gebhart/patrepeval huggingface dataset:
How to Monitor Scale Inhibitor Squeeze Using Simple TRF Tracers (2015)

Abstract Mineral scale deposition in oilfield reservoirs has caused millions of dollars in damage every year. The most common remedy to the build-up of scale inside well bores and the surrounding reservoir is the periodical “squeeze” treatment by inhibitor additives. The real-time and on-site control of inhibitor concentration during production remains one of the big challenges. Indeed, current techniques of inhibitor monitoring that use elemental analysis appear too complex for an efficient long-term industrial solution. With this in mind, we have developed a simple and accurate method for scale inhibitor quantification in production waters based on the use of time-resolved fluorescence (TRF) tracers. The characteristic luminescence signature (lifetime value, emission and excitation spectra) of TRF tracers allows the reliable tracking of inhibitors additives. Moreover, their long-lifetime luminescence signal can significantly increase the signal to noise ratio thanks to the suppression of organic oil residual background emission. Our experimental tests on produced water collected from different sites confirm the detection of a larger variety of inhibitors i.e. for carboxylates, phosphonates and sulphonates by simple post-chelation with TRF tracers at low concentration. Indeed, the non-fluorescent inhibitor species have been switched to fluorescent compound by the addition of few amounts of tracer in order to be detectable and quantified at sub-ppm concentrations. The coupling between TRF tracers and specific TRF spectrofluorometer apparatus then open new and accurate ways for the online and/or on-site monitoring of scale inhibitors for better risk management of flow assurance during production.
Über Pyrrolidin‐3‐ und Pyrazolin‐4‐spiro‐1′‐isothiochromane und ‐isochromane. 12. Mitt. über Untersuchungen in der Isochroman‐ und Isothiochroman‐Reihe (1974)

Abstract Aus 1‐Cyan‐isothiochroman bzw. ‐isochroman sind durch Umsetzung mit Chloracetonitril 1‐Cyan‐1‐cyanmethyl‐isothiochroman ( 1a ) bzw. ‐isochroman ( 1c ) zugänglich, die sich durch Verseifung in 2,5‐Dioxo‐pyrrolidin‐(3‐spiro‐1′)‐isothiochroman ( 2a ) bzw. ‐isochroman ( 2c ) überführen lassen. – 1‐Cyan‐isothiochroman‐1‐carbonsäuremethylester ( 4 ) und Hydrazin können zu 3‐Amino‐5‐oxo‐pyrazolin‐ bzw. 3‐Imino‐5‐oxo‐pyrazolidin‐(4‐spiro‐ 1′)‐isothiochroman ( 6 bzw. 5 ) kondensiert werden.
Measurement of serum hyaluronic acid in patients with chronic hepatitis C and its relationship to liver histology (2000)

Serum HA measurement may be clinically useful to non-invasively assess the degree of fibrosis and cirrhosis. Further prospective studies are warranted to determine the clinical utility of HA as a non-invasive marker of liver fibrosis.
From Cloning to a Commercial Realization: Human Alpha Interferon (1990)

Recent applications of recombinant DNA techniques have enabled the cloning of several interesting human genes, leading to the production of rare biologicals in abundant quantities. We review here the discovery, early characterization, cloning, and expression of Interferon Alfa-2B (IFN alpha-2b or Intron A) as a therapeutic at Schering-Plough Research. IFN alpha-2a is marketed by Hoffman LaRoche under the trade name Roferon. The studies on the expression, purification, biology, and clinical aspects of this interferon offer a plethora of information on one of the earliest recombinant DNA based drugs to reach the market place.
Inhibition of Hypoxia‐Induced Gene Transcription by Substituted Pyrazolyl Oxadiazoles: Initial Lead Generation and Structure–Activity Relationships (2013)

The transcription factors hypoxia-inducible factor-1 and -2 (HIF-1 and HIF-2) orchestrate a multitude of processes that allow tumor cells to survive under conditions of low oxygen and nutrients, and that lead to resistance to some apoptotic pathways and facilitate invasion and metastasis. Therefore, inhibition of transactivation by HIF has become an attractive target in cancer research. Herein we present the results of a cell-based screening approach that led to the discovery of substituted 1H-pyrazole-3-carboxamides. Chemical optimization of the hit class with respect to potency and metabolic stability is described; it resulted in novel 5-(1H-pyrazol-3-yl)-1,2,4-oxadiazoles that inhibit the hypoxia-induced accumulation of HIF-1α and HIF-2α. The HIF inhibitory potency in the screening cell system was improved from IC₅₀ 190 to 0.7 nM, and significant parts of the SAR are disclosed. For a key compound, the ability to suppress the hypoxia-induced expression of HIF target genes was studied in A549 human lung adenocarcinoma cells. The same compound shows a favorable pharmacokinetic profile in rats after i.v. and p.o. administration.
Cystic Fibrosis Locus Defined by a Genetically Linked Polymorphic DNA Marker (1985)

