood of responders, increased infiltration of responder tumors by CD8+ cells and interleukin-17+ cells, and decreased infiltration of responder tumors by CD11b+Gr-1+ cells and FoxP3+ cells. Furthermore, serum ELISAs revealed a significant elevation of transforming growth factor-beta in nonresponders as compared with responders. Interestingly, CD8+ T cells isolated from responders and nonresponders have equivalent cytotoxic activity in vitro. Taken together, our data suggest that established tumors may escape immunosurveillance by preventing clonal expansion of tumor-specific CTL without inducing anergy.
Lymphocyte inhibitor of TRAIL (TNF-related apoptosis-inducing ligand): a new receptor protecting lymphocytes from the death ligand TRAIL. (1998)

Apoptosis can be triggered by the engagement of cell surface receptors by their ligands. A growing number of receptors belonging to the TNF receptor family have been identified that contain a conserved cytoplasmic death domain. These include Fas, TNF-R1, lymphocyte-associated receptor of death (LARD), DR4, and TNF-related apoptosis-inducing ligand receptor inducer of cell killing-2 (TRICK2). The latter two are receptors for the cytotoxic ligand TNF-related apoptosis-inducing ligand (TRAIL), and one of the paradoxes raised by the cloning of these molecules was why do most cells not die upon contact with the widely expressed TRAIL molecule? This is a particular problem for lymphocytes that express DR4 and TRICK2 and are in constant circulation through TRAIL-expressing tissues. We have cloned LIT (lymphocyte inhibitor of TRAIL), which lacks a death domain. LIT is expressed predominantly on PBL, where it can competitively inhibit TRAIL-induced apoptosis through DR4/TRICK2, and may function to modulate lymphocyte sensitivity to TRAIL.
REAL-TIME MUTUAL-INFORMATION-BASED LINEAR REGISTRATION ON THE CELL BROADBAND ENGINE PROCESSOR (2007)

Emerging multi-core processors are able to accelerate medical imaging applications by exploiting the parallelism available in their algorithms. We have implemented a mutual-information-based 3D linear registration algorithm on the Cell Broadband Enginetrade (CBE) processor, which has nine processor cores on a chip and has a 4-way SIMD unit for each core. By exploiting the highly parallel architecture and its high memory bandwidth, our implementation with two CBE processors can compute mutual information for about 33 million pixel pairs in a second. This implementation is significantly faster than a conventional one on a traditional microprocessor or even faster than a previously reported custom-hardware implementation. As a result, it can register a pair of 256times256times30 3D images in one second by using a multi-resolution method. This paper describes our implementation with a focus on localized sampling and speculative packing techniques, which reduce the amount of the memory traffic by 82%
Pharmacodynamics of cisplatin in human head and neck cancer: correlation between platinum content, DNA adduct levels and drug sensitivity in vitro and in vivo (1998)

Total platinum contents and cisplatin-DNA adduct levels were determined in vivo in xenografted tumour tissues in mice and in vitro in cultured tumour cells of head and neck squamous cell carcinoma (HNSCC), and correlated with sensitivity to cisplatin. In vivo, a panel of five HNSCC tumour lines growing as xenografts in nude mice was used. In vitro, the panel consisted of five HNSCC cell lines, of which four had an in vivo equivalent. Sensitivity to cisplatin varied three- to sevenfold among cell lines and tumours respectively. However, the ranking of the sensitivities of the tumour lines (in vivo), also after reinjection of the cultured tumour cells, did not coincide with that of the corresponding cell lines, which showed that cell culture systems are not representative for the in vivo situation. Both in vitro and in vivo, however, significant correlations were found between total platinum levels, measured by atomic absorption spectrophotometry (AAS), and tumour response to cisplatin therapy at all time points tested. The levels of the two major cisplatin-DNA adduct types were determined by a recently developed and improved 32P post-labelling assay at various time points after cisplatin treatment. Evidence is presented that the platinum-AG adduct, in which platinum is bound to guanine and an adjacent adenine, may be the cytotoxic lesion because a significant correlation was found between the platinum-AG levels and the sensitivities in our panel of HNSCC, in vitro as well as in vivo. This correlation with the platinum-AG levels was established at 1 h (in vitro) and 3 h (in vivo) after the start of the cisplatin treatment, which emphasizes the importance of early sampling.