gebhart/patrepeval huggingface dataset:
Bacterial Cell-to-Cell Signaling in the Gastrointestinal Tract (2005)

The gastrointestinal (GI) tract is the site of the largest and most complex environment in the mammalian host. In the adult human, the total microbial population (ca. 1014 cells) is estimated to exceed the total number of mammalian cells by at least an order of magnitude ([5][1]). The GI tract
Multimapper: Data Density Sensitive Topological Visualization (2018)

Mapper is an algorithm that summarizes the topological information contained in a dataset and provides an insightful visualization. It takes as input a point cloud which is possibly high-dimensional, a filter function on it and an open cover on the range of the function. It returns the nerve simplicial complex of the pullback of the cover. Mapper can be considered a discrete approximation of the topological construct called Reeb space, as analysed in the 1-dimensional case by [Carri et al.,]. Despite its success in obtaining insights in various fields such as in [Kamruzzaman et al., 2016], Mapper is an ad hoc technique requiring lots of parameter tuning. There is also no measure to quantify goodness of the resulting visualization, which often deviates from the Reeb space in practice. In this paper, we introduce a new cover selection scheme for data that reduces the obscuration of topological information at both the computation and visualisation steps. To achieve this, we replace global scale selection of cover with a scale selection scheme sensitive to local density of data points. We also propose a method to detect some deviations in Mapper from Reeb space via computation of persistence features on the Mapper graph.
Oracle8 Data Warehousing (1998)

From the Publisher:
A practical guide to successful data warehouse analysis,build,and roll-out. 
Your Expert Guide to Building and Launching Your Data Warehouse Data warehousing  large-scale data storage and analysis  is among the most important areas of enterprise computing today. Master data warehousing with the book officially authorized by Oracle Corporation,the leading provider of data warehousing solutions to Fortune 1000 companies. 
Written by a solid team of Oracle and data warehousing experts  Oracle8 Data Warehousing is your tactical guide to every important facet of data warehousing with Oracle8. Whether you are a database administrator,an information technology manager,or a data warehouse team member,you'll find this book loaded with valuable advice on planning,building,rolling out,and maintaining your data warehouse for optimal performance. 
This book will help you to: 

Understand the Oracle Express Server data warehousing solution. Investigate the physical components of a data warehouse including table size,expansion,disk stripping,and table partitioningBuild an effective warehousing team and gain real-world insight into the business rationale that secures essential management buy-inOptimize the Oracle8 server for decision support. Make critical technical decisions such as choosing RAID technology,running the cost-based optimizer,as well as using read-only table space and warehouse refresh mechanismsConvert a legacy database system into an Oracle datawarehouse. Gain a complete overview of data extraction,transformation,and loading into the Oracle8 repositoryLearn the basics of ROLAP,MOLAP,and OLAP


From general concepts to Oracle8's specific warehousing capabilities,Oracle8 Data Warehousing is all you need.
Comparison of the effectiveness of (+/-)-1,2-bis(3,5-dioxopiperazinyl-1-yl)propane (ICRF-187) and N-acetylcysteine in preventing chronic doxorubicin cardiotoxicity in beagles. (1985)

