gebhart/patrepeval huggingface dataset:
Tumor Lectinology: At the Intersection of Carbohydrate Chemistry, Biochemistry, Cell Biology, and Oncology (1988)

Abstract The scientific description of lectins, a class of sugar‐binding proteins distinct from both sugar‐specific enzymes and antibodies, began nearly 100 years ago. The natural ligands of lectins include the sugar moieties of cell glycoproteins, glycolipids, and proteoglycans. Lectins can selectively recognize these potential information‐storing or ‐transferring structural elements and so contribute to regulating biological processes. Plant lectins are now a well‐established means of characterizing and localizing glycoconjugate‐bound sugar determinants. However, work on endogenous lectins is still confronted by many open questions, whose answers require detailed experiments using a suitable model system. Tumors offer an obvious model, particularly since they allow the possible diagnostic and therapeutic uses of lectins to be explored directly. Tumor lectinology employs a broad range of methods, from the chemical synthesis of the sugar components of neoglycoproteins, and their use to seek out cellular sugar receptors with histochemical and cell‐biological techniques, to the biochemical and immunological characterization of the lectins expressed by tumor cells and the use of homology analysis to find further functional domains. The outlook for clinical applications depends on the harmonious integration of these disparate disciplines in tumor lectinology.
Splicing mutations in the CHO DHFR gene preferentially induced by (+/-)-3 alpha,4 beta-dihydroxy-1 alpha,2 alpha-epoxy-1,2,3,4- tetrahydrobenzo[c]phenanthrene. (1990)

Cultured Chinese hamster ovary (CHO) cells were treated with the polycyclic aromatic hydrocarbon racemic 3 alpha,4 beta-dihydroxy-1 alpha,2 alpha-epoxy-1,2,3,4- tetrahydrobenzo[c]phenanthrene. Mutants deficient in dihydrofolate reductase activity were isolated. A carcinogen treatment at 0.1 microM yielded at 46% survival of the treated population and an induced frequency of mutation of 1.7 x 10(-4), 10(3)-fold greater than the spontaneous rate. By polymerase chain reaction amplification and direct DNA sequencing, we determined the base changes in 38 mutants. Base substitutions accounted for 78% (30/38) of the mutations. We obtained, in addition, four frameshift and four complex mutations. The preferred type of mutation was transversion (A.T----T.A and G.C----T.A) occurring in 69% of the analyzed mutants. A purine was on the 3' side of the putative adduct site in every mutant. Mutations were favored at sequences AGG, CAG, and AAG (the underlined base is the target). Surprisingly, 42% of the mutations created mRNA splicing defects (16/38), especially at splice acceptor sites for each of the five introns. Thus, this chemical carcinogen may recognize some aspect of DNA structure in regions corresponding to pre-mRNA splice sites.
Introducing Predictive Analytics: Opportunities (2007)

Abstract Energy companies' data bases hold the potential for tremendous advantage. Moreover, they are growing exponentially, fed by a mounting array of sources including ERP systems, sensory networks, machine instrumentation, credit card transactions, loyalty programs, and increasing multi-media and other unstructured data. Yet analyzing and extracting value from large datasets has always been a problem due to the sheer volume of data and consequent "signal to noise" problems. To unlock some of this value, BP have launched a "predictive analytics" initiative, investigating pattern recognition techniques that find correlations and relationships in large datasets. This form of analysis is not new, but pilots in previous years have not resulted in significant implementation. However, recent advances in computing power coupled with more sophisticated applications, easy-to-use interfaces and easier access to data, have made predictive analytics a more valuable, practical tool for wide scale corporate adoption. And now, with more data available from sensor enabled applications, predictive analytics presents an opportunity to make all aspects of our field operations more efficient and effective. A particular distinction of these techniques is that the models used are data-driven, and do not rely on a fundamental understanding of the first principles involved. This means that predictive analytics can be particularly useful where the underlying scientific principles are complex and difficult to model precisely. Data driven models can be created with reduced effort and often without the need for in-depth skills used to create models from first principles. To take advantage of these techniques, the Digital &amp; Communications Chief Technology Office (CTO) has been leading a program to introduce predictive analytics across all business segments and operations in BP. In so doing, we have been working closely with our segment specific technology teams, FIELD OF THE FUTURE, Refining Technology and our Exploration and Production Digital &amp; Communications Technology teams. Having established connections with over 50 "predictive analytics" vendors, CTO is working with business units and functions and have completed a number of proof of concept (POC) trials utilizing a variety of innovative vendor solutions This paper describes a number of these POCs and presents the value proposition for data driven predictive analytics.
Characterization of Fortilin, a Novel Antiapoptotic Protein (2001)

