gebhart/patrepeval huggingface dataset:
A New Model for Matching Fracturing Fluid Flowback Composition (2007)

Abstract Recovery of fracturing fluid is considered a critical aspect for achieving production performance that meets the expectations of fracture treatment designs. Fluid recovery is often described simply as a percentage of load recovery on a volume basis, without consideration of the composition of the recovered water. Some of this water may in fact be formation water and not original load water at all. Analysis of the ionic composition of the water can determine whether the recovered water is formation water or treatment water. This paper describes a new model that embodies the physics of flow during back-production of a fracturing treatment and incorporates a chemistry "layer" that allows for matching fracturing fluid flowback compositions. The model accommodates formation water having a separate composition from the fracturing fluid. The movements of sodium, potassium, chloride, sulfate, carbohydrate, boron, etc. are modeled during shut-in and production. The compositions of the produced water calculated by the simulator were compared to field production samples. The process of matching the produced water analyses after the fracturing treatment first required a good match of the produced water rates as a function of both time and the produced gas rates. Reservoir and fracture properties were optimized to match the water production. The ionic composition of the flowback water was then matched by adjusting various parameters that might affect how the water was recovered from the reservoir. The information obtained by adjusting these parameters includes relative permeability curves, capillary pressure curves, and some fracture structure details. Deviations of the model from the observed return profiles indicated areas where the understanding of fluid chemistry and physics of flow might be improved.
Gene Repair Using Chimeric RNA/DNA Oligonucleotides (1999)

An experimental strategy has been developed for the site-specific alteration of genomic DNA. The approach is based on the observation that oligonucleotides containing complementary RNA/DNA hybrid regions are more active than duplex DNA in homologous pairing reactions in vitro. The chimeric molecules are designed with a homologous targeting sequence comprised of a DNA region flanked by blocks of 2'-O-methyl RNA residues (the chimeric strand), its complementary all-DNA strand, thymidine hairpin caps, a single-strand break, and a double-stranded clamp region. The oligonucleotide can align in perfect register with a genomic target except for the designed single base pair mismatch, which is recognized and corrected by harnessing the cell's endogenous DNA repair system. The mechanism of repair has been studied using mammalian cell-free extracts and bacterial systems and has revealed a mismatch correction pathway distinct from homologous recombination. The chimeric molecules have been demonstrated to be effective in the alteration of single nucleotides in episomal and genomic DNA in cell culture, as well as genomic DNA of cells in situ. This is a potentially powerful strategy for gene repair for the myriad hepatic genetic diseases caused by point mutations.
How Big Is Too Big? (2021)

The vertical rectus abdominis flap has been a workhorse flap for perineal reconstruction. Defect size does not affect risk of partial flap necrosis, complete flap loss, infection, abdominal fascial dehiscence, ventral hernia, or seroma, which supports the utility of VRAM flap for perineal reconstruction. Larger perineal defects are associated with increased risk for major wound complications, which required reoperation, regardless of age or BMI. Future studies should be performed to determine if there is a maximum defect size cutoff that limits the utility of VRAM flap reconstruction or to develop a predictive model to assess the risk of major wound complications based on defect size.
Very low zero-dispersion wavelength predicted for single-mode modified-total-internal-reflection crystal fibre (2004)

A zero-dispersion wavelength (λZD) below 600 nm has been predicted for a pure silica modified-total-internal-reflection (M-TIR) single-mode crystal fibre with a 1 µm pitch. The fibre is single mode from at least 250 nm, i.e., from well below λZD. Both a method for designing single-mode crystal fibres using an anti-guiding structure and a fast calculation scheme for investigating the structure for different pitch sizes are proposed.
Molecular Biology for the Environment: an EC-US hands-on Course in Environmental Biotechnology (2004)

One of the central goals of this activity is to bring together young scientists (at the late Ph.D. or early postdoctoral stages of their careers) in a forum that should result in future collaborations. The course is designed to give scientists hands-on experience in modern, up-to-date biotechnological methods at the interface between molecular biology and environmental biotechnology for the analysis of microorganisms and their activities with regard to the remediation of pollutants in the environment.
STANDING LAPAROSCOPIC-GUIDED UTERINE BIOPSY IN A SOUTHERN WHITE RHINOCEROS (CERATOTHERIUM SIMUM SIMUM) (2000)

