gebhart/patrepeval huggingface dataset:
Investigation of a High Temperature Organic Water Shutoff Gel: Reaction Mechanisms (2006)

Summary Water production during oil and gas recovery is a longstanding problem that is becoming critical with maturing fields worldwide. Lifting, processing, treating, and reinjection of the unwanted water add to the overall oil production costs. Also, water disposal may pose environmental problems. Recent statistical studies indicate that processing unwanted water costs the oil industry nearly U.S. $40 billion per year. Polymer gels have been widely used as blocking agents for excessive water production. In this study, two different polymers were crosslinked with polyethyleneimine (PEI). The first is a copolymer of polyacrylamide tert-butyl acrylate (PAtBA), and the second is a polyacrylamide (PAM). The PAtBA/PEI system was previously shown to be stable at temperatures up to 160°C, typical of those encountered in deep oil and gas reservoirs. However, the crosslinking mechanisms of this system at high temperatures have not been well defined. This study examined the structural changes of PAtBA using C-13 nuclear magnetic resonance (NMR) spectroscopy. Understanding these changes is a first step toward the identification of the crosslinking mechanisms of PAtBA and PAM with PEI. This will have a strong impact on the design of water shutoff treatments utilizing these systems. Introduction As oil and gas fields mature, larger volumes of water are produced. Separating, treating, and disposing this water add extra costs to the petroleum production. It has been reported that the petroleum industry spends several tens of billions of dollars to deal with excessive water production (Bailey et al. 2000). Hydrophilic polymer gels have been widely used to reduce (Zaitoun and Kohler 1988) or completely block (Hutchins et al. 1996.water from its producing zones. Polyacrylamides have been the most commonly used base polymers crosslinked with either inorganic or organic crosslinkers. Inorganic crosslinkers include Cr+3, Al+3, and Zr+4 and have been mostly utilized to crosslink partially hydrolyzed polyacrylamide (HPAM). Inorganically crosslinked gels result from the ionic bonding between the negatively charged carboxylate groups and the multivalent cation (Prud'homme et al. 1983; Lockhart 1994; te Nijenhuis et al. 2003). Organic crosslinkers were introduced to obtain gels that are stable over a wider temperature range (Moradi-Araghi 1991; Albonico et al. 1994; Hardy et al. 1999). This is possible because in this case, the crosslinking is done by a covalent bonding, which is much more stable than ionic bonds. The covalent bonds often involve the amide groups on the polymer backbone. A typical example of an organically crosslinked gel is the polyacrylamide-phenol/formaldehyde system, which has been reported to be stable at 121 DEGREE C for 13.3 years (Moradi-Araghi 2000, 1993). However, its toxicity has limited its broad use in the field. Chemical alternatives for the phenol/formaldehyde system were also reported (Moradi-Araghi 1994; Dovan et al. 1997).
Facile Procedure for Generating Side Chain Functionalized Poly(α-hydroxy acid) Copolymers from Aldehydes via a Versatile Passerini-Type Condensation (2010)

A general method for synthesizing alpha-hydroxy N-acylindoles in one-pot via an acid-catalyzed condensation of a convertible isonitrile with water and various aldehydes is presented. These intermediates were incorporated into poly(alpha-hydroxy acid) copolymers bearing residues with functionalizable side chains, which could be further modified through Cu(I)-catalyzed azide-alkyne cylcoaddition reactions. This versatile synthetic strategy provides access to side chain functionalized poly(alpha-hydroxy acid) copolymers from readily available aldehydes, making it potentially useful as an approach to synthesize biodegradable polymers with new, tunable properties.
The Origin and Evolution of Dino Fest (1994)

Late in the summer of 1993, Robert Hall, Chairman of the Department of Geology, Indiana University-Purdue University at Indianapolis (IUPUI) thought it would be a good idea to invite a couple of dinosaur workers to campus to capitalize on the frenzy of enthusiasm for dinosaurs that the movie, Jurassic Park , had generated. However, what originally was to have been a couple of guest lectures quickly evolved into a three-day affair that was probably the first scientific conference–certainly the first paleontologic conference–for the general public, raising important issues about public involvement in science.
CXCR4–SDF-1 signaling is active in rhabdomyosarcoma cells and regulates locomotion, chemotaxis, and adhesion (2002)