Apoptosis is meticulously controlled in living organisms. Its dysregulation has been shown to play a key role in a number of human diseases, including neoplastic, cardiovascular, and degenerative disorders. Bcl-2 family member proteins and inhibitors of apoptosis proteins are two major negative regulators of apoptosis. We report here the characterization of novel antiapoptotic protein, fortilin, which we identified through yeast two-hybrid library screening. Sequence analysis of fortilin revealed it to be a 172-amino acid polypeptide highly conserved from mammals to plants. Fortilin is structurally unrelated to either Bcl-2 family member proteins or inhibitors of apoptosis proteins. Northern blot analysis showed the fortilin message to be ubiquitous in normal tissue but especially abundant in the liver, kidney, and small intestine. Western blot analysis using anti-fortilin antibody showed more extensive expression in cancerous cell lines (H1299, MCF-7, and A549) than in cell lines derived from normal tissue (HEK293). Immunocytochemistry using HeLa cells transiently expressing FLAG-tagged fortilin and immunohistochemistry using human breast ductal carcinoma tissue and anti-fortilin antibody both showed that fortilin is predominantly localized in the nucleus. Functionally, the transient overexpression of fortilin in HeLa cells prevented them, in a dose-dependent fashion, from undergoing etoposide-induced apoptosis. Consistently, U2OS cells stably expressing fortilin protected the cells from cell death induced by etoposide over various concentrations and durations of exposure. In addition, fortilin overexpression inhibited caspase-3-like activity as assessed by the cleavage of fluorogenic substrate benzyloxycarbonyl-DEVD-7-amido-4-(trifluoromethyl)coumarin. Furthermore, the antisense depletion of fortilin from breast cancer cell line MCF-7 was associated with massive cell death. These data suggest that fortilin represents a novel antiapoptotic protein involved in cell survival and apoptosis regulation.
Systemic Inflammation Alters the Kinetics of Cerebrovascular Tight Junction Disruption after Experimental Stroke in Mice (2008)

Systemic inflammatory events, such as infection, increase the risk of stroke and are associated with worse outcome, but the mediators of this clinically important effect are unknown. Our aim here was to elucidate mechanisms contributing to the detrimental effects of systemic inflammation on mild ischemic brain injury in mice. Systemic inflammation was induced in mice by peripheral interleukin-1beta (IL-1beta) challenge and focal cerebral ischemia by transient middle cerebral artery occlusion (MCAo). Systemic inflammation caused an alteration in the kinetics of blood-brain barrier (BBB) disruption through conversion of a transient to a sustained disruption of the tight junction protein, claudin-5, and also markedly exacerbated disruption to the cerebrovascular basal lamina protein, collagen-IV. These alterations were associated with a systemic inflammation-induced increase in neurovascular gelatinolytic activity that was mediated by a fivefold increase in neutrophil-derived matrix metalloproteinase-9 (MMP-9) in the brains of IL-1beta-challenged mice after MCAo. Specific inhibition of MMP-9 abrogated the effects of systemic inflammation on the sustained but not the acute disruption of claudin-5, which was associated with phosphorylation of cerebrovascular myosin light chain. MMP-9 inhibition also attenuated the deleterious impact of systemic inflammation on brain damage, edema, neurological deficit, and incidence of hemorrhagic transformation. These data indicate that a transformation from transient to sustained BBB disruption caused by enhanced neutrophil-derived neurovascular MMP-9 activity is a critical mechanism underlying the exacerbation of ischemic brain injury by systemic inflammation. These mechanisms may contribute to the poor clinical outcome in stroke patients presenting with antecedent infection.
Evaluation of the performances of several four-antenna systems in a reverberation chamber (2007)

