gebhart/patrepeval huggingface dataset:
Through Bit Logging: A New Method To Acquire Log Data, And A First Step On The Road To Through Bore Drilling (2004)

Through Bit Logging (TBL) has been developed over the last few years by Shell and Reeves Oilfield Services (together with industry partners) as a cost-effective and operationally efficient alternative to standard wireline conveyance and LWD. In the new system the logging tools are conveyed via the drillstring and pass into open hole through a specially designed bit, with formation evaluation data being acquired with wireline tools for surface readout, or with memory tools while tripping drill pipe out of the well. The Reeves logging tools are latest technology, small diameter (2.25-inch OD) oilfield tools with low power consumption suitable for both wireline and batterymemory operations. They have completed 17,000 nonTBL operations, providing mainly quad-combo data. Reeves also have a 2.4-inch OD formation pressure tester which is run through the bit on wireline for realtime pressure evaluation. The TBL method has been tested in a number of semivertical wells drilled by Shell, and is ready for commercial use. It saves tripping time, reduces open hole exposure, and is particularly well suited as a lowcost solution for difficult well environments. The next stage is now under development with industry partners. Through Bore Drilling (TBD) uses a drilling assembly with directional drilling and MWD functionality that has a through bore capability to allow tools to be deployed, and other operations to be carried out. TBD is particularly well suited to deviated, horizontal, and extended reach wells where trip-time costs and risks are particularly significant. TBD is an entirely new approach in which the drilling assembly and bit provide more than the drilling function - they are a conduit and a gateway to the borehole and formation. Through this gateway it is possible to perform various operations, including (but not limited to) logging and placement of cement. This can be likened to laparoscopic (keyhole) operations in the medical world, where numerous functions are carried out through a simple conduit brought into place once only. The paper summarises the TBL method and trials to date, and discusses the latest developments around the Through Bore Drilling system.
Improved analysis of the outage performance in cellular systems (2002)

The performance of cellular systems is studied, in terms of average and worst-case outage probability. The approach is based on a new analysis which allows one to take into account the assignment of a mobile to the most favorable cell site, instead of the closest one. Other features, such as power control and diversity, are included, and the sensitivity of the performance to the fading parameter is studied. The study of the outage performance of the TDMA cellular system can be used for the computation of the interference statistics, by taking into account features such as log-normal shadowing, deterministic path loss, power control and best cell site selection.
The Punaglandins: 10-Chloroprostanoids from the Octocoral Telesto riisei (1994)

Telesto riisei, an octocoral from Hawaii, produces nineteen highly functionalized prostanoids, the punaglandins, which are characterized by various oxygenation at C-5, -6, -7, and -12, and a 10-chloro-9-cyclopentenone moiety. The absolute stereochemistry of the 10-chloroprostanoids is epimeric to that of the Pacific marine prostanoids without halogen. The punaglandins have shown anti-inflammatory and antitumor activity. A synthetic 10-thiomethyl derivative enhances in vivo mineralization in human osteoblasts.
Comprehensive feature analysis for sample classification with comprehensive two‐dimensional LC (2010)

Comprehensive two-dimensional LC (LC x LC) is a powerful tool for analysis of complex biological samples. With its multidimensional separation power and increased peak capacity, LC x LC generates information-rich, but complex, chromatograms, which require advanced data analysis to produce useful information. An important analytical challenge is to classify samples on the basis of chromatographic features, e.g., to extract and utilize biomarkers indicative of health conditions, such as disease or response to therapy. This study presents a new approach to extract comprehensive non-target chromatographic features from a set of LC x LC chromatograms for sample classification. Experimental results with urine samples indicate that the chromatographic features generated by this approach can be used to effectively classify samples. Based on the extracted features, a support vector machine successfully classified urine samples by individual, before/after procedure, and concentration with leave-one-out and replicate K-fold cross-validation. The new method for comprehensive chromatographic feature analysis of LC x LC separations provides a potentially powerful tool for classifying complex biological samples.
Short prokaryotic Argonautes provide defence against incoming mobile genetic elements through NAD <sup>+</sup> depletion (2021)

