gebhart/patrepeval huggingface dataset:
Short Radius Drilling Technology Utilizing Mobile Service/Workover Rig (1989)

Abstract The paper will discuss a multi-well, short radius lateral drilling project in a gas producing shale formation in northern Michigan. A description of short radius drilling tools and associated equipment, and the mobile service rig and auxiliary equipment will be presented. Drilling and completion procedures including mobilization, de-mobilization, rig-up and rig-down will be summarized, along with graphical representations of time curves, cost curves and directional section profiles. The benefits of packaging multiple services and how it may apply to establishment and development of a learning curve will be evaluated. Limitations of both the short radius lateral equipment, and the mobile service rig will be reviewed, along with available optional equipment that is compatible with both systems. The economics of utilizing a mobile service rig versus a conventional drilling rig will be discussed.
Pre-processing Agilent microarray data (2007)

Simple loess normalization without background subtraction resulted in low variance fold changes that more reliably ranked gene expression than the other methods. While t-statistics and other measures that take variation into account, including Agilent's z-statistic, can also be used to reliably select differentially expressed genes, fold changes are a standard measure of differential expression for exploratory work, cross platform comparison, and biological interpretation and can not be entirely replaced. Although dye effects are small for most genes, many array features are affected. Therefore, an experimental design that incorporates dye swaps or a common reference could be valuable.
Pharmacokinetics and Distribution of [35S]Methylsulfonylmethane following Oral Administration to Rats (2007)

Methylsulfonylmethane (MSM) is a sulfur-containing compound found in a wide range of human foods including fruits, vegetables, grains, and beverages. More recently, it has been marketed as a dietary supplement worldwide. The objective of this study was to evaluate the pharmacokinetic profile and distribution of radiolabeled MSM in rats. Male Sprague-Dawley rats were administered a single oral dose of [35S]MSM (500 mg/kg), and blood levels of radioactivity were determined at different time points for up to 48 h. Tissue levels of radioactivity at 48 and 120 h and urine and fecal radioactivity levels were measured at different time points for up to 120 h following [35S]MSM administration to rats. Oral [35S]MSM was rapidly and efficiently absorbed with a mean tmax of 2.1 h, Cmax of 622 microg equiv/mL, and AUC0-inf of 15124 h.microg equiv/mL. The t1/2 was 12.2 h. Soft tissue distribution of radioactivity indicated a fairly homogeneous distribution throughout the body with relatively lower concentrations in skin and bone. Approximately 85.8% of the dose was recovered in the urine after 120 h, whereas only 3% was found in the feces. No quantifiable levels of radioactivity were found in any tissues after 120 h, indicating complete elimination of [35S]MSM. The results of this study suggest that [35S]MSM is rapidly absorbed, well distributed, and completely excreted from the body.
Usefulness of procalcitonin for diagnosis of sepsis in the intensive care unit (2002)

In the present study PCT was found to be a more accurate diagnostic parameter for differentiating SIRS and sepsis, and therefore daily determinations of PCT may be helpful in the follow up of critically ill patients.
Structure of β-Ketoacyl-[acyl carrier protein] Reductase from Escherichia coli:  Negative Cooperativity and Its Structural Basis, (2001)

The structure of beta-ketoacyl-[acyl carrier protein] reductase (FabG) from Escherichia coli was determined via the multiwavelength anomalous diffraction technique using a selenomethionine-labeled crystal containing 88 selenium sites in the asymmetric unit. The comparison of the E. coli FabG structure with the homologous Brassica napus FabG.NADP(+) binary complex reveals that cofactor binding causes a substantial conformational change in the protein. This conformational change puts all three active-site residues (Ser 138, Tyr 151, and Lys 155) into their active configurations and provides a structural mechanism for allosteric communication between the active sites in the homotetramer. FabG exhibits negative cooperative binding of NADPH, and this effect is enhanced by the presence of acyl carrier protein (ACP). NADPH binding also increases the affinity and decreases the maximum binding of ACP to FabG. Thus, unlike other members of the short-chain dehydrogenase/reductase superfamily, FabG undergoes a substantial conformational change upon cofactor binding that organizes the active-site triad and alters the affinity of the other substrate-binding sites in the tetrameric enzyme.
On Combinatorial DNA Word Design (2001)