A polymorphic DNA marker has been found genetically linked, in a set of 39 human families, to an autosomal recessive gene that causes cystic fibrosis (CF), a disease affecting one in 2000 Caucasian children. The DNA marker (called D0CRI-917) is also linked to the PON locus, which by independent evidence is linked to the CF locus. The best estimates of the genetic distances are 5 centimorgans between the DNA marker and PON and 15 centimorgans between the DNA marker and the CF locus, meaning that the location of the disease gene has been narrowed to about 1 percent of the human genome (about 30 million base pairs). Although the data are consistent with the interpretation that a single locus causes cystic fibrosis, the possibility of genetic heterogeneity remains. The discovery of a linked DNA polymorphism is the first step in molecular analysis of the CF gene and its causative role in the disease.
New prostheses for use in bypass grafts with special emphasis on polyurethanes (2002)

Vascular bypass procedures using traditional prosthetic grafts such as polytetrafluoroethylen (PTFE) and polyethylene tetraphthlate (Dacron) are prone to failure when used in low flow states such as in below knee bypass and when the diameter of the graft is less than 6 mm. A major factor in this is compliance mismatch between the graft and the diseased vessel, which may cause intimal hyperplasia at the distal anastomosis. PTFE and Dacron are rigid grafts with poor compliance. By improving the compliance of the prosthetic graft it is hoped that patency will improve. Recent advances in polyurethane chemistry have developed materials that do not degrade and which allow compliance matching of the graft to the patient's vasculature. It is now possible to manufacture biologically and haemodynamically compatible grafts with small diameter from these polyurethane graft materials. This review will focus on the lack of compliance in current vascular bypass grafts and the promise of the new polyurethane polymers in a new generation of small-bore bypass grafts.
Dendritic Cells Augment Choroidal Neovascularization (2008)

These results suggest a role for DCs in promoting angiogenesis and lesion growth in laser-induced CNV. The present data suggest that DCs may represent potential cellular targets for therapeutic intervention in wet ARMD.
Negative Regulation of Mixed Lineage Kinase 3 by Protein Kinase B/AKT Leads to Cell Survival (2003)

Mixed lineage kinase 3 (MLK3) is a mitogen-activated protein kinase kinase kinase (MAPKKK) that activates c-jun N-terminal kinase (JNK) and can induce cell death in neurons. By contrast, the activation of phosphatidylinositol 3-kinase and AKT/protein kinase B (PKB) acts to suppress neuronal apoptosis. Here, we report a functional interaction between MLK3 and AKT1/PKBalpha. Endogenous MLK3 and AKT1 interact in HepG2 cells, and this interaction is regulated by insulin. The interaction domain maps to the C-terminal half of MLK3 (amino acids 511-847), and this region also contains a putative AKT phosphorylation consensus sequence. Endogenous JNK, MKK7, and MLK3 kinase activities in HepG2 cells are significantly attenuated by insulin treatment, whereas the phosphatidylinositol 3-kinase inhibitors LY294002 and wortmannin reversed the effect. Finally, MLK3-mediated JNK activation is inhibited by AKT1. AKT phosphorylates MLK3 on serine 674 both in vitro and in vivo. Furthermore, the expression of activated AKT1 inhibits MLK3-mediated cell death in a manner dependent on serine 674 phosphorylation. Thus, these data provide the first direct link between MLK3-mediated cell death and its regulation by a cell survival signaling protein, AKT1.
Catalytic nanomaterials for amplified biosensing (2018)