Argonaute (Ago) proteins are found in all three domains of life. The so-called long Agos are composed of four major domains (N, PAZ, MID, and PIWI) and contribute to RNA silencing in eukaryotes (eAgos) or defence against invading mobile genetic elements in prokaryotes (pAgos). The majority (~60%) of pAgos identified bioinformatically are shorter (comprised of only MID and PIWI domains) and are typically associated with Sir2, Mrr or TIR domain-containing proteins. The cellular function and mechanism of short pAgos remain enigmatic. Here, we show that Geobacter sulfurreducens short pAgo and the NAD + -bound Sir2-protein form a stable heterodimeric complex. The GsSir2/Ago complex presumably recognizes invading plasmid or phage DNA and activates the Sir2 subunit, which triggers endogenous NAD + depletion and cell death, and prevents the propagation of invading DNA. We reconstituted NAD + depletion activity in vitro and showed that activated GsSir2/Ago complex functions as a NADase that hydrolyses NAD + to ADPR. Thus, short Sir2-associated pAgos provide defence against phages and plasmids and underscores the diversity of mechanisms of prokaryotic Agos.
From a Binary to a Quaternary Cocrystal: An Unusual Supramolecular Synthon (2019)

Abstract Formation of a stoichiometric quaternary cocrystal consisting of resorcinol ( RES ), tetramethylpyrazine ( TMP ), phenazine ( PHE ) and pyrene ( PYR ) is described. A closed tetrameric resorcinol‐heterocycle synthon, unusual in that it has two different linker bases rather than just one, is observed in this four‐component solid. The tetrameric synthon is formed by two RES molecules and the two pyridine bases TMP and PHE . The stoichiometric quaternary cocrystal grows in an epitaxial fashion on the surfaces of a RES.PHE binary cocrystal which is initially obtained from the mother liquor. By indexing the common crystal faces of the binary and quaternary cocrystals, and noting that no ternary solid is obtained, a plausible mechanism has been proposed for the formation of this rare supramolecular architecture.
Similarity Retrieval of Drawings and Its Application to Plant Control and Maintenance (1994)

We are developing a drawing image database system that stores plant diagrams. The system scans, recognizes and stores plant diagrams. Users can then refer to any parts of the diagrams according to their needs.Similarity retrieval, a retrieval where users show sample diagrams to describe what they want, is realized by defining a similarity measure between drawing images. The measure is based on graph representations of drawing images and it is effective for retrieval of drawing images that describe logical meaning by their structure.In this paper, a fast retrieval method that features two-level matching between graph representations is proposed. By combining rough matching and detailed matching, the average response time is reduced to 2.8 seconds, which is about one sixth of the former method. It is confirmed that the response time is adequate for applications at plant control and maintenance.
Fragmentation of the Lamellae and Fractionation of Polymer Coils upon Mixing Poly(dimethylacrylamide) with the Lamellar Phase of Aerosol OT in Water (2005)

The lamellar mesophase formed by surfactant 1,4-bis(2-ethylhexyl) sodium sulfosuccinate (AOT) in deuterated water is mixed with poly(dimethylacrylamide) (PDMAA) polymers of low molecular weight (Mn= (2-20) x 10(3)). The mixtures separate into microphases (lamellar plus isotropic polymer solution). Their microstructures are studied by microscopy, small-angle X-ray scattering (SAXS), and deuterium NMR (2H NMR). According to SAXS, the lamellar phase fractionates the molecular weight distribution of the polymer, by dissolving only chains with coil sizes smaller than the thickness of the water layers between lamellae, and keeping larger chains segregated from the lamellar phase. The fraction of polymer that is segregated from the lamellar phase grows with Mn of the polymer. In 2H NMR, there are two signals, a quadrupolar doublet (water molecules hydrating the anisotropic lamellar phase contribute to this doublet) and a singlet (water molecules in the isotropic polymer solution contribute to this singlet). These two signals are deconvoluted to analyze the phases. Mixing with the polymer produces the partial dispersion of the lamellar phase into small fragments (microcrystallites). The structure of these microcrystallites is such that they conserve the regular long period spacing of the macrophase, and are thus identified in SAXS, but they are smaller than the minimum size required to produce quadrupolar splitting (about 4 microm), and therefore, in 2H NMR, they contribute to the singlet. 2H NMR can thus not distinguish between small microcrystallites and an isotropic polymer solution segregated from the lamellar phase; instead small microcrystallites are detected as an apparent increase of the isotropic solution. The degree of dispersion produced by the polymer in the lamellar phase is correlated with the degree of segregation that the polymer suffers. Thus, much greater dispersion into microcrystallites is produced by the higher Mn polymers than by the lower Mn polymers (in the range covered by the present samples, although with a much higher molecular weight sample (3 x 10(6)) that is totally segregated no such microcrystallites were detected).
Failure of physiologic doses of pure UVA or UVB to induce lesions in photosensitive cutaneous lupus erythematosus: implications for phototesting (2006)

