gebhart/patrepeval huggingface dataset:
Pushing the Envelope for Polymer Flooding Towards High-temperature and High-salinity Reservoirs with Polyacrylamide Based Ter-polymers (2011)

Abstract Polymer flooding is a mature EOR technique successfully applied in both sandstone and carbonate reservoirs and it is expected to have much wider applications in the future. However, it is currently limited mainly by a combination of reservoir temperature and make-up brine salinity and hardness, as synthetic polymers can chemically and thermally degrade at high temperature and salinity. This paper reports the results of an ongoing study aimed at finding polymers that can enlarge the application envelope of polymer flooding to, for example, high-temperature and high-salinity Middle Eastern carbonate reservoirs. In this study thermal stability of a number of commercially available polymers was tested at 120°C in various brines. The polymers investigated are partially hydrolyzed polyacrylamide (HPAM) based co- and ter-polymers functionalized with 2-Acrylamido-2-Methylpropane Sulfonate (AMPS) and/or n-Vinyl Pyrrolidone (n-VP) monomers. These monomers provide tolerance to divalent ions and protection to hydrolysis at higher temperatures. The thermal stability tests showed a clear relationship between the polymer stability and the concentration of the functionalizing monomer. Incorporation of the AMPS monomer alone does not stabilize the polymer in brines which contain divalent ions. The additional incorporation of n-VP demonstrates a stabilizing effect which is optimal at a concentration of 35-50%. The optimal ter-polymer is stable at 120°C in brines with salinity up to 200,000 ppm TDS and divalent ion concentration up to 18,000 ppm for more than 180 days. Another challenge to polymer flooding is the adsorption of polymers onto the reservoir rock. The adsorption of the terpolymers on carbonate core material was investigated in this study as a function of the polymer type and pH. This is the first work to prove the feasibility of polymer flooding at temperatures up to 120°C in high-salinity reservoirs in the presence of a high concentration of divalent ions. These results will significantly enlarge the application envelope for polymer flooding.
Improved Chou-Fasman method for protein secondary structure prediction (2006)

Our method has greatly improved Chou-Fasman method. It is able to predict protein secondary structure as good as current popular methods. By locating nucleation regions with refined wavelet transform technology and by calculating propensity factors with larger size data set, it is likely to get a better result.
Facile, Regioselective [4 + 2] Cycloaddition Involving 1-Aryl-4-phenyl-1-azadienes and Allenic Esters:  An Efficient Route to Novel Substituted 1-Aryl-4-phenyl-1,4-dihydropyridines (2001)

[reaction: see text]1-Aryl-4-phenyl-1-azadienes undergo facile, regioselective [4 + 2] cycloaddition to the C2,C3 pi-bond of allenic esters in refluxing benzene, and the formed adducts undergo a 1,3-H shift to afford novel 2-alkyl-1-aryl-3-ethoxycarbonyl-4-phenyl-1,4-dihydropyridines (78-97%). However, when the reaction is carried at room temperature, besides the [4 + 2] addition, the [2 + 2] mode of addition involving C=N of azadiene and C3,C4 pi-bond of allenic esters also intervenes. The resulting N-aryl-2-ethoxy-carbonyl-methylidene-4-styrylazetidines (17-28%) undergo reorganization on silica gel to afford 2-cyclohexen-1-ones.
Mesenchymal stem cell secretes microparticles enriched in pre-microRNAs (2009)

Intercellular exchange of protein and RNA-containing microparticles is an increasingly important mode of cell-cell communication. Here we investigate if mesenchymal stem cells (MSCs) known for secreting therapeutic paracrine factors also secrete RNA-containing microparticles. We observed that human embryonic stem cell (hESC)-derived MSC conditioned medium contained small RNAs (less than 300 nt) encapsulated in cholesterol-rich phospholipid vesicles as evidenced by their RNase sensitivity only in the presence of a sodium dodecyl sulfate-based cell lysis buffer, phospholipase A2 and a chelator of cholesterol, cyclodextrin and the restoration of their lower than expected density by detergent or phospholipase A2 treatment. MicroRNAs (miRNAs) such as hsa-let-7b and hsa-let-7g were present in a high precursor (pre)- to mature miRNA ratio by microarray analysis and quantitative reverse transcription-polymerase chain reaction. The pre-miRNAs were cleaved to mature miRNA by RNase III in vitro. High performance liquid chromatography-purified RNA-containing vesicles have a hydrodynamic radius of 55-65 nm and were readily taken up by H9C2 cardiomyocytes. This study suggests that MSCs could facilitate miRNA-mediated intercellular communication by secreting microparticles enriched for pre-miRNA.
Two mouse models reveal an actionable PARP1 dependence in aggressive chronic lymphocytic leukemia (2017)