We consider the problem of designing DNA codes, namely sets of equi-length words over the alphabet [A, C, G, T] that satisfy certain combinatorial constraints. This problem is motivated by the task of reliably storing and retrieving information in synthetic DNA strands for use in DNA computing or as molecular bar codes in chemical libraries. The primary constraints that we consider, defined with respect to a parameter d, are as follows: for every pair of words w, x in a code, there are at least d mismatches between w and x if w not equal x and also between the reverse of w and the Watson-Crick complement of x. Extending classical results from coding theory, we present several upper and lower bounds on the maximum size of such DNA codes and give methods for constructing such codes. An additional constraint that is relevant to the design of DNA codes is that the free energies and enthalpies of the code words, and thus the melting temperatures, be similar. We describe dynamic programming algorithms that can (a) calculate the total number of words of length n whose free energy value, as approximated by a formula of Breslauer et al. (1986) falls in a given range, and (b) output a random such word. These algorithms are intended for use in heuristic algorithms for constructing DNA codes.
Production of plant growth substances by rhizosphere mycoflora of broad bean and cotton (1975)

The culture filtrates of the rhizosphere fungi of broad bean (Vicia faba L.) and cotton (Gossypium barbadense L.) were analysed for the presence of plant growth substances of auxin and gibberellins nature. Bioassay test and chromatographic analysis indicated that these fungi, each synthesized different auxins in their culture medium. These auxins were indole compounds. Similarly the rhizosphere fungi produced in their culture medium some gibberellins and gibberellin-like substances.
Intrinsicn-type versusp-type doping asymmetry and the defect physics of ZnO (2001)

ZnO typifies a class of materials that can be doped via native defects in only one way: either n type or p type. We explain this asymmetry in ZnO via a study of its intrinsic defect physics, including ${\mathrm{Zn}}_{\mathrm{O}},$ ${\mathrm{Zn}}_{i},$ ${\mathrm{V}}_{\mathrm{O}},$ ${\mathrm{O}}_{i},$ and ${V}_{\mathrm{Zn}}$ and n-type impurity dopants, Al and F. We find that ZnO is n type at Zn-rich conditions. This is because (i) the Zn interstitial, ${\mathrm{Zn}}_{i},$ is a shallow donor, supplying electrons; (ii) its formation enthalpy is low for both Zn-rich and O-rich conditions, so this defect is abundant; and (iii) the native defects that could compensate the n-type doping effect of ${\mathrm{Zn}}_{i}$ (interstitial O, ${\mathrm{O}}_{i},$ and Zn vacancy, ${V}_{\mathrm{Zn}}),$ have high formation enthalpies for Zn-rich conditions, so these ``electron killers'' are not abundant. We find that ZnO cannot be doped p type via native defects $({\mathrm{O}}_{i},{V}_{\mathrm{Zn}})$ despite the fact that they are shallow (i.e., supplying holes at room temperature). This is because at both Zn-rich and O-rich conditions, the defects that could compensate p-type doping ${(V}_{\mathrm{O}}{,\mathrm{}\mathrm{Zn}}_{i},{\mathrm{Zn}}_{\mathrm{O}})$ have low formation enthalpies so these ``hole killers'' form readily. Furthermore, we identify electron-hole radiative recombination at the ${V}_{\mathrm{O}}$ center as the source of the green luminescence. In contrast, a large structural relaxation of the same center upon double hole capture leads to slow electron-hole recombination (either radiative or nonradiative) responsible for the slow decay of photoconductivity.
Azathioprine/6-mercaptopurine toxicity: The role of the TPMT gene (2008)