This investigation examined the potential of N-acetylcysteine (NAC) and ICRF-187, alone and in combination, to protect against chronic doxorubicin cardiotoxicity. Adult beagles of either sex (7.3 to 12.5 kg) were given doxorubicin (1.75 mg/kg i.v.) either alone or 30 min after either ICRF-187 (25 mg/kg i.p.), NAC (200 mg/kg i.p.), or ICRF-187 (25 mg/kg i.p.) and NAC (200 mg/kg i.p.) at 3-week intervals. Control dogs received ICRF-187 (25 mg/kg i.p.), NAC (200 mg/kg i.p.), ICRF-187 (25 mg/kg i.p.) and NAC (200 mg/kg i.p.), or 0.9% NaCl solution without doxorubicin. The experiment was terminated 3 weeks after the seventh injection (total doxorubicin dose, 12.25 mg/kg). Three animals pretreated with NAC and one pretreated with ICRF-187 before receiving doxorubicin died or were in poor condition and were killed before the end of the study. The frequency and extent of myocardial lesions (vacuolization and myofibrillar loss) were assessed on a scale of 0 to 4+. Such lesions were present in all six dogs given doxorubicin alone and were marked to severe (3+ to 4+) in five of these dogs and moderate (2+) in one. Lesions of comparable severity (2+ to 4+) were also apparent in the hearts of dogs given the combination of NAC and doxorubicin. In contrast, no abnormalities (lesion score 0) were found in the hearts of three of six dogs given doxorubicin and ICRF-187 and in four of six dogs given doxorubicin following the combination of ICRF-187 and NAC; the remaining animals in these two groups had minimal lesions. At the dosage regimen used in the present experiments, doxorubicin, NAC, or ICRF-187 alone or in combination did not cause alterations in lungs, liver, kidney, or small intestine. Decreases in WBC count, RBC count, and hemoglobin occurred in dogs given doxorubicin with or without the various pretreatments. Thus, pretreatment with ICRF-187 was effective and pretreatment with NAC was ineffective in reducing chronic doxorubicin cardiotoxicity.
[An early detection of recurrence using reverse transcriptase-polymerase chain reaction (RT-PCR) and methylation-specific polymerase chain reaction (MSP) from peripheral blood in patients after gastrectomy]. (2006)

Several molecular approaches, using peripheral blood of patients with cancers, have been assessed recently for ability to detect various primary and recurrent cancers at an early stage. One is the reverse transcriptase polymerase chain reaction (RT-PCR) analysis, which can detect a small number of circulating cancer cells. Another is the methylation-specific polymerase chain reaction (MSP), which detects tumor-specific alterations of cell-free serum DNA released from tumor into the circulation by necrosis and/or apoptosis. In the present study, we set out to assess the diagnostic value of the RT-PCR assay and the MSP assay for an early detection of recurrent diseases in patients after curative gastrectomy. Two of the 25 patients (8%) exhibited a CEA specific signal in their peripheral blood. On the other hand, seven patients (28%) showed aberrant methylation of the promoter region of at least one gene (3 patients for p16, 3 for E-cadherin, 3 for RARbeta genes, and 1 for CDH4 respectively). No abnormal signal was detected in sera from volunteers who served as controls. Of 10 patients who developed recurrences, a CEA-specific signal and aberrant methylation was demonstrated in plasma samples of 1 and 4 patients, respectively. One patient, without definite findings of recurrence at the time of analysis, developed recurrences 6 months later. Both assays can serve as markers that allow selection of those cases requiring more intensive screening and aggressive postoperative treatment.
Galanin‐Galanin Receptor Systems in the Hypothalamic Paraventricular and Supraoptic Nuclei: Some Recent Findings and Future Challenges aa (1998)

Galanin and galanin receptors are widely distributed within the central nervous system, but historically much research has been focused on hypothalamic galanin systems including those in the preoptic area, paraventricular nucleus (PVN), supraoptic nucleus (SON), and median eminence. In early studies, galanin mRNA, immunoreactivity, and binding sites were detected in neurons of the SON and both the magnocellular and parvocellular regions of the PVN, all of which also contain vasopressin, oxytocin, and several other peptides. This article briefly reviews some important recent studies of the electrophysiologic effects of galanin on magno-cellular neurons in vitro; regulation of galanin expression by the physiologic stimulus of lactation; the role of parvocellular galanin systems in energy balance, body weight, and obesity; and the regional and cellular localization of galanin and galanin receptor mRNAs in the PVN/SON. In relation to the latter issue, two distinct galanin receptor subtypes, GalR1 and GalR2, have now been cloned and characterized. In situ hybridization histochemical studies of rat brain by several groups have consistently demonstrated GalR1 mRNA in the SON and PVN, in the magnocellular and parvocellular regions. By contrast, our recent experiments using [35S]-labeled oligonucleotide probes detected GalR2 mRNA enriched in the parvocellular, not the magnocellular regions of the PVN, and the transcripts were not detected in the SON, whereas studies by other using a digoxigenin-labeled RNA probe have detected GalR2 mRNA in the SON (and PVN). Nonetheless, given the known effects of hyperosmotic stimuli, changes in metabolic status, and various hormones on galanin synthesis and release and the ability of galanin to regulate the electrical and secretory activity of magnocellular neurons, it will be of interest to determine any possible (differential) regulation of galanin receptor subtype expression and the pre- and postsynaptic roles of GalR1 and GalR2 receptors in magnocellular and parvocellular neurons.
Gamma secretase inhibition promotes hypoxic necrosis in mouse pancreatic ductal adenocarcinoma (2012)