Chronic lymphocytic leukemia (CLL) remains an incurable disease. Two recurrent cytogenetic aberrations, namely del(17p), affecting TP53, and del(11q), affecting ATM, are associated with resistance against genotoxic chemotherapy (del17p) and poor outcome (del11q and del17p). Both del(17p) and del(11q) are also associated with inferior outcome to the novel targeted agents, such as the BTK inhibitor ibrutinib. Thus, even in the era of targeted therapies, CLL with alterations in the ATM/p53 pathway remains a clinical challenge. Here we generated two mouse models of Atm- and Trp53-deficient CLL. These animals display a significantly earlier disease onset and reduced overall survival, compared to controls. We employed these models in conjunction with transcriptome analyses following cyclophosphamide treatment to reveal that Atm deficiency is associated with an exquisite and genotype-specific sensitivity against PARP inhibition. Thus, we generate two aggressive CLL models and provide a preclinical rational for the use of PARP inhibitors in ATM-affected human CLL.ATM and TP53 mutations are associated with poor prognosis in chronic lymphocytic leukaemia (CLL). Here the authors generate mouse models of Tp53- and Atm-defective CLL mimicking the high-risk form of human disease and show that Atm-deficient CLL is sensitive to PARP1 inhibition.
NEUTRALIZING ANTIVIRAL B CELL RESPONSES (1997)

Neutralizing antiviral B cell responses differ in various aspects from the many usually measured B cell responses specific for protein in adjuvants. In particular, such neutralizing antiviral B cell responses are more rapidly induced, reach higher titers, are longer lived, and are efficiently generated without adjuvants. Evidence is summarized here that the repetitiveness of many viral antigens is a key factor responsible for the efficiency of these B cell responses, amplifying B cells early and rapidly for potent IgM responses and also for efficient switching to IgG. The data reviewed indicate that B cells discriminate antigen patterns via the degree of surface Ig-cross-linking and use antigen repetitiveness as a self/nonself discriminator.
Serodiagnosis of Burkholderia mallei Infections in Horses: State‐of‐the‐art and Perspectives (2005)

Burkholderia mallei causes glanders or farcy in solipeds, a disease that must be reported to the OIE (Office International des Epizooties, Paris, France). The number of reported outbreaks has increased steadily during the last decade. Serodiagnosis is hampered by the considerable number of false-positives and -negatives of the internationally prescribed tests. The major problem leading to low sensitivity and specificity of complement fixation test (CFT) and enzyme-linked immunosorbent assay (ELISA) has been linked to the test antigens currently used, i.e. crude preparations of whole cells. Future perspectives for the development and evaluation of serological test kits using well-characterized single antigens are discussed in the light of recent molecular research on B. mallei and the closely related saprozoonotic agent B. pseudomallei.
Susceptibility of p53 Unstructured N Terminus to 20 S Proteasomal Degradation Programs the Stress Response (2009)

The N-terminal transcription activation domain of p53 is intrinsically unstructured. We show in vitro and in vivo that this domain initiates p53 degradation by the 20 S proteasome in a ubiquitin-independent fashion. The decay of metabolically labeled p53 follows biphasic kinetics with an immediate fast phase that is ubiquitin-independent and a second slower phase that is ubiquitin-dependent. The 20 S proteasome executes the first phase by default, whereas the second phase requires the 26 S proteasome. p53 N-terminal binding proteins, such as Hdmx, can selectively block the first phase of degradation. Remarkably, gamma-irradiation inhibits both p53 decay phases, whereas UV selectively negates the second phase, giving rise to discrete levels of p53 accumulation. Our data of a single protein experiencing double mode degradation mechanisms each with unique kinetics provide the mechanistic basis for programmable protein homeostasis (proteostasis).
Clinical, Biochemical, and Genetic Heterogeneity in Short-Chain Acyl-Coenzyme A Dehydrogenase Deficiency (2006)

SCADD is far more common than assumed previously, and clinical symptoms in SCADD are nonspecific, generally uncomplicated, often transient, and not correlated with specific ACADS genotypes. Because SCADD does not meet major newborn screening criteria, including a lack of clinical significance in many patients and that it is not possible to differentiate diseased and nondiseased individuals, it is not suited for inclusion in newborn screening programs at the present time.
Recent advances in rechargeable battery materials: a chemist’s perspective (2009)

The constant increase in global energy demand, together with the awareness of the finite supply of fossil fuels, has brought about an imperious need to take advantage of renewable energy sources. At the same time, concern over CO(2) emissions and future rises in the cost of gasoline has boosted technological efforts to make hybrid and electric vehicles available to the general public. Energy storage is a vital issue to be addressed within this scenario, and batteries are certainly a key player. In this tutorial review, the most recent and significant scientific advances in the field of rechargeable batteries, whose performance is dependent on their underlying chemistry, are covered. In view of its utmost current significance and future prospects, special emphasis is given to progress in lithium-based technologies.
Local Sharing as a Predominant Determinant of Synaptic Matrix Molecular Dynamics (2006)