This paper results from a short-term mission granted by the COST 284 where the antenna-design competences of the LEAT have been gathered with the measurement skills of Chalmers Institute of Technology. Three multi-antenna prototypes have been characterized in the Bluetest reverberation chamber in terms of total efficiency and diversity gain. Particularly the performances of an initial four-antenna system with poor isolation have been evaluated with and without the presence of a phantom head and then we characterized in the same manner two prototypes with highly decoupled antennas. The paper especially focused on demonstrating that the neutralization technique is still giving improvements in the presence of the user's head.
Strict Criteria Should Be Applied in the Diagnosis of Encapsulated Follicular Variant of Papillary Thyroid Carcinoma (2002)

Papillary thyroid carcinoma (PTC) is defined on the basis of the cytologic features, and, thus, in contrast with follicular carcinoma, demonstration of invasion is not required to establish a diagnosis of malignancy. Although most PTCs show an admixture of papillary structures and follicles, some are composed entirely of follicles—the follicular variant of PTC. For the examples that are nonencapsulated, the diagnosis usually poses no problems, because the invasive growth and accompanying sclerosis leave no doubt about the malignant nature of the process. It is a different story for encapsulated neoplasms composed exclusively of follicles and lacking capsular and vascular invasion—the distinction between follicular adenoma and follicular variant of PTC rests on the pathologist’s perception of the nuclear characteristics of the follicular cells. If the pathologist believes that the nuclear features are compatible with those of PTC, a diagnosis of malignancy (PTC) is made just on that basis. However, the nuclei very often show some but not all of the nuclear features of PTC, eg, pale nuclei alone, making a clear-cut diagnosis difficult. If the case is sent out for consultation opinion, more often than not, divergent opinions are obtained, which reflects a lack of uniform diagnostic criteria.
Regulation of Exopolysaccharide Production by Lactococcus lactis subsp. cremoris by the Sugar Source (1999)

Lactococcus lactis produced more exopolysaccharide (EPS) on glucose than on fructose as the sugar substrate, although the transcription level of the eps gene cluster was independent of the sugar source. A major difference between cells grown on the two substrates was the capacity to produce sugar nucleotides, the EPS precursors. However, the activities of the enzymes required for the synthesis of nucleotide sugars were not changed upon growth on different sugars. The activity of fructosebisphosphatase (FBPase) was by far the lowest of the enzymes involved in precursor formation under all conditions. FBPase catalyzes the conversion of fructose-1, 6-diphosphate into fructose-6-phosphate, which is an essential step in the biosynthesis of sugar nucleotides from fructose but not from glucose. By overexpression of the fbp gene, which resulted in increased EPS synthesis on fructose, it was proven that the low activity of FBPase is indeed limiting not only for EPS production but also for growth on fructose as a sugar source.
DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon–intron structure (2013)

DNA methylation is known to regulate transcription and was recently found to be involved in exon recognition via cotranscriptional splicing. We recently observed that exon–intron architectures can be grouped into two classes: one with higher GC content in exons compared to the flanking introns, and the other with similar GC content in exons and introns. The first group has higher nucleosome occupancy on exons than introns, whereas the second group exhibits weak nucleosome marking of exons, suggesting another type of epigenetic marker distinguishes exons from introns when GC content is similar. We find different and specific patterns of DNA methylation in each of the GC architectures; yet in both groups, DNA methylation clearly marks the exons. Exons of the leveled GC architecture exhibit a significantly stronger DNA methylation signal in relation to their flanking introns compared to exons of the differential GC architecture. This is accentuated by a reduction of the DNA methylation level in the intronic sequences in proximity to the splice sites and shows that different epigenetic modifications mark the location of exons already at the DNA level. Also, lower levels of methylated CpGs on alternative exons can successfully distinguish alternative exons from constitutive ones. Three positions at the splice sites show high CpG abundance and accompany elevated nucleosome occupancy in a leveled GC architecture. Overall, these results suggest that DNA methylation affects exon recognition and is influenced by the GC architecture of the exon and flanking introns.
Highly selective evanescent modal filter for two-mode optical fibers (1986)