Pancreatic ductal adenocarcinoma (PDA) is a highly lethal disease that is refractory to medical intervention. Notch pathway antagonism has been shown to prevent pancreatic preneoplasia progression in mouse models, but potential benefits in the setting of an established PDA tumor have not been established. We demonstrate that the gamma secretase inhibitor MRK003 effectively inhibits intratumoral Notch signaling in the KPC mouse model of advanced PDA. Although MRK003 monotherapy fails to extend the lifespan of KPC mice, the combination of MRK003 with the chemotherapeutic gemcitabine prolongs survival. Combination treatment kills tumor endothelial cells and synergistically promotes widespread hypoxic necrosis. These results indicate that the paucivascular nature of PDA can be exploited as a therapeutic vulnerability, and the dual targeting of the tumor endothelium and neoplastic cells by gamma secretase inhibition constitutes a rationale for clinical translation.
L-Type Amino Acid Transporter 1 (LAT1) Expression in Canine Mammary Gland Tumors (2012)

L-type amino acid transporter 1 (LAT1), an isoform of amino acid transport system L, transports branched or aromatic amino acids essential for fundamental cellular activities such as cellular growth, proliferation and maintenance. This amino acid transporter recently has received attention because of its preferential and up-regulated expression in a variety of human tumors, in contrast to its limited distribution and low-level expression in normal tissues. In this study, to explore the feasibility of using LAT1 expression as a molecular marker in mammary gland tumors (MGT), we performed a comparative study of LAT1 expression at the mRNA and protein levels in normal mammary gland cells and tumor cells. Conventional RT-PCR and Western blotting were performed on MGT tissues from 16 dogs and normal organs from nine healthy dogs. LAT1 expression was detected in ten of the 16 MGT patients. As is the case in human tissues, LAT1 showed limited expressional distribution in normal canine organs. For quantitative expressional comparison, extensive real-time RT-PCR was performed on mRNA samples from 53 MGT patients. The comparison demonstrated that LAT1 mRNA levels from MGT tissues were 20 times higher than those in normal mammary gland tissues. Additionally, histologically invasive MGT showed a higher expression of LAT1 than non-invasive tumors. These findings suggest that LAT1 could be a clinical marker and therapeutic target for invasive malignant MGT.
Analogues of LNA (Locked Nucleic Acid): Synthesis of the 2′-Thio-LNA Ribothymidine and 5-Methylcytidine Phosphoramidites (2004)

The bicyclic 2′-thio-LNA ribothymidine phosphoramidite (13) has been synthesised using a strategy making the synthesis of 2′-thio-LNA convergent with the syntheses of LNA and 2′-amino-LNA. The key step was the formation of anhydro-nucleoside 4 that prevented unwanted oxetane (3) formation during debenzylation of the 3′-OBn group, while concomitantly furnishing the necessary inversion of configuration at the C2′ position. No oxetane was observed even under basic conditions. We believe that this is due to the rigid tricyclic anhydro-nucleoside limiting the conformational freedom of the furanose, thereby preventing the formation of a strained tetracyclic system. After removal of the benzyl protection group the liberated 3′-OH group (5) was easily benzoylated (6) and the anhydro-nucleoside ring opened to give the threo configured nucleoside 7. The 2′-thio-LNA ribothymidine phosphoramidite was synthesised in 9 steps from anhydro-nucleoside 4 in 30% yield. The 2′-thio-LNA 5-methylcytidine phosphoramidite was synthesised from nucleoside 12 using standard protocols.
Cementum and Periodontal Wound Healing and Regeneration (2002)