Accurate, timely, and sensitive diagnosis is the first step in appropriately treating disease. The development of diagnostics that can be used in non-hospital and point-of-care (PoC) settings is key for democratizing access to disease diagnosis and treatment when it is most effective. The application of PoC diagnostics in early disease detection is often limited due to insufficient sensitivity for the short time frames and limited resources available in these settings. To overcome these challenges, this thesis presents the synthesis, characterization, and application of catalytic nanomaterials for signal amplification and enhanced sensitivity in PoC diagnostic platforms. The nanomaterials developed here span a broad size regime from 1.5 nm clusters of atoms to 300 nm diameter particles and have been demonstrated for use in both in vitro and in vivo biosensing platforms. The platinum and gold nanomaterials exhibited robust and efficient peroxidase-like activity in their ability to oxidize chromogenic substrates in the presence of hydrogen peroxide to generate additional colored signals that could be used for amplification of disease detection, even after exposure to harsh conditions such as elevated temperatures. The larger catalytic nanomaterials were employed as extraordinarily stable and highly amplifying labels in a simple paper-based lateral flow assay (LFA). The nanocatalyst-labeled LFA surpassed the sensitivities of both commercial and published reports to date for paper-based detection of p24, one of the earliest and most conserved biomarkers of HIV. The smaller catalytic nanoclusters were efficiently renally cleared and were deployed in a modular nanosensor platform to monitor disease-associated protease activity in vivo. Catalytic activity of cleared gold nanoclusters in collected urine provided a simple, sensitive, and rapid colorimetric urinary readout of disease state. The clinical utility of both platforms presented here was investigated through detection of acute phase HIV in clinical human plasma samples using the nanocatalyst-labeled LFA, and successful non-invasive detection of tumors in a mouse model of colorectal cancer using the protease-nanosensors with colorimetric urinary readout. This thesis demonstrates the broad applicability and versatility of catalytic nanoparticle amplification for use in disease detection. A pipeline for further development of both sensing platforms for detection of other biomolecules at the PoC is presented.
Augmented Production of Panton‐Valentine Leukocidin Toxin in Methicillin‐Resistant and Methicillin‐SusceptibleStaphylococcus aureusIs Associated with Worse Outcome in a Murine Skin Infection Model (2009)

The role of Panton-Valentine leukocidin (PVL) in Staphylococcus aureus infections is controversial. We used a mouse model of skin infection to compare the virulence of methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) strains with different levels of PVL production. Differences in PVL production were not associated with mutations in the genes lukS-PV and lukF-PV. However, MSSA and MRSA strains that produced high levels of PVL caused larger skin abscesses, higher bacterial burdens, and more tissue inflammation than did low-PVL-producing strains. Together, these data suggest that (1) the effect of PVL on the pathogenesis of staphylococcal infection may depend on the level of toxin produced and (2) many strains of MSSA that cause soft-tissue infections produce higher levels of PVL than do MRSA strains.
Atlas of Heart Failure (2008)

Epidemiology of Heart Failure.- Molecular and Cellular Basis of Heart Failure.- Pathologic Etiologies of Heart Failure.- Cardiac Remodeling.- Cardiac Function in Heart Failure.- Neurohormones, Renal and Vascular.- Clinical Syndromes of Acute and Chronic Heart Failure.- Diuretics and Digitalis.- Renin-Angiotensin-Aldosterone System Inhibition.- Beta-Blockers.- New Approaches to Therapy.- Cardiac Resynchronization Therapy.- Diastolic Heart Failure.- Management of the Hospitalized Patient.- Mechanical Assist Devices.- Transplantation.
Recombinant Human Parvovirus B19 Vectors: Erythroid Cell-Specific Delivery and Expression of Transduced Genes (1998)

A novel packaging strategy combining the salient features of two human parvoviruses, namely the pathogenic parvovirus B19 and the nonpathogenic adeno-associated virus type 2 (AAV), was developed to achieve erythroid cell-specific delivery as well as expression of the transduced gene. The development of such a chimeric vector system was accomplished by packaging heterologous DNA sequences cloned within the inverted terminal repeats of AAV and subsequently packaging the DNA inside the capsid structure of B19 virus. Recombinant B19 virus particles were assembled, as evidenced by electron microscopy as well as DNA slot blot analyses. The hybrid vector failed to transduce nonerythroid human cells, such as 293 cells, as expected. However, MB-02 cells, a human megakaryocytic leukemia cell line which can be infected by B19 virus following erythroid differentiation with erythropoietin (N. C. Munshi, S. Z. Zhou, M. J. Woody, D. A. Morgan, and A. Srivastava, J. Virol. 67:562-566, 1993) but lacks the putative receptor for AAV (S. Ponnazhagan, X.-S. Wang, M. J. Woody, F. Luo, L. Y. Kang, M. L. Nallari, N. C. Munshi, S. Z. Zhou, and A. Srivastava, J. Gen. Virol. 77:1111-1122, 1996), were readily transduced by this vector. The hybrid vector was also found to specifically target the erythroid population in primary human bone marrow cells as well as more immature hematopoietic progenitor cells following erythroid differentiation, as evidenced by selective expression of the transduced gene in these target cells. Preincubation with anticapsid antibodies against B19 virus, but not anticapsid antibodies against AAV, inhibited transduction of primary human erythroid cells. The efficiency of transduction of primary human erythroid cells by the recombinant B19 virus vector was significantly higher than that by the recombinant AAV vector. Further development of the AAV-B19 virus hybrid vector system should prove beneficial in gene therapy protocols aimed at the correction of inherited and acquired human diseases affecting cells of erythroid lineage.
Biodegradable Nanogels Prepared by Atom Transfer Radical Polymerization as Potential Drug Delivery Carriers:  Synthesis, Biodegradation, in Vitro Release, and Bioconjugation (2007)

Stable biodegradable nanogels cross-linked with disulfide linkages were prepared by inverse miniemulsion atom transfer radical polymerization (ATRP). These nanogels could be used for targeted drug delivery scaffolds for biomedical applications. The nanogels had a uniformly cross-linked network, which can improve control over the release of encapsulated agents, and the nanogels biodegraded into water-soluble polymers in the presence of a biocompatible glutathione tripeptide, which is commonly found in cells. The biodegradation of nanogels can trigger the release of encapsulated molecules including rhodamine 6G, a fluorescent dye, and Doxorubicin (Dox), an anticancer drug, as well as facilitate the removal of empty vehicles. Results obtained from optical fluorescence microscope images and live/dead cytotoxicity assays of HeLa cancer cells suggested that the released Dox molecules penetrated cell membranes and therefore could suppress the growth of cancer cells. Further, OH-functionalized nanogels were prepared to demonstrate facile applicability toward bioconjugation with biotin. The number of biotin molecules in each nanogel was determined to be 142,000, and the formation of bioconjugates of nanogels with avidin was confirmed using optical fluorescence microscopy.
On the Maximum Throughput of a Combined Input-Crosspoint Queued Packet Switch (2006)

Combined input-crosspoint buffered (CICB) packet switches have been of research interest in the last few years because of their high performance. These switches provide higher performance than input-buffered (IB) packet switches while requiring the crosspoint buffers run at the same speed as that of the input buffers in IB switches. Recently, it has been shown that CICB switches with one-cell crosspoint buffers, virtual output queues, and simple input and output arbitrations, provide 100% throughput under uniform traffic. However, it is of general interest to know the maximum throughput that a CICB switch, with no speedup, can provide under admissible traffic. This paper analyzes the throughput performance of a CICB switch beyond uniform traffic patterns and shows that a CICB switch with one-cell crosspoint buffers can provide 100% throughput under admissible traffic while using no speedup.
Electrosynthesis of Benzolactones by Nickel-Catalyzed Carboxylation of Epoxide-Functionalized Aromatic Halides (2000)

The electrochemical, nickel-catalyzed carbon dioxide incorporation into 2-haloaryl epoxides led chemoselectively to different carboxylated products according to the nature of the substrate and to the catalytic system. Whereas terminal epoxide derivatives led to cyclic carbonates in good yields, disubstituted epoxides reacted through a first carbon-halogen bond carboxylation followed by epoxide ring opening. Five-membered ring benzolactones were selectively formed with cyclam as the ligand, whereas 6-membered ring isocoumarine derivatives were obtained using 2,2′-bipyridine.
SchemaPath: Extending XML Schema for Co-Constraints (2004)

PDF and gzipped PostScript formats via anonymous FTP from the area ftp.cs.unibo.it:/pub/TR/UBLCS or via WWW at
Biological Response Modifier Activity of an Exopolysaccharide fromPaenibacillus jamilaeCP-7 (2001)

An extracellular polysaccharide was purified from culture supernatants of Paenibacillus jamilae CP-7, a gram-positive bacillus that was isolated from compost prepared with olive mill wastewaters. The extracellular polysaccharide was produced under aerobic conditions in a medium containing olive mill wastewaters (80% [vol/vol]). This exopolymer had a low level of acute toxicity when it is administered to BALB/c mice by the intraperitoneal route