Transrectal ultrasonography of a 35-yr-old captive female southern white rhinoceros (Ceratotherium simum simum) with a history of chronic mucohemorrhagic vulvar discharge revealed right transmural uterine horn enlargement. Abdominal laparoscopic surgery, although extremely difficult because of inadequate instrumentation, permitted uterine visualization and biopsy. Standing anesthesia, incorporating butorphanol and azaperone together with local anesthetic infiltration, facilitated the laparoscopy. A leiomyoma was suspected on the basis of history, physical examination, ultrasonographic appearance, and histopathology. Prior rhinoceros laparoscopies have failed, primarily from limitations imposed by recumbency.
Requirement of Staphylococcus aureus ATP-Binding Cassette-ATPase FhuC for Iron-Restricted Growth and Evidence that It Functions with More than One Iron Transporter (2006)

In Staphylococcus aureus, fhuCBG encodes an ATP-binding cassette (ABC) transporter that is required for the transport of iron(III)-hydroxamates; mutation of either fhuB or fhuG eliminates transport. In this paper, we describe construction and characterization of an S. aureus fhuCBG deletion strain. The delta fhuCBG::ermC mutation not only resulted in a strain that was incapable of growth on iron(III)-hydroxamates as a sole source of iron but also resulted in a strain which had a profound growth defect in iron-restricted laboratory media. The growth defect was not a result of the inability to transport iron(III)-hydroxamates since S. aureus fhuG::Tn917 and S. aureus fhuD1::Km fhuD2::Tet mutants, which are also unable to transport iron(III)-hydroxamates, do not have similar iron-restricted growth defects. Complementation experiments demonstrated that the growth defect of the delta fhuCBG::ermC mutant was the result of the inability to express FhuC and that this was the result of an inability to transport iron complexed to the S. aureus siderophore staphylobactin. Transport of iron(III)-staphylobactin is dependent upon SirA (binding protein), SirB (permease), and SirC (permease). S. aureus expressing FhuC with a Walker A K42N mutation could not utilize iron(III)-hydroxamates or iron(III)-staphylobactin as a sole source of iron, supporting the conclusion that FhuC, as expected, functions with FhuB, FhuG, and FhuD1 or FhuD2 to transport iron(III)-hydroxamates and is the "genetically unlinked" ABC-ATPase that functions with SirA, SirB, and SirC to transport iron(III)-staphylobactin. Finally, we demonstrated that the delta fhuCBG::ermC strain had decreased virulence in a murine kidney abscess model.
Dihydrofolate synthetase and folylpolyglutamate synthetase: direct evidence for intervention of acyl phosphate intermediates (1988)

The transfer of 17O and/or 18O from (COOH-17O or -18O) enriched substrates to inorganic phosphate (Pi) has been demonstrated for two enzyme-catalyzed reactions involved in folate biosynthesis and glutamylation. COOH-18O-labeled folate, methotrexate, and dihydropteroate, in addition to [17O]-glutamate, were synthesized and used as substrates for folylpolyglutamate synthetase (FPGS) isolated from Escherichia coli, hog liver, and rat liver and for dihydrofolate synthetase (DHFS) isolated from E. coli. Pi was purified from the reaction mixtures and converted to trimethyl phosphate (TMP), which was then analyzed for 17O and 18O enrichment by nuclear magnetic resonance (NMR) spectroscopy and/or mass spectroscopy. In the reactions catalyzed by the E. coli enzymes, both NMR and quantitative mass spectral analyses established that transfer of the oxygen isotope from the substrate 18O-enriched carboxyl group to Pi occurred, thereby providing strong evidence for an acyl phosphate intermediate in both the FPGS- and DHFS-catalyzed reactions. Similar oxygen-transfer experiments were carried out by use of two mammalian enzymes. The small amounts of Pi obtained from reactions catalyzed by these less abundant FPGS proteins precluded the use of NMR techniques. However, mass spectral analysis of the TMP derived from the mammalian FPGS-catalyzed reactions showed clearly that 18O transfer had occurred.
Interactively Exploring Hierarchical Results (2002)