The extracellular matrix (ECM) of cementum resembles other mineralized tissues in composition; however, its physiology is unique, and it contains molecules that have not been detected in other tissues. Cementum components influence the activities of periodontal cells, and they manifest selectivity toward some periodontal cell types over others. In light of emerging evidence that the ECM determines how cells respond to environmental stimuli, we hypothesize that the local environment of the cementum matrix plays a pivotal role in maintaining the homeostasis of cementum under healthy conditions. The structural integrity and biochemical composition of the cementum matrix are severely compromised in periodontal disease, and the provisional matrix generated during periodontal healing is different from that of cementum. We propose that, for new cementum and attachment formation during periodontal regeneration, the local environment must be conducive for the recruitment and function of cementum-forming cells, and that the wound matrix is favorable for repair rather than regeneration. How cementum components may regulate and participate in cementum regeneration, possible new regenerative therapies using these principles, and models of cementoblastic cells are discussed.
deltex, a locus interacting with the neurogenic genes, Notch, Delta and mastermind in Drosophila melanogaster. (1990)

Abstract The Notch locus of Drosophila melanogaster, which codes for a transmembrane protein sharing homology with the mammalian epidermal growth factor, is one of a small number of zygotically acting genes, the so called neurogenic loci, which are necessary for the correct segregation of neural from epidermal lineages during embryogenesis. In an attempt to identify genes whose products may interact with that of Notch, we designed a genetic screen aimed at identifying suppressors of certain Notch mutations which are known to affect the extracellular epidermal growth factor homologous domain of Notch. Mutations in two neurogenic loci were identified as suppressors: Delta, whose product was recently shown to interact with Notch and mastermind. In addition, a third, X-linked gene was shown capable of acting as a suppressor. We show that this gene is the deltex locus, characterize the phenotype of deltex mutations, and demonstrate both a maternal and zygotic action of the locus. All deltex alleles behave as recessive viables affecting wing, ocellar and eye morphology. There are allele specific interactions between deltex and various Notch alleles; for example, deltex mutants with a reduced dosage of wild-type Notch die as pupae. deltex also interacts with Delta and mastermind in a fashion that is formally analogous to its interaction with Notch. These results emphasize the special relationship between Notch, Delta and mastermind suggested by previous work and indicate that deltex is likely to play an important role in the same genetic circuitry within which these three neurogenic loci operate.
Fries Reaction. Part-XII: Preparation of Hydroxydiarylsulphones (1976)

University Department of Chemistry, Saurashtra University, Bhavnagar. <em>Manuscript received 11 December 1975 ; revised 6 April 1976, accepted 8 April 1976.</em> A few Hydroxyarylsulphones have been prepared by the Fries migration of the aryl-\(p\)-chloro­benzenesulphonates of phenol, \(o\)-cresol, \(m\)-cresol, \(o\)-chlorophenol, \(o\)-nitrophenol, \(a\)-naphthol in absence of solvent at elevated temperatures (130<sup>°</sup>-140<sup>°</sup>). The type of isomer (ortho or pare) has been supported by ultra-violet spectra study.
Workflow and process synchronization with interaction expressions and graphs (2002)

Current workflow management technology does not provide adequate means for inter-workflow coordination as concurrently executing workflows are considered completely independent. While this simplified view might suffice for one application domain or the other, there are many real-world application scenarios where workflows, though independently modeled in order to remain comprehensible and manageable, are semantically interrelated. As pragmatical approaches, like merging interdependent workflows or inter-workflow message passing, do not satisfactorily solve the inter-workflow coordination problem, interaction expressions and graphs are proposed as a simple yet powerful formalism for the specification and implementation of synchronization conditions in general and inter-workflow dependencies in particular. In addition to a graph based semi-formal interpretation of the formalism, a precise formal semantics, an equivalent operational semantics, an efficient implementation of the latter, and detailed complexity analyses have been developed, allowing the formalism to be actually applied to solve real-world problems like inter-workflow coordination.
Spectral observations of the extreme ultraviolet background (1991)