We hypothesized that the CXC chemokine receptor-4 (CXCR4)-stromal-derived factor-1 (SDF-1) axis may be involved in metastasis of CXCR4(+) tumor cells into the bone marrow and lymph nodes, which secrete the alpha-chemokine SDF-1. To explore this hypothesis, we phenotyped by fluorescence-activated cell sorter analysis various human tumor cell lines for expression of CXCR4 and found that it was highly expressed on several rhabdomyosarcoma (RMS) cell lines. We also observed that cell lines derived from alveolar RMS, which is characterized by recurrent PAX3- and PAX7-FKHR gene fusions and is associated with a poor prognosis, expressed higher levels of CXCR4 than lines derived from embryonal RMS. Furthermore, transfer of a PAX3-FKHR gene into embryonal RMS cell activates CXCR4 expression. Because alveolar RMS frequently metastasizes to the bone marrow and lymph nodes, it seems that the CXCR4-SDF-1 axis could play an important role in this process. These findings prompted us to determine whether SDF-1 regulates the metastatic behavior of RMS cells. Accordingly, we found that, although SDF-1 did not affect proliferation or survival of these cell lines, it induced in several of them (1) phosphorylation of mitogen-activated protein kinase p42/44; (2) locomotion; (3) directional chemotaxis across membranes covered by laminin, fibronectin, or Matrigel; (4) adhesion to laminin, fibronectin, and endothelial cells; and (5) increased MMP-2 and diminished tissue inhibitors of metalloproteinases secretion. The small-molecule CXCR4-specific inhibitor, T140, effectively blocked the in vitro responses of RMS cells to SDF-1. On the basis of these observations we suggest that the CXCR4-SDF-1 axis may play an important role in tumor spread and metastasis of RMS cells to bone marrow and that molecular strategies aimed at inhibiting this axis could thus prove to be useful therapeutic measures.
Production of maternal-zygotic mutant zebrafish by germ-line replacement (2002)

We report a generally applicable strategy for transferring zygotic lethal mutations through the zebrafish germ line. By using a morpholino oligonucleotide that blocks primordial germ cell (PGC) development, we generate embryos devoid of endogenous PGCs to serve as hosts for the transplantation of germ cells derived from homozygous mutant donors. Successful transfers are identified by the localization of specifically labeled donor PGCs to the region of the developing gonad in chimeric embryos. This strategy, which results in the complete replacement of the host germ line with donor PGCs, was validated by the generation of maternal and maternal-zygotic mutants for the miles apart locus. This germ-line replacement technique provides a powerful tool for studying the maternal effects of zygotic lethal mutations. Furthermore, the ability to generate large clutches of purely mutant embryos will greatly facilitate embryological, genetic, genomic, and biochemical studies.
U-Net (1995)

The U-Net communication architecture prowdes processeswith a virtual view of a network interface to enable user-Ievel accessto high-speed communication dewces. The architecture, implemented on standard workstations using offthe-shelf ATM communication hardware, removes the kernel from the communication path, while stall prowdmg full
Cyclic polymers: Synthetic strategies and physical properties (2009)

Abstract Syntheses of cyclic polymers including cyclic homopolymers, cyclic block copolymers, sun‐shaped polymers, and tadpole polymers are discussed on the basis of a differentiation between synthetic methods and synthetic strategies (e.g., polycondensation, ring–ring equilibration, or ring‐expansion polymerization). Furthermore, all synthetic methods are classified as kinetically or thermodynamically controlled reactions. Characteristic properties of cyclic polymers such as smaller hydrodynamic volume, lower melt viscosities, and higher thermostabilities are compared to the properties of their linear counterparts. Furthermore, the nanophase separation of cyclic diblock copolymers is discussed. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 251–284, 2010
Signal transduction pathways in the mitogenic response to G protein-coupled neuropeptide receptor agonists (1998)