Recent studies suggest that central nervous system synapses can persist for weeks, months, perhaps lifetimes, yet little is known as to how synapses maintain their structural and functional characteristics for so long. As a step toward a better understanding of synaptic maintenance we examined the loss, redistribution, reincorporation, and replenishment dynamics of Synapsin I and ProSAP2/Shank3, prominent presynaptic and postsynaptic matrix molecules, respectively. Fluorescence recovery after photobleaching and photoactivation experiments revealed that both molecules are continuously lost from, redistributed among, and reincorporated into synaptic structures at time-scales of minutes to hours. Exchange rates were not affected by inhibiting protein synthesis or proteasome-mediated protein degradation, were accelerated by stimulation, and greatly exceeded rates of replenishment from somatic sources. These findings indicate that the dynamics of key synaptic matrix molecules may be dominated by local protein exchange and redistribution, whereas protein synthesis and degradation serve to maintain and regulate the sizes of local, shared pools of these proteins.
Highly Active, Air-Stable Versatile Palladium Catalysts for the C−C, C−N, and C−S Bond Formations via Cross-Coupling Reactions of Aryl Chlorides (2001)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTHighly Active, Air-Stable Versatile Palladium Catalysts for the C−C, C−N, and C−S Bond Formations via Cross-Coupling Reactions of Aryl ChloridesGeorge Y. Li, Gang Zheng, and Andrew F. NoonanView Author Information The DuPont Company, Central Research and Development Department, Experimental Station, P.O. Box 80328, Wilmington, Delaware 19880-0328 [email protected]Cite this: J. Org. Chem. 2001, 66, 25, 8677–8681Publication Date (Web):November 15, 2001Publication History Received27 July 2001Published online15 November 2001Published inissue 1 December 2001https://pubs.acs.org/doi/10.1021/jo010764chttps://doi.org/10.1021/jo010764cbrief-reportACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views3498Altmetric-Citations304LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Anions,Catalysts,Cross coupling reaction,Ligands,Thiols Get e-Alerts
The phenotypic and functional characteristics of umbilical cord blood and peripheral blood natural killer cells (2009)

Allogeneic hematopoietic cell transplantation can be curative for patients with high-risk acute leukaemia. Umbilical cord blood (UCB) is an increasingly used source of allogeneic stem cells for patients who are in need of a transplant, but do not have a sibling donor. This review highlights the similarities and differences between the natural killer (NK) cells obtained from adult peripheral blood (PB) and UCB. These two cell sources show similar percentages of NK cells, including the major CD56(dim) and CD56(bright) subpopulations. UCB also contains an additional CD56-CD16+ subset, not typically found in PB. In addition, there are a number of progenitor cell populations in UCB that can give rise to NK cells. Some studies showed that UCB NK cells express a relatively higher percentage of inhibitory receptors (CD94/NKG2A and killer-cell immunoglobulin-like receptors) and less adhesion molecules. Resting UCB NK cells also show significantly less cytotoxicity compared to PB NK cells. However, following cytokine stimulation, the cytotoxicity of UCB NK cells can be rapidly increased to levels that are comparable to PB NK cells. Activation and expansion protocols for UCB NK cells are briefly reviewed. Lastly, we outline the early use of UCB NK cells in clinical trials.
Bacterial Overgrowth in Jejunal and Ileal Disease (1983)

The number of bacteria recovered in anaerobic cultures of jejunal secretions was significantly higher in a group of 10 patients with jejunal disease and stagnation of gut content in the proximal small bowel than in a group of 10 patients with similar conditions in the distal ileum. Some overlap in bacterial numbers occurred between patients with jejunal disease, ileal disease, and healthy controls, whereas production of fermentation gas in anaerobic media supplemented with glucose occurred only in cultures from the patients with jejunal disease. The 14C-glycocholic acid test showed increased output of breath 14CO2 in both patient groups, whereas faecal 14C was significantly increased only in patients with ileal disease. Increased breath hydrogen excretion after glucose ingestion was recorded in 8 of 10 patients with jejunal disease only. Breath methane excretion, previously found in 44% of healthy subjects, was absent in all of 28 patients with Crohn's disease of the small, indicating that these patients have a gut flora that is different from that of the healthy population.
In vivo study of the effect of antiviral acyclic nucleotide phosphonate (R)-9-[2- (phosphonomethoxy) propyl]adenine (PMPA, tenofovir) and its prodrug tenofovir disoproxil fumarate on rat microsomal cytochrome P450 (2008)