The potential role of wavelengths outside the UVA and UVB range in the photo-induction of cutaneous lupus skin lesions needs to be investigated, and there is a need to standardize phototesting equipment and procedures for patients with cutaneous lupus erythematous.
TSLP Promotes Induction of Th2 Differentiation but Is Not Necessary during Established Allergen-Induced Pulmonary Disease (2013)

Thymic stromal lymphopoietin (TSLP) has been implicated in the development of allergic inflammation by promoting Th2-type responses and has become a potential therapeutic target. Using in vitro T cell differentiation cultures we were able to validate that TSLP played a more critical role in the early development of Th2 immune responses with less significant enhancement of already developed Th2 responses. Adoptive transfer of naive DO11.10 ovalbumin-specific T cells followed by airway exposure to ovalbumin showed an early impairment of Th2 immune response in TSLP-/- mice compared to wild type mice during the development of a Th2 response. In contrast, transfer of already differentiated Th2 cells into TSLP-/- mice did not change lung pathology or Th2 cytokine production upon ovalbumin challenge compared to transfer into wild type mice. An allergen-induced Th2 airway model demonstrated that there was only a difference in gob5 expression (a mucus-associated gene) between wild type and TSLP-/- mice. Furthermore, when allergic animals with established disease were treated with a neutralizing anti-TSLP antibody there was no change in airway hyperreponsiveness (AHR) or Th2 cytokine production compared to the control antibody treated animals, whereas a change in gob5 gene expression was also observed similar to the TSLP-/- mouse studies. In contrast, when animals were treated with anti-TSLP during the initial stages of allergen sensitization there was a significant change in Th2 cytokines during the final allergen challenge. Collectively, these studies suggest that in mice TSLP has an important role during the early development of Th2 immune responses, whereas its role at later stages of allergic disease may not be as critical for maintaining the Th2-driven allergic disease.
Towards the scalable implementation of a user level anomaly detection system (2003)

Traditional intrusion detection systems can be broadly classified as misuse and anomaly detectors. Misuse detectors attempt detection by matching the current system/user activity against known signatures and patterns. As opposed to this, anomaly detection works by developing a reference graph and comparing the ongoing activity against it. Any significant deviation is flagged as an intrusion. Anomaly detection is more promising because of its potential to detect unseen types of attacks. However, both techniques have conventionally relied on audit trails sampled deep inside the system via probes and the sheer size of the data allows only after-the-fact and off line detection. In recent past, there have been efforts to capture the semantics of system activity for more rapid detection and this can typically be done at levels closer to the user. In our earlier works related to this effort, we presented a scheme and a reasoning framework to detect intrusions based on the encapsulated user intent. This paper addresses the scalability and implementation aspects of the system by introducing concepts such as workspaces and meta-operations. Although this security system is a general anomaly detection system, it is amenable to operator fault recovery. While encryption provides secure communication channels, it leaves the end points exposed. Our security system has the additional capability of handling insider attacks relevant in this context.
Gender Difference of Circulating Ghrelin and Leptin Concentrations in Chronic <i>Helicobacter pylori</i> Infection (2009)

There should be a gender difference to circulating total ghrelin levels, but not leptin levels, in response to H. pylori infection and its related chronic gastritis.
Supplementary Table 1 from Synthesis and biological analysis of new curcumin analogues bearing an enhanced potential for the medicinal treatment of cancer (2023)

Supplementary Table 1 from Synthesis and biological analysis of new curcumin analogues bearing an enhanced potential for the medicinal treatment of cancer
Gordonia crocea sp. nov. and Gordonia spumicola sp. nov. isolated from sludge of a wastewater treatment plant (2020)