Neuropeptides, including mammalian bombesin-like peptides, act as potent cellular growth factors and have been implicated in a variety of normal and abnormal processes, including development, inflammation, and malignant transformation. These signaling peptides exert their characteristic effects on cellular processes by binding to specific G protein-coupled receptors (GPCR) on the surface of their target cells. Typically, the binding of a neuropeptide to its cognate GPCR triggers the activation of multiple signal transduction pathways that act in a synergistic and combinatorial fashion to relay the mitogenic signal to the nucleus and promote cell proliferation. A rapid increase in the synthesis of lipid-derived second messengers with subsequent activation of protein phosphorylation cascades is an important early response to neuropeptides. An emerging theme in signal transduction is that these agonists also induce rapid and coordinate tyrosine phosphorylation of cellular proteins including the nonreceptor tyrosine kinase p125fak and the adaptor proteins p130cas and paxillin. This tyrosine phosphorylation pathway depends on the integrity of the actin cytoskeleton and requires functional Rho. The purpose of this article is to review recent advances in unraveling the pathways that play a role in transducing mitogenic and migratory responses induced by G protein-coupled neuropeptide receptor agonists.
Repression of insulin gene expression by adenovirus type 5 E1a proteins. (1987)

Insulin gene transcription relies on enhancer and promoter elements which are active in pancreatic beta cells. We showed that adenovirus type 5 infection of HIT T-15 cells, a transformed hamster beta cell line, represses insulin gene transcription and mRNA levels. Using expression plasmids transiently introduced into HIT T-15 cells, we showed that adenovirus type 5 E1a transcription regulatory proteins repress insulin enhancer-promoter element activity as assayed with a surrogate xanthine-guanine phosphoribosyltransferase gene. We relate E1a repression of the insulin gene to other examples of repression of enhancer-dependent genes by E1a and discuss the possible relationship of this repression to insulin gene regulation.
Reliability of signals from a chronically implanted, silicon-based electrode array in non-human primate primary motor cortex (2005)

Multiple-electrode arrays are valuable both as a research tool and as a sensor for neuromotor prosthetic devices, which could potentially restore voluntary motion and functional independence to paralyzed humans. Long-term array reliability is an important requirement for these applications. Here, we demonstrate the reliability of a regular array of 100 microelectrodes to obtain neural recordings from primary motor cortex (MI) of monkeys for at least three months and up to 1.5 years. We implanted Bionic (Cyberkinetics, Inc., Foxboro, MA) silicon probe arrays in MI of three Macaque monkeys. Neural signals were recorded during performance of an eight-direction, push-button task. Recording reliability was evaluated for 18, 35, or 51 sessions distributed over 83, 179, and 569 days after implantation, respectively, using qualitative and quantitative measures. A four-point signal quality scale was defined based on the waveform amplitude relative to noise. A single observer applied this scale to score signal quality for each electrode. A mean of 120 (+/- 17.6 SD), 146 (+/- 7.3), and 119 (+/- 16.9) neural-like waveforms were observed from 65-85 electrodes across subjects for all recording sessions of which over 80% were of high quality. Quantitative measures demonstrated that waveforms had signal-to-noise ratio (SNR) up to 20 with maximum peak-to-peak amplitude of over 1200 microv with a mean SNR of 4.8 for signals ranked as high quality. Mean signal quality did not change over the duration of the evaluation period (slope 0.001, 0.0068 and 0.03; NS). By contrast, neural waveform shape varied between, but not within days in all animals, suggesting a shifting population of recorded neurons over time. Arm-movement related modulation was common and 66% of all recorded neurons were tuned to reach direction. The ability for the array to record neural signals from parietal cortex was also established. These results demonstrate that neural recordings that can provide movement related signals for neural prostheses, as well as for fundamental research applications, can be reliably obtained for long time periods using a monolithic microelectrode array in primate MI and potentially from other cortical areas as well.
Motor cortical activity during drawing movements: population representation during sinusoid tracing (1993)