The thiopurine drugs azathioprine (AZA) and 6-mercaptopurine (6-MP) are widely used in medicine, including inflammatory bowel diseases (IBD). Thiopurine drugs undergo S-methylation catalysed by thiopurine methyltransferase (TPMT) to methylmercaptopurine or oxidation to thiouric acid via xanthine oxidase (XO). Altered TPMT activity predominantly results from single nucleotide polymorphisms (SNPs) in the TPMT gene, which is located on chromosome 6p22.3.In the general population TPMT enzyme activity is normal in 89%, intermediate in approximately 11% and absent in approximately 0.3% of cases. The prevalence of the most frequent single nucleotide polymorphisms (SNPs) in the TPMT gene has been reported to vary worldwide. The mechanisms of AZA/6-MP action are currently unknown. Pharmacogenetics of AZA/6-MP represents an interesting field of research with direct implications in clinical practice. AZA/6- MP metabolization steps, the impact of TPMT gene SNPs on toxicity prediction as well as the 6p loci analysis represents a challenging field of research in IBD and other diseases. When possible, TPMT genotyping prior to the initiation of AZA/6-
MP should be considered to decrease the risk of severe adverse event as well as to identify patients who might benefit from higher doses. Clinicians should be aware that TPMT SNPs do not explain all leucopenic events and that TPMT measurements cannot replace the need for continued monitoring of leucocyte counts in AZA/6-MP treated patients.
A two-dimensional simulation of organic transistors (1997)

In this paper, we analyze the operation of organic thin-film transistors (TFT's) using two-dimensional (2-B) numerical simulation to: (1) validate the use of simple MOSFET theory to describe the above-threshold behavior; (2) clarify the subthreshold characteristics, and short-channel effects; and (3) illustrate the operation of organic bilayer devices. Our analysis clarifies a number of issues that can help in device design. We also point out differences between the material parameters used in Si-MOSFET and organic FET simulation, and discuss the circumstances under which a semiconductor device simulator can be used for the simulation of organic transistors.
15‐Deoxy‐Δ12,14‐prostaglandin J2 (15d‐PGJ2) protects neurons from oxidative death via an Nrf2 astrocyte‐specific mechanism independent of PPARγ (2012)

Astrocytes are critical for the antioxidant support of neurons. Recently, we demonstrated that low level hydrogen peroxide (H(2) O(2) ) facilitates astrocyte-dependent neuroprotection independent of the antioxidant transcription factor Nrf2, leaving the identity of the endogenous astrocytic Nrf2 activator to question. In this study, we show that an endogenous electrophile, 15-deoxy-Δ12,14-prostaglandin J2 (15d-PGJ2), non-cell autonomously protects neurons from death induced by depletion of the major antioxidant glutathione. Nrf2 knockdown in astrocytes abrogated 15d-PGJ2's neuroprotective effect as well as 15d-PGJ2 facilitated Nrf2-target gene induction. In contrast, knockdown of the transcription factor peroxisome proliferator activated-receptor gamma (PPARγ), a well-characterized 15d-PGJ2 target, did not alter 15d-PGJ2 non-cell autonomous neuroprotection. In addition, several PPARγ agonists of the thiazolidinedione (TZD) family failed to induce neuroprotection. Unexpectedly, however, the TZD troglitazone (which contains a chromanol moiety found on vitamin E) induced astrocyte-mediated neuroprotection, an effect which was mimicked by the vitamin E analogs alpha-tocopherol or alpha-tocotrienol. Our findings lead to two important conclusions: (i) 15d-PGJ2 induces astrocyte-mediated neuroprotection via an Nrf2 but not PPARγ mediated pathway, suggesting that 15d-PGJ2 is a candidate endogenous modulator of Nrf2 protective pathways in astrocytes; (ii) selective astrocyte treatment with analogs or compounds containing the chromanol moiety of vitamin E facilitates non-cell autonomous neuroprotection.
Salmonella invasion of nonphagocytic cells induces formation of macropinosomes in the host cell (1994)

Salmonella typhimurium induced massive uptake of extracellular fluid in epithelial cells in the form of macropinosomes. The appearance of macropinosomes in the infected cell was related to the induction of membrane ruffling during bacterial invasion. A noninvasive S. typhimurium invA mutant did not trigger such effects in the host cell. Similarly, S. typhimurium invA mutants that invaded via the invasin protein from Yersinia pseudotuberculosis or adhered to the host cell via the afimbrial AFA-I adhesin from Escherichia coli did not trigger formation of macropinosomes. In contrast to the formation of macropinosomes in macrophages, the appearance of macropinosomes in S. typhimurium-infected epithelial cells did not require microtubules. These data suggest that massive uptake of extracellular fluid in S. typhimurium-infected epithelial cells is an event related to the invasion mechanisms used by this pathogen.
High-Efficiency Millimeter-Wave Energy-Harvesting Systems With Milliwatt-Level Output Power (2016)