Two novel actinobacteria, designated NBRC 107696<sup>T</sup> and NBRC 107697<sup>T</sup>, were isolated from sludge samples from a wastewater treatment plant and their taxonomic positions were investigated by a polyphasic approach. The cells of the strains were aerobic, rod-shaped, non-motile and non-endospore-forming. The strains contained glutamic acid, alanine and <i>meso</i>-diaminopimelic acid in the peptidoglycan. Galactose and arabinose were detected as cell-wall sugars. The predominant menaquinone was identified as MK-9(H<sub>2</sub>) and the major fatty acids were C<sub>16 : 0</sub>, C<sub>18 : 1</sub>ω9c and C<sub>16 : 1</sub>ω7c. The DNA G+C contents of NBRC 107696<sup>T</sup> and NBRC 107697<sup>T</sup> were 68.07 and 68.99 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequence comparisons revealed that NBRC 107696<sup>T</sup> and NBRC 107697<sup>T</sup> were a clade with members of the genus <i>Gordonia</i>. The highest 16S rRNA gene sequence similarity values were obtained with <i>Gordonia araii</i> IFM 10211<sup>T</sup> (98.9 %) for NBRC 107697<sup>T</sup>, and <i>Gordonia malaquae</i> IMMIB WWCC-22<sup>T</sup>, <i>Gordonia neofelifaecis</i> AD-6<sup>T</sup> and <i>Gordonia humi</i> CC-12301<sup>T</sup> (98.1 %) for NBRC 107696<sup>T</sup>, respectively. The digital DNA-DNA relatedness data coupled with the combination of genotypic and phenotypic data indicated that the two strains are representatives of two novel separate species. The names proposed to accommodate these two strains are <i>Gordonia spumicola</i> sp. nov. and <i>Gordonia crocea</i> sp. nov., and the type strains are NBRC 107696<sup>T</sup> (=IFM 10067<sup>T</sup>=TBRC 11239<sup>T</sup>) and NBRC 107697<sup>T</sup> (=IFM 10881<sup>T</sup>=TBRC 11240<sup>T</sup>), respectively.
Relation of Intracellular K+ and Steroidogenesis in Isolated Adrenal Zona Glomerulosa and Fasciculata Cells (1975)

1. Intracellular K+ content, water spaces and corticosterone output were measured in isolated zona glomerulosa and zona fasciculata-reticularis cell suspensions of rat adrenal cortex, after incubation in vitro under conditions designed to alter steroidogenesis. 2. Intracellular K+ of unpurified zona glomerulosa cells was not altered after stimulation of corticosterone output with serotonin. Similarly, with zona glomerulosa cells purified by unit gravity sedimentation, no change in intracellular K+ was detected after stimulation of steroidogenesis with serotonin or angiotensin II. 3. In high-potassium medium (final concentration 8.4 mmol/1), parallel increases in intracellular K+ and corticosterone output were observed with both purified zona glomerulosa cells. However, a similar increase in intracellular K+ also occurred in high-potassium medium with zona fasciculata cells, whose steroid output is unresponsive to external potassium concentration ([K+]). 4. Ouabain at 10(-5) mol/1 depressed the intracellular [K+] of glomerulosa cells but did not alter basal or stimulated corticosterone output. Similar results were obtained with fasciculata cells. 5. Ouabain at 5 times 10(-4) mol/1 further depressed intracellular [K-+] of glomerulosa cells and inhibited basal and stimulated corticosterone output. However, this concentration of ouabain also inhibited steroidogenesis in fasciculata cells. 6. These results demonstrate a variety of situations where changes in intracellular [K+] are dissociated from those in corticosterone output and indicate that intracellular [K+] cannot be the sole mechanism regulating steroidogenesis under these conditions.
Restoration of dopamine transporter density in the striatum of fetal ventral mesencephalon-grafted, but not sham-grafted, MPTP-treated parkinsonian monkeys (1996)