1. Monkeys were trained to trace sinusoids with their index fingers on a planar surface. During this task, both the direction and speed of movement varied continuously. Activity of individual units in the precentral gyrus contralateral to the moving arm was recorded as the task was performed. These cells responded to passive movement of the shoulder and/or elbow. The relation between discharge rate and movement direction for these individual cells could be described with a cosine tuning function. 2. Data recorded as the sinusoid was traced were divided into 100 bins as each cell was studied during the experiment. In each bin, the activity of a particular cell was represented by a vector. The vector ("cell vector") pointed in the direction of finger movement that corresponded to the highest rate of neuronal discharge. This direction, referred to as the preferred direction, corresponded to the peak of the cosine tuning function. The direction of the vector was constant between bins, but the magnitude of this cell's vector was a function of the instantaneous discharge rate. 3. This cell vector is a hypothetical contribution of a single cell to the population response comprised of 554 similarly derived vectors from different cells. The population response was represented as the vector that resulted from forming the sum of the vector contributions from the individual cells. A separate calculation was made for each bin, resulting in 100 population vectors for each sinusoid. 4. Within a given time series of population vectors, their lengths and directions varied in a consistent relation to the tangential velocity of the drawing movement.(ABSTRACT TRUNCATED AT 250 WORDS)
A Non-Invasive Approach to Detecting Organ Rejection by MRI: Monitoring the Accumulation of Immune Cells At the Transplanted Organ (2004)

Organ transplantation is the generally preferred medical procedure of treatment for patients with end-stage organ failure. The immunological reaction of rejection is a major cause of functional failure in transplant patients. The current "gold standard" for detecting or confirming graft rejection following solid organ transplantation requires biopsy samples in order to detect immune cell (e.g., T-cells, macrophages, etc.) infiltration into the graft and other pathological changes. This procedure is not only invasive, having associated risks, but is also prone to sampling errors that can yield false negative results. To circumvent the need for biopsies, we are developing magnetic resonance imaging (MRI) techniques to monitor the accumulation of immune cells at the transplanted organ as a means to detect graft rejection. By labeling immune cells with an MRI contrast agent, dextran-coated ultrasmall superparamagnetic iron oxide (USPIO) particles, we can monitor the accumulation of these labeled immune cells at the rejecting graft as a non-invasive method to detect graft rejection. Cells can be labeled ex vivo and then infused into the animal, or MRI contrast agents can be introduced directly into the animal in vivo. Our results show excellent correlation among the MRI signal intensity due to the USPIO-labeled macrophages at the rejecting graft, immuno-staining for macrophages, histo-pathology for graft rejection, and the iron staining of tissue samples. In this article, we shall give a summary of our progress from detecting single immune cells in vitro to monitoring the accumulation of immune cells in vivo at the transplanted kidneys, hearts, and lungs in our rat models for organ transplantation by MRI.
Effectiveness of Donor Natural Killer Cell Alloreactivity in Mismatched Hematopoietic Transplants (2002)

T cells that accompany allogeneic hematopoietic grafts for treating leukemia enhance engraftment and mediate the graft-versus-leukemia effect. Unfortunately, alloreactive T cells also cause graft-versus-host disease (GVHD). T cell depletion prevents GVHD but increases the risk of graft rejection and leukemic relapse. In human transplants, we show that donor-versus-recipient natural killer (NK)-cell alloreactivity could eliminate leukemia relapse and graft rejection and protect patients against GVHD. In mice, the pretransplant infusion of alloreactive NK cells obviated the need for high-intensity conditioning and reduced GVHD. NK cell alloreactivity may thus provide a powerful tool for enhancing the efficacy and safety of allogeneic hematopoietic transplantation.
The presence of an RHD pseudogene containing a 37 base pair duplication and a nonsense mutation in Africans with the Rh D-negative blood group phenotype (2000)