olecular biologists and geneticistsseek to understand the function ofgenes, including the more than 6,000genes in the yeast genome and theestimated 40,000 genes in the humangenome. Recently developed for genome analysis,DNA microarrays—also known as gene arrays orgene chips—usually consist of glass or nylon sub-strates that measure 1 × 3 inches or smaller. Thesechips contain speciﬁc DNA gene samples spottedin an array by a robotic printing device.Researchers spread ﬂuorescently labeled messen-ger RNA (mRNA) from an experimental conditiononto the DNA gene samples in the array. ThismRNA binds (hybridizes) strongly with some DNAgene samples and weakly with others. Finally, alaser scans the array and sensors detect the fluo-rescence levels, indicating the strength with whichthe sample expresses each gene.Experimental conditions can include types of can-cers, diseased organisms, or normal tissues.Microarray experiments typically have from 100 to20,000 DNA gene samples and from two to 80experimental conditions. These experiments pro-duce data sets containing the proﬁles that includeexpression levels for each DNA gene sample undereach experimental condition.Researchers often use mathematical clusteringmethods to discover interesting patterns in theselarge data sets.
Verify Results of Network Intrusion Alerts Using Lightweight Protocol Analysis (2006)

We propose a method to verify the result of attacks detected by signature-based network intrusion detection systems using lightweight protocol analysis. The observation is that network protocols often have short meaningful status codes saved at the beginning of server responses upon client requests. A successful intrusion that alters the behavior of a network application server often results in an unexpected server response, which does not contain the valid protocol status code. This can be used to verify the result of the intrusion attempt. We then extend this method to verify the result of attacks that still generate valid protocol status code in the server responses. We evaluate this approach by augmenting Snort signatures and testing on real world data. We show that some simple changes to Snort signatures can effectively verify the result of attacks against the application servers, thus significantly improve the quality of alerts
A placebo controlled clinical trial of buprenorphine as a treatment for opioid dependence (1995)

Large-scale placebo controlled clinical trials assessing the efficacy of medications for the treatment of drug dependence have generally been limited to alcohol, cocaine and nicotine dependent populations. The purpose of the present study was to assess the early (1-2 week) clinical effectiveness of buprenorphine versus placebo in an opioid dependent population. The study used a parallel-group design with a behavioral choice component to compare buprenorphine (a mu-opioid partial agonist) to placebo for the treatment of opioid dependence. Opioid dependent volunteer patients participated in a 14-day study to assess the effectiveness and patient acceptance of this new pharmacotherapy for the treatment of opioid dependence. Patients were randomly assigned to placebo (n = 60) or 2 mg (n = 60) or 8 mg (n = 30) daily sublingual buprenorphine. All doses were administered double-blind. On days 6-13 all patients could request a dose change, knowing that their new dose would be randomly chosen from the remaining 2 alternatives. Compared to placebo, patients given buprenorphine (independent of dose) showed greater time on initial dose, requested fewer dose changes, used less illicit opioids (assessed by urinalysis), and rated dose adequacy higher. These results demonstrate that a placebo controlled study with a behavioral choice component is an effective means of assessing the potential efficacy and acceptability of new pharmacotherapies for opioid dependence.
Papilloma incidence in FoxN1<sup><i>nu/nu</i></sup> mice infected with MmuPV1 DNA. (2017)

&lt;p&gt;Papilloma incidence in FoxN1&lt;sup&gt;&lt;i&gt;nu/nu&lt;/i&gt;&lt;/sup&gt; mice infected with MmuPV1 DNA.&lt;/p&gt;
Coating PTFE vascular prostheses with a fibroblastic matrix improves cell retention when subjected to blood flow (1998)