Transplantation of fetal dopamine neurons to the adult striatum potentially offers a means to reverse the striatal dopamine deficiency that characterizes Parkinson's disease. Many investigations in rodents have supported the hope that neural grafting may be a useful treatment for parkinsonism. However, clinical studies have generally produced more modest improvements in motor abnormalities than observed in lower species. It is possible that the number of fetal dopamine neurons that survive transplantation is insufficient to restore dopaminergic innervation of the large human striatum to a level where striking recovery is obtained. In fact, there has been no quantitative study of graft outgrowth to indicate what portion of the dopamine-depleted striatum might be reinnervated with present techniques. Furthermore, it has been speculated that regeneration of the host dopamine system in response to the implantation surgery may play an important role in the beneficial effects of neural grafting in primates. The present study used nine 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated parkinsonian monkeys to investigate these issues. Sham implantation procedures produced no increase in either dopamine transporter density (measured by quantitative autoradiography) or tissue dopamine concentration (measured by HPLC) in the striatum of MPTP-treated monkeys. In sham-grafted and nonimplanted MPTP-treated monkeys, the striatal dopamine concentration was reduced by 99%, based on analysis of 16 sampled sites in the caudate nucleus and putamen of each monkey. No behavioral recovery was seen in the sham-grafted and nonimplanted MPTP-treated groups. In contrast, transplantation of fetal dopamine neurons to the caudate nucleus or putamen of MPTP-treated monkeys resulted in a significant elevation of dopamine transporter density and dopamine levels in the grafted striatal nucleus. Each grafted MPTP-treated monkey received ventral mesencephalon dopamine neurons from one donor harvested during putative neurogenesis. Donor ventral mesencephalon was divided equally and implanted into six sites either in the caudate nucleus or putamen. One graft site in each monkey was examined by dopamine transporter autoradiography. In sections in which graft fibers were present, a mean of one-third of the volume of the grafted nucleus was occupied by an elevated density of dopamine transporters. This increase in dopamine transporter density was defined to be at least 5-10% of the control density. However, full behavioral recovery was not observed in the grafted MPTP-treated group. These data provide no support for the hypothesis that regeneration of the host dopamine system occurs in response to a sham implantation procedure in severely parkinsonian monkeys. The current study illustrates the power of the applied techniques for delineating the relationship between the level of host dopamine depletion, the extent of graft-induced dopaminergic restoration, and behavioral recovery.
Shifts in Vedolizumab Utilization Across the United States Are Associated With Improved Outcomes (2018)

Introduction: Early experiences after initial availability of drugs are impacted by use in high-risk or refractory patients waiting for alternative therapies (“warehouse effect”). This study aimed to compare treatment pattern and treatment outcomes with vedolizumab (VDZ) over time after launch. Methods: A time-trend analysis was performed with 2 data sets: 1) VICTORY consortium (n=1,087), a multicenter, tertiary referral center, collaborative cohort study for VDZ use in routine practice, and 2) Truven MarketScan Database (n=2,574), a nationally representative claims database. Time of VDZ treatment initiation was grouped into 2 periods: first 12 months of VDZ launch (Era 1; May 2014-June 2015), and subsequent 24 months (Era 2; July 2015-June 2017). Consortium outcomes assessed were 12-month cumulative rates for clinical remission (CREM; resolution of disease-related symptoms) and mucosal healing (MH; Mayo endoscopic subscore of 0 or 1 for ulcerative colitis [UC], absence of ulcers or erosions for Crohn's disease [CD]). Truven outcomes assessed were 12-month rates for inflammatory bowel disease (IBD)-related hospitalization and surgery. Results: Era 2 UC and CD patients were more often biologic naive in both VICTORY and Truven data sets (Table 1). In the VICTORY cohort, Era 2 CD patients had higher 12-month cumulative rates of CREM (40% vs 31%; P=0.03) and MH (58% vs 42%; PPP=0.006). This trend was not seen for CD in the Truven cohort for IBD-related hospitalization (16.6% vs 14.6%; P=0.46) or IBD-related surgery (16.8% vs 17.8%; P=0.71). Conclusion: There has been a shift in positioning of VDZ over the past 3 years toward using VDZ in less refractory patients, with a more pronounced shift toward early use in UC than in CD. This shift was accompanied by lower rates of IBD-related hospitalization and surgery for UC. For CD, although clinical practice data would suggest improved clinical outcomes over time, we did not observe a significant shift in IBD-related hospitalization or surgery. Further studies are needed to understand whether early VDZ use in CD impacts disease-related complications.583 Figure 1. Baseline Demographics