Efficient and selective coupling between a single-mode fiber and the LP(11) mode of a double-mode fiber is demonstrated in an evanescent directional coupler. With greater than 90% coupling to the LP(11) mode, suppression of the coupled power to the lower-order LP(01) mode was measured to be at least 24 dB. This device has application as a modal filter for the construction of in-line all-fiber optical components.
Prevalence of Neurological Involvement and Malformative/systemic Syndromes in A- and V-pattern Strabismus (2012)

Neurological involvement and malformative/systemic syndromes seem to be more evident in patients presenting with A- and V-pattern strabismus.
Multipoint Fiber-Optic Hot-Spot Sensing Network Integrated Into High Power Transformer for Continuous Monitoring (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> A multipoint fiber-optic temperature sensor network integrated inside a power transformer for continuous monitoring of hot-spots on windings, cellulose insulations, and oil, is demonstrated and tested. The temperature sensors are based on proprietary encapsulated fiber Bragg grating (FBG) sensors and the optical interrogation unit uses a special designed narrowband high power broadband fiber source. The fiber-optic sensing network is integrated into a 20 MVA, 345/<formula formulatype="inline"><tex>$\surd 3$</tex></formula> kV <formula formulatype="inline"><tex>$-20$</tex></formula> kV power transformer (CORE type) having 12 temperature sensing points, distributed over several physical locations inside the transformer (windings, cellulose insulators, magnetic circuit, and cooling oil entrance and exit). </para>
3-D EM exploration of the hepatic microarchitecture – lessons learned from large-volume in situ serial sectioning (2016)

To-date serial block-face scanning electron microscopy (SBF-SEM) dominates as the premier technique for generating three-dimensional (3-D) data of resin-embedded biological samples at an unprecedented depth volume. Given the infancy of the technique, limited literature is currently available regarding the applicability of SBF-SEM for the ultrastructural investigation of tissues. Herein, we provide a comprehensive and rigorous appraisal of five different SBF-SEM sample preparation protocols for the large-volume exploration of the hepatic microarchitecture at an unparalleled X, Y and Z resolution. In so doing, we qualitatively and quantitatively validate the use of a comprehensive SBF-SEM sample preparation protocol, based on the application of heavy metal fixatives, stains and mordanting agents. Employing the best-tested SBF-SEM approach, enabled us to assess large-volume morphometric data on murine parenchymal cells, sinusoids and bile canaliculi. Finally, we integrated the validated SBF-SEM protocol with a correlative light and electron microscopy (CLEM) approach. The combination of confocal scanning laser microscopy and SBF-SEM provided a novel way to picture subcellular detail. We appreciate that this multidimensional approach will aid the subsequent research of liver tissue under relevant experimental and disease conditions.
<title>Building an integrated clinical and research network</title> (1996)

At the Georgetown University Medical Center Department of Radiology we are currently involved in integrating three diverse networks into a coherent whole. We are installing a new Radiology Information System (RIS) and a new Picture Archiving and Communication System (PACS) as well as upgrading our existing research network, which provides Internet access, to add office automation tools. To accomplish this, many issues have to be resolved. Users of the different systems have different requirements and must have different levels of access to data on the various systems. For example, researchers need access to Internet resources and e-mail while data from the clinical systems must be protected from the outside world. Physicians and some other users on the non-clinical network also require fast and convenient access to the RIS and PACS for clinical uses. Parts of the network should be shielded from the heavy image traffic created by the PACS. On the other hand, because clinical data is also used for research, a connection between the networks is necessary. Our solution for providing adequate access for all users, assuring confidentiality for patient data, and managing network traffic will be described.
Dark Rearing Rescues P23H Rhodopsin-Induced Retinal Degeneration in a TransgenicXenopus laevisModel of Retinitis Pigmentosa: A Chromophore-Dependent Mechanism Characterized by Production of N-Terminally Truncated Mutant Rhodopsin (2007)