An investigation was made into the effect of blood flow on endothelial cells (EC) and mesothelial cells (MC) seeded on a vascular expanded polytetrafluoroethylene (ePTFE) prosthesis coated with a fibroblastic matrix. Endothelial cells were obtained from the external jugular vein and MC from the omentum. To test the performance of prostheses, a custom designed, femoral "ex vivo" circuit was developed in mongrel dogs. Four study groups were established: a control group, A1, where prostheses were uncoated and seeded with EC; a second control group, A2, where prostheses were uncoated and seeded with MC; group B1 where prostheses were coated with a fibroblastic matrix and seeded with EC; and group B2 where coated prostheses were seeded with MC. All cells were labeled with 111Indium oxine (10 microCi/mL) before seeding. After the seeded cells had formed a monolayer on the ePTFE prostheses (which took approximately 24 h) the prostheses were placed in the "ex vivo" circuit. The rates of blood flow to which prostheses were exposed were measured at the point of inflow (117.5 +/- 12.50 mL/min, mean +/- SD) and outflow (72.6 +/- 14.3 mL/min). MC showed a greater baseline radionuclide uptake than did EC. The cells of groups B1 and B2 adhered sufficiently to the fibroblastic matrix and covered enough of the prosthetic surface to be positioned in the "ex vivo" circuit (76.90 +/- 8.24% surface covered in EC-seeded prostheses and 71.65 +/- 6.23% in MC-seeded prostheses). After exposure to blood flow the quantity of radionuclide-labeled cells and the prosthetic surface covered by them were greatly reduced though the fibroblast-coated prostheses showed greater cell retention.
Size and Zeta Potential Clicked Germination Attenuation and Anti-Sporangiospores Activity of PEI-Functionalized Silver Nanoparticles against COVID-19 Associated Mucorales (Rhizopus arrhizus) (2022)

The SARS-CoV-2 infections in Indian people have been associated with a mucormycotic fungal infection caused by the filamentous fungi <i>Rhizopus arrhizus</i>. The sporangiospores of <i>R. arrhizus</i> are omnipresent in the environment and cause infection through inhalation or ingestion of contaminated air and foods. Therefore, the anti-sporangiospore activity of polyethyleneimine functionalized silver nanoparticles (PEI-f-Ag-NPs) with variable size and surface charge as a function of the molecular weight of PEI was explored. The results showed that both PEI-f-AgNP-1 and PEI-f-AgNP-2, potentially, attenuated the germination and reduced the viability of sporangiospores. Furthermore, the results showed that the minimum inhibitory concentration (MIC) values of both PEI-f-AgNP-1 and PEI-f-AgNP-2 (1.65 and 6.50 μg/mL, respectively) were dependent on the nanoparticle size and surface ζ potentials. Similarly, the sporangiospore germination inhibition at MIC values was recorded, showing 97.33% and 94% germination inhibition, respectively, by PEI-f-AgNP-1 and 2 within 24 h, respectively. The confocal laser scanning microscopy, SEM-EDS, and confocal Raman spectroscopy investigation of PEI-f-Ag-NPs treated sporangiospores confirmed size and surface charge-dependent killing dynamics in sporangiospores. To the best of our knowledge, this is the first investigation of the polyethyleneimine functionalized silver nanoparticle-mediated size and surface charge-dependent anti-sporangiospore activity against <i>R. arrhizus,</i> along with a possible antifungal mechanism.
An Optimization Approach for Components Built by Fused Deposition Modeling with Parametric Internal Structures (2014)

Additive manufacturing processes are employed to create physical models from three-dimensional (3D) computer-aided design (CAD) math data. A solid model or water-tight surface model is used as the input, which is sliced into layers, and travel paths are created for each layer. The object is built by layer by layer stacking, with supporting structures for overhanging geometry and undercuts being created where necessary (process dependent). Fused deposition modeling (FDM) is an additive fabrication process that builds a part from extruded filaments of a melted thermoplastic. Several studies have focused on the depositing parameters; however, none of them have characterized internal support structures in different geometrical arrangements. The incorporation of reconfigurable parametric internal matrix structures based on primitive elements will balance the mechanical properties, the material usage and the build time. Parametric internal structures are designed, and compressive test components built and tested both experimentally and using simulation tools to depict the compressive characteristics. Extensive physical testing is done as the components built by the FDM process have anisotropic properties. The material usage, build time, and loading characteristics are captured for a variety of parametric structures (solid, shell, orthogonal, hexagonal, pyramid) build orientations, and internal densities (loose, compact). From this data, a model is developed that serves as a predictive tool to: (i) estimate the mechanical properties and (ii) calculate the build time and materials utilized based on various internal structural configurations for the component's application. A model that generates an optimal solution (minimum material, minimum build time, etc.) needs to be developed. Using the collected data as a foundation, an optimization model that considers the build time, material usage, surface finish, interior geometry, strength characteristics, and related parameters is presented and can be used to assist designers making informed decision with respect to strength, material usage and time, etc. is developed using the Genetic Algorithm approach.
The role of colony‐stimulating factor in granulopoiesis (1980)