The total content of rat liver microsomal cytochrome P450 (CYP) significantly decreased after repeated i.p. administration of the antiviral agent tenofovir ((R)-9-[2-(phosphonomethoxy)propyl] adenine) and tenofovir disoproxil at a daily dose 25 mg/kg, although the content of liver microsomal protein did not change. The decrease of the CYP content was accompanied by concomitant increase of the amount of inactive CYP form, cytochrome P420. This effect was confirmed by a parallel study of the activities of selected CYP forms, CYP2E1 (p-nitrophenol hydroxylation) and CYP1A2 (7-ethoxyresorufin deethylation). The activity (expressed relatively to the protein content) of both CYP forms decreased significantly following the decrease of the total CYP. On the other hand, the CYP2E1 activity expressed relatively to the decreasing total CYP content remained unchanged. However, CYP1A2 activity also decreased when calculated relatively to the total native CYP content indicating lower stability of this form. Semiquantitative RT-PCR showed no significant changes in expression of major rat liver microsomal CYP forms after tenofovir treatment. In conclusion, repeated administration of tenofovir in higher doses led to significant decrease of the relative proportion of active liver microsomal CYPs accompanied by a conversion of these enzymes to the inactive form (CYP420) maintaining the sum of CYP proteins unchanged.
The RGD Domain of Human Osteopontin Promotes Tumor Growth and Metastasis through Activation of Survival Pathways (2010)

Unlike prior reports, our data suggest that the RGD domain of both OPN-A and B promote tumor growth and metastasis mainly by protecting cells against apoptosis under stressed conditions and not via migration or invasion. Future inhibitors directed against OPN should target multiple isoforms and should inhibit cell survival mechanisms that involve the RGD domain, FAK phosphorylation and NF-kappaB activation.
A First-Generation Multiplex Biomarker Analysis of Urine for the Early Detection of Prostate Cancer (2008)

Although prostate-specific antigen (PSA) serum level is currently the standard of care for prostate cancer screening in the United States, it lacks ideal specificity and additional biomarkers are needed to supplement or potentially replace serum PSA testing. Emerging evidence suggests that monitoring the noncoding RNA transcript PCA3 in urine may be useful in detecting prostate cancer in patients with elevated PSA levels. Here, we show that a multiplex panel of urine transcripts outperforms PCA3 transcript alone for the detection of prostate cancer. We measured the expression of seven putative prostate cancer biomarkers, including PCA3, in sedimented urine using quantitative PCR on a cohort of 234 patients presenting for biopsy or radical prostatectomy. By univariate analysis, we found that increased GOLPH2, SPINK1, and PCA3 transcript expression and TMPRSS2:ERG fusion status were significant predictors of prostate cancer. Multivariate regression analysis showed that a multiplexed model, including these biomarkers, outperformed serum PSA or PCA3 alone in detecting prostate cancer. The area under the receiver-operating characteristic curve was 0.758 for the multiplexed model versus 0.662 for PCA3 alone (P = 0.003). The sensitivity and specificity for the multiplexed model were 65.9% and 76.0%, respectively, and the positive and negative predictive values were 79.8% and 60.8%, respectively. Taken together, these results provide the framework for the development of highly optimized, multiplex urine biomarker tests for more accurate detection of prostate cancer.
Online nonlinear reference shaping with end-point position feedback for human-like smooth reaching motion (2009)

A nonlinear reference shaping method for manipulators which are operated in living environments is proposed. It generates an intermediate reference position, and by connecting the position and the manipulator's endpoint with virtual spring and damper, the robot acceleration is moderated and smooth reaching motion is realized. By feeding back the hand position of the manipulator to the proposed reference shaping controller, the motion of the robot becomes pliant against external forces applied to it without generating excessive pushing forces and large acceleration. Furthermore, according to the initial/desired hand position, the parameter of the reference shaping controller is changed dynamically to avoid large acceleration and generate smoother, human-like reaching motions. The convergence performance to a target hand position is never decreased with the proposed method. The validity of the proposed method is shown through computer simulations on a planar 4-DOF manipulator.
Pairing Devices with Good Quality Output Interfaces (2008)

The operation of achieving authenticated key agreement between two human-operated devices over a short range wireless communication channel, such as Bluetooth or Wi-Fi, is known as "pairing". The devices being paired are ad hoc in nature, i.e., they can not be assumed to have a prior context (such as pre-shared secrets) or a common trusted on- or off-line authority. However, the devices can generally be connected using auxiliary physical channel(s) (such as audio or visual) that can be authenticated by the user(s) of the devices. These authenticatable channels can be used to form a basis for pairing.In this paper, we present the results of a user study of a technique used to pair two devices (such as two cell phones) which have good quality output interfaces in the form of a display, speaker, and/or vibration.