To elucidate the molecular mechanisms underlying the light-sensitive retinal degeneration caused by the rhodopsin mutation P23H, which causes retinitis pigmentosa (RP) in humans, we expressed Xenopus laevis, bovine, human, and murine forms of P23H rhodopsin in transgenic X. laevis rod photoreceptors. All P23H rhodopsins caused aggressive retinal degeneration associated with low expression levels and retention of P23H rhodopsin in the endoplasmic reticulum (ER), suggesting involvement of protein misfolding and ER stress. However, light sensitivity varied dramatically between these RP models, with complete or partial rescue by dark rearing in the case of bovine and human P23H rhodopsin, and no rescue for X. laevis P23H rhodopsin. Rescue by dark rearing required an intact 11-cis-retinal chromophore binding site within the mutant protein and was associated with truncation of the P23H rhodopsin N terminus. This yielded an abundant nontoxic approximately 27 kDa form that escaped the ER and was transported to the rod outer segment. The truncated protein was produced in the greatest quantities in dark-reared retinas expressing bovine P23H rhodopsin and was not observed with X. laevis P23H rhodopsin. These results are consistent with a mechanism involving enhanced protein folding in the presence of 11-cis-retinal chromophore, with ER exit assisted by proteolytic truncation of the N terminus. This study provides a molecular mechanism for light sensitivity observed in other transgenic models of RP and for phenotypic variation among RP patients.
Galactomannan detection in computerized tomography‐based broncho‐alveolar lavage fluid and serum in haematological patients at risk for invasive pulmonary aspergillosis (2003)

We determined the value of galactomannan (GM) detection in computerized tomography (CT)-based broncho-alveolar lavage (BAL) fluid and serum for the diagnosis of invasive pulmonary aspergillosis (IPA) in haemato-oncological patients with neutropenia. CT of the thorax and BAL were performed systematically at predefined clinical indications. GM was determined by sandwich enzyme-linked immunosorbent assay; the clinicians were unaware of the results. Of 160 patients, 17 patients (10.6%) presented with proven, probable or suspected IPA. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of GM detection in CT-based BAL fluid were all 100%. For GM detection in serially sampled serum, the sensitivity was 47%, the specificity 93%, the PPV 73% and the NPV 82%. A non-blinded follow-up study was performed to validate these results. In this study, 22 of 198 patients (11.1%) presented with IPA, and the sensitivity, specificity, PPV and NPV of GM detection in CT-based BAL fluid were 85%, 100%, 100% and 88% respectively. None of BAL fluids obtained after antifungal treatment of 3 d or more were positive. These results indicate that, when CT is used systematically and at an early stage, GM detection in CT-based BAL fluid has a high PPV for diagnosing IPA early in untreated patients.
Emerging roles of the tumor-associated stroma in promoting tumor metastasis (2012)

The stroma in human carcinomas consists of extracellular matrix and various types of non-carcinoma cells, mainly leukocytes, endothelial cells, fibroblasts, myofibroblasts and bone marrow-derived progenitors. The tumor-associated stroma actively supports tumor growth by stimulating neo-angiogenesis, as well as proliferation and invasion of apposed carcinoma cells. It has long been accepted that alterations within carcinoma cells mediate metastasis in a cell-autonomous fashion. Recent studies have, however, suggested an additional notion that cancer cells instigate local and systemic changes in the tumor microenvironment and contribute to niche formation for metastasis. Research, aiming to establish the roles of the tumor-associated stroma in facilitating the spread of carcinoma cells into distant organs, has provided an abundance of data and greater knowledge of the biology of metastatic carcinoma cells and associated stromal cells. This has stimulated further advances in the development of novel therapeutic approaches targeting tumor metastasis.