The output power level and the power conversion efficiency (PCE) rate of the energy-harvesting systems are vital factors in realizing effective millimeter-wave wireless power transfer solutions that can power battery-less and charge coil-free smart everyday objects. Two 60-GHz energy harvesters that use a tuned complementary cross-coupled oscillator-like rectifying circuitry in 40-nm digital CMOS process are presented. They harvest energy at power rates and peak PCE levels in excess of 1 mW and 30%. These figures are significantly higher than those of the prior art. In one design, two rectifier stages are in a cascode configuration to produce higher dc output voltage levels at the low-current regime. Novel theoretical analyses of the unique rectifying circuitry of the single-stage and two-stage cascode harvesters are presented, which formulate all of the key specifications.
EcoTILLING for the identification of allelic variation in the powdery mildew resistance genes mlo and Mla of barley (2006)

Abstract In this investigation the successful implementation of a CEL I‐based mutation detection technique for the discovery and detection of DNA polymorphism in the genes mlo and Mla of barley is described. The technique is called EcoTILLING, which is a high‐throughput method to detect and discover new point mutations and small insertions/deletions in DNA. That the method not only reveals polymorphism between different alleles but can also be used as a powerful genetic marker is demonstrated. The genes mlo and Mla are involved in the defence of barley against the fungal pathogen powdery mildew. The powdery mildew resistance gene mlo is a single copy gene, whereas multiple alleles exist at the Mla locus. With EcoTILLING it was possible to identify point mutations and deletions in each of the 11 mlo mutants tested. For Mla 25 natural barley variants were tested, and although the identification was complex due to the presence of highly similar paralogues of Mla , most of the recently identified alleles from Hordeum vulgare ssp. spontaneum were identified. This method offers the possibility to combine different mlo alleles with different Mla alleles from wild barley to obtain cultivars with more durable resistance.
[Clinical and rheological efficacy of troxerutin in obstetric gynecology]. (1991)

The success of treatment aimed at improving manifestations of venous insufficiency appears today to be closely linked to a therapeutic impact on blood viscosity and the macrorheological parameters upon which it depends. This double-blind placebo-controlled trial of troxerutine was designed to evaluate changes during treatment in rheological abnormalities in 60 women with vulval varicosities and venous insufficiency of the lower limbs, half in the context of premenstrual syndrome and half in pregnant women from the 4th month on. Initial examination revealed no significant difference between the treated and control groups from a clinical and rheological standpoint in the gynecological and obstetric categories. Analysis of results showed that a high dose of troxerutine was associated with a very marked improvement in symptomatic parameters by the first month of treatment with a significant correlation between clinical criteria and rheological parameters in pregnant women as well as in those with a premenstrual syndrome. These data were confirmed by excellent acceptability as well as subjective assessment by patients after 4 months' treatment at the dosage of 4 g/d.
The effects of N-3 polyunsaturated fatty acids on the generation of platelet-activating factor-acether by human monocytes. (1987)

Human leukocytes generate platelet-activating factor (PAF-acether), a lipid mediator of inflammation, from membrane alkyl phospholipids through the release of arachidonic acid or other fatty acids at the 2-position and subsequent acetylation. Because it was previously demonstrated that fish oil fatty acids suppress human leukocyte arachidonic acid release and metabolism, separate experiments were conducted to investigate the effects of dietary fish oil supplementation and in vitro incubation with fish oil fatty acids on calcium ionophore-stimulated PAF-acether generation in human monocytes. In subjects on their regular diets, a 4-hr incubation of monocyte monolayers with an optimally effective concentration of arachidonic acid of 1 micrograms/ml resulted in a 64% increase of calcium ionophore-induced net PAF-acether generation from 7.75 +/- 0.78 ng/10(6) cells for untreated monolayers to 12.70 +/- 1.21 ng/10(6) cells (mean +/- SEM). Treatment of monolayers with eicosapentaenoic acid (EPA) at the optimal concentration of 1 micrograms/ml decreased net PAF-acether generation by 28%. However, treatment of monocyte monolayers with docosahexaenoic acid did not appreciably affect net PAF-acether generation. The changes in PAF-acether release with each fatty acid added in vitro paralleled those in total PAF-acether generation; the percentage PAF-acether release remained unaffected. Three weeks of dietary supplementation with 18 g MaxEPA daily, providing 3.2 g EPA did not affect the PAF-acether generation of calcium ionophore-stimulated human monocyte monolayers. However, 6 weeks of dietary supplementation resulted in a 47% decrease of net total PAF-acether generation and a concomitant 59% decline in net PAF-acether release; the percentage release of PAF-acether was not affected. Thus, whether added to the diet or introduced in vitro, fish oil-derived fatty acids suppress PAF-acether generation by human monocyte monolayers.
Event Related Potentials and Time Estimation (1977)

ABSTRACT Event related potentials (ERPs) recorded from the scalp of man were studied during a time estimation task. The principal ERP correlate of mental activity associated with time estimation appeared to be a CNV wave followed by a late positive shift. Latency of CNV termination was correlated with temporal judgments. There was some evidence that the onset of CNV termination occurred prior to the estimated time of occurrence of cortical motor command signals associated with production of the temporal judgments.
Characterization of resident and migratory dendritic cells in human lymph nodes (2012)

Dendritic cells (DCs) initiate adaptive immune responses in lymph nodes (LNs). In mice, LN DCs can be divided into resident and tissue-derived populations, the latter of which migrate from the peripheral tissues. In humans, different subsets of DCs have been identified in the blood, spleen, and skin, but less is known about populations of resident and migratory tissue-derived DCs in LNs. We have analyzed DCs in human LNs and identified two populations of resident DCs that are present in all LNs analyzed, as well as in the spleen and tonsil, and correspond to the two known blood DC subtypes. We also identify three main populations of skin-derived migratory DCs that are present only in skin-draining LNs and correspond to the DC subsets found in the skin. Resident DCs subsets induce both Th1 and Th2 cytokines in naive allogeneic T lymphocytes, whereas the corresponding blood subsets failed to induce efficient Th2 polarization. LN-resident DCs also cross-present antigen without in vitro activation, whereas blood DCs fail to do so. Among migratory DCs, one subset was poor at both CD4(+) and CD8(+) T cell activation, whereas the other subsets induced only Th2 polarization. We conclude that in humans, skin-draining LNs host both resident and migratory DC subsets with distinct functional abilities.
Sequentially timed all-optical mapping photography (STAMP) utilizing spectral filtering (2015)

We propose and experimentally demonstrate a new method called SF-STAMP for sequentially timed all-optical mapping photography (STAMP) that utilizes spectral filtering. SF-STAMP is composed of a diffractive optical element (DOE), a band-pass filter, and two Fourier transform lenses. Using a linearly frequency-chirped pulse and converting the wavelength to the time axis, we realize single-shot ultrafast burst imaging. As an experimental demonstration of SF-STAMP, we monitor the dynamics of a laser ablation using a linearly frequency-chirped broadband pulse (>100 nm) that is temporally stretched up to ~40 ps. This imaging method is expected to be effective for investigating ultrafast dynamics in a diverse range of fields, such as photochemistry, plasma physics, and fluidics.
ASAP, a systematic annotation package for community analysis of genomes (2003)

ASAP (a systematic annotation package for community analysis of genomes) is a relational database and web interface developed to store, update and distribute genome sequence data and functional characterization (https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm). ASAP facilitates ongoing community annotation of genomes and tracking of information as genome projects move from preliminary data collection through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources. ASAP supports three levels of users: public viewers, annotators and curators. Public viewers can currently browse updated annotation information for Escherichia coli K-12 strain MG1655, genome-wide transcript profiles from more than 50 microarray experiments and an extensive collection of mutant strains and associated phenotypic data. Annotators worldwide are currently using ASAP to participate in a community annotation project for the Erwinia chrysanthemi strain 3937 genome. Curation of the E. chrysanthemi genome annotation as well as those of additional published enterobacterial genomes is underway and will be publicly accessible in the near future.