Antigens of the Rh blood group system are encoded by 2 homologous genes, RHD and RHCE, that produce 2 red cell membrane proteins. The D-negative phenotype is considered to result, almost invariably, from homozygosity for a complete deletion of RHD. The basis of all PCR tests for predicting fetal D phenotype from DNA obtained from amniocytes or maternal plasma is detection of the presence of RHD. These tests are used in order to ascertain the risk of hemolytic disease of the newborn. We have identified an RHD pseudogene (RHD psi) in Rh D-negative Africans. RHDpsi contains a 37 base pair (bp) insert in exon 4, which may introduce a stop codon at position 210. The insert is a sequence duplication across the boundary of intron 3 and exon 4. RHDpsi contains another stop codon in exon 6. The frequency of RHDpsi in black South Africans is approximately 0.0714. Of 82 D-negative black Africans, 66% had RHDpsi, 15% had the RHD-CE-D hybrid gene associated with the VS+ V- phenotype, and only 18% completely lacked RHD. RHDpsi is present in about 24% of D-negative African Americans and 17% of D-negative South Africans of mixed race. No RHD transcript could be detected in D-negative individuals with RHDpsi, probably as a result of nonsense-mediated mRNA decay. Existing PCR-based methods for predicting D phenotype from DNA are not suitable for testing Africans or any population containing a substantial proportion of people with African ethnicity. Consequently, we have developed a new test that detects the 37 bp insert in exon 4 of RHDpsi. (Blood. 2000; 95:12-18)
The biochemistry of CYFRA 21—1 and other cytokeratin-tests (1995)

Soluble forms of keratins in human sera seem to be useful analytes for the monitoring of cancer patients. CYFRA 21-1 is a new test measuring keratin 19 in human blood. The test was developed as sandwich ELISA based on two monoclonal antibodies, both reacting with keratin 19. The epitopes recognised by the antibodies are located on the rod region of the molecule. In sera from malignant patients CYFRA 21-1 detects immunoreactive compounds which appear to be larger than keratin 19 itself, indicating the presence of oligomers in these sera. In a comparison study the reactivity of other keratin tests (TPA, TPS, TPAcyk) with the keratins 8, 18 and 19 were measured both in solution and on immunoblots. The reactivity pattern was found to be different what may explain the different diagnostic properties of the individual tests.
Named entity recognition with a maximum entropy approach (2003)

The named entity recognition (NER) task involves identifying noun phrases that are names, and assigning a class to each name. This task has its origin from the Message Understanding Conferences (MUC) in the 1990s, a series of conferences aimed at evaluating systems that extract information from natural language texts. It became evident that in order to achieve good performance in information extraction, a system needs to be able to recognize names. A separate subtask on NER was created in MUC-6 and MUC-7 (Chinchor, 1998).
A pthA Homolog from Xanthomonas axonopodis pv. citri Responsible for Host-Specific Suppression of Virulence (2007)

Strains of the plant-pathogenic bacterium Xanthomonas axonopodis pv. citri are differentiated into two groups with respect to aggressiveness (normal and weak) on Citrus grandis cultivars but not on other Citrus species such as Citrus sinensis. Random mutagenesis using the transposon Tn5 in X. axonopodis pv. citri strain KC21, which showed weak aggressiveness on a C. grandis cultivar, was used to isolate mutant KC21T46, which regained a normal level of aggressiveness on the cultivar. The gene inactivated by the transposon, hssB3.0, was shown to be responsible for the suppression of virulence on C. grandis. Sequence analysis revealed it to be a new member of the pthA homologs, which was almost identical in sequence to the other homologs except for the number of tandem repeats in the central region of the gene. hssB3.0 appears to be a chimera of other pthA homologs, pB3.1 and pB3.7, and could have been generated by recombination between these two genes. Importantly, in X. axonopodis pv. citri, hssB3.0 was found in all of the tested isolates belonging to the weakly aggressive group but not in the isolates of the normally aggressive group. Isolation of the virulence-deficient mutant KC21T14 from KC21, in which the pathogenicity gene pthA-KC21 was disrupted, showed that hssB3.0 induces a defense response on the host but partially interrupts canker development elicited by the pathogenicity gene in this bacterium.
Intraperitoneal Cisplatin plus Intravenous Cyclophosphamide versus Intravenous Cisplatin plus Intravenous Cyclophosphamide for Stage III Ovarian Cancer (1996)

As compared with intravenous cisplatin, intraperitoneal cisplatin significantly improves survival and has significantly fewer toxic effects in patients with stage III ovarian cancer and residual tumor masses of 2 cm or less.