A grazing incidence spectrometer was designed to measure the diffuse extreme ultraviolet background. It was flown on a sounding rocket, and data were obtained on the diffuse background between 80 and 650 angstroms. These are the first spectral measurements of this background below 520 angstroms. Several emission features were detected, including interplanetary He I 584 angstroms emission and geocoronal He II 304 angstroms emission. Other features observed may originate in a hot ionized interstellar gas, but if this interpretation is correct, gas at several different temperatures is present. The strongest of these features is consistent with O V emission at 630 angstroms. This emission, when combined with upper limits for other lines, restricts the temperature of this component to 5.5 < log T < 5.7, in agreement with temperatures derived from O VI absorption studies. A power-law distribution of temperatures is consistent with this feature only if the power-law coefficient is negative, as is predicted for saturated evaporation of clouds in a hot medium. In this case, the O VI absorption data confine the filling factor of the emission of f < or = 4% and the pressure to more than 3.7 x 10(4) cm-3 K, substantially above ambient interstellar pressure. Such a pressure enhancement has been predicted for clouds undergoing saturated evaporation. Alternatively, if the O V emission covers a considerable fraction of the sky, it would be a major source of ionization. A feature centered at about 99 angstroms is well fitted by a cluster of Fe XVIII and Fe XIX lines from gas at log T = 6.6-6.8. These results are consistent with previous soft X-ray observations with low-resolution detectors. A feature found near 178 angstroms is consistent with Fe X and Fe XI emission from gas at log T = 6; this result is consistent with results from experiments employing broad-band soft X-ray detectors.
The molecular biology and functions of the granulocyte-macrophage colony-stimulating factors (1986)

Rapid progress has occurred recently in characterizing the molecular nature of the specific glycoprotein colony-stimulating factors (CSFs) controlling the proliferation; and some functional activities of granulocytes and monocyte-macrophages. All four known murine CSFs have been purified, and cDNAs for two have been cloned and expressed by mammalian and bacterial cells. Similarly, three human CSFs have been purified, and cDNAs for two cloned and expressed. This work has opened up the exciting prospects of testing the effects of these recombinant CSFs on hematopoiesis in vivo. Each CSF has a broader range of hematopoietic target cells than previously suspected, and it is now clear that the CSFs are not simply proliferative stimuli but can also regulate the functional activity of mature cells. There are increasing reasons to believe that these CSFs will be useful therapeutic agents in stimulating hematopoietic regeneration in leukopenic states and the functional activity of granulocytes and monocytes in infections.
<title>Early detection of Internet worm activity by metering ICMP destination unreachable messages</title> (2002)

Early warning of active worm propagation over the Internet is of vital importance to first responders. Knowing an active worms characteristics very early in its propagation can significantly reduce the damage it may cause. In this paper we propose an early warning system that uses ICMP Destination Unreachable (ICMP-T3) messages to identify the random scanning behavior of worms. Participating routers across the Internet send Blind Carbon Copies of all their locally generated ICMP-T3 messages to a central collection point. There all the incoming messages are compared for similarities. Incoming messages are abstracted and patterns identified. Using the methods discussed in this paper we identify 'blooms' of activity that are a clear signature of worm propagation. Preliminary test results have shown that actively spreading worms can be identified in the first few minutes after they are launched. By using the characteristics gathered in those early stages, action can be taken and widespread damage might be avoided.
Design, Synthesis, and Biological Evaluation of New Inhibitors of the Endocannabinoid Uptake:  Comparison with Effects on Fatty Acid Amidohydrolase (2003)

A new series of arachidonic acid derivatives were synthesized and evaluated as inhibitors of the endocannabinoid uptake. Most of them are able to inhibit anandamide uptake with IC(50) values in the low micromolar range (IC(50) = 0.8-24 microM). In general, the compounds had only weak effects upon CB(1), CB(2), and VR(1) receptors (K(i) > 1000-10000 nM). In addition, there was no obvious relationship between the abilities of the compounds to affect anandamide uptake and to inhibit anandamide metabolism by fatty acid amidohydrolase (FAAH; IC(50) = 30-113 microM). This indicates that the compounds do not exert their effects secondarily to FAAH inhibition. It is hoped that these compounds, particularly the most potent in this series (compound 5, UCM707, with IC(50) values for anandamide uptake and FAAH of 0.8 and 30 microM, respectively), will provide useful tools for the elucidation of the role of the anandamide transporter system in vivo.