Abstract The proliferation and maturation of granulocytic‐monocytic stem cells appears to be controlled by a series of closely related glycoproteins termed “colony‐stimulating factors” (CSFs). Recently, we devised a 6‐step scheme for the purification of murine fibroblast (L‐cell)‐derived CSF. Ten liter pools of conditioned media were concentrated by ultrafiltration, precipitated by ethanol, and separated on DEAE cellulose, Con‐A Sepharose, and Sephadex G 150. The CSF was separated from trace contaminants, including endotoxin, by density gradient centrifugation. The purified material was radioiodinated and used to define the serum half‐life and in vivo distribution. Following IV injection there was a biphasic serum clearance with a t½ of 24–40 min and 2–2½ hours in the first and second phases. Approximately 25% of the tracer was excreted in the urine at 6 h; however, urinary radioactivity was due to low molecular weight peptides. Simultaneous studies by radioimmunoassay showed a similar rapid serum clearance of unlabeled CSF but virtually no urinary CSF activity. Thus, assays for urinary CSF may not provide useful measures of in vivo CSF activity. Further in vitro studies have defined the interaction of CSF with responsive cells in the marrow. Varying doses of CSF were incubated with 10 7 marrow cells for intervals of 24–48 h. The major increment in cell‐associated radioactivity occurred between 6 and 16 h. The reaction was saturable with 1–2 ng/ml CSF. Binding was prevented by cold CSF, but not by other proteins. Irradiation yielded only a minimal reduction in CSF binding. The interaction of CSF with marrow cells appeared to require new protein synthesis, as binding was completely inhibited by cycloheximide and puromycin. Irradiated mice injected with antibodies to CSF showed an inhibition of granulopoiesis by marrow cells in peritoneal diffusion chambers; however, granulopoiesis in the intact bone marrow was unaffected. Granulpoiesis in long‐term marrow cultures was also unaffected by anti‐CSF. These different responses may be due to accelerated clearance of injected CSF in nonirradiated mice or to extensive stromal interactions that modulate and perhaps control granulocytic differentiation in the intact bone marrow microenvironment.
K-Means Cloning: Adaptive Spherical K-Means Clustering (2018)

We propose a novel method for adaptive K-means clustering. The proposed method overcomes the problems of the traditional K-means algorithm. Specifically, the proposed method does not require prior knowledge of the number of clusters. Additionally, the initial identification of the cluster elements has no negative impact on the final generated clusters. Inspired by cell cloning in microorganism cultures, each added data sample causes the existing cluster ‘colonies’ to evaluate, with the other clusters, various merging or splitting actions in order for reaching the optimum cluster set. The proposed algorithm is adequate for clustering data in isolated or overlapped compact spherical clusters. Experimental results support the effectiveness of this clustering algorithm.
Compact genome of the Antarctic midge is likely an adaptation to an extreme environment (2014)

The midge, Belgica antarctica, is the only insect endemic to Antarctica, and thus it offers a powerful model for probing responses to extreme temperatures, freeze tolerance, dehydration, osmotic stress, ultraviolet radiation and other forms of environmental stress. Here we present the first genome assembly of an extremophile, the first dipteran in the family Chironomidae, and the first Antarctic eukaryote to be sequenced. At 99 megabases, B. antarctica has the smallest insect genome sequenced thus far. Although it has a similar number of genes as other Diptera, the midge genome has very low repeat density and a reduction in intron length. Environmental extremes appear to constrain genome architecture, not gene content. The few transposable elements present are mainly ancient, inactive retroelements. An abundance of genes associated with development, regulation of metabolism and responses to external stimuli may reflect adaptations for surviving in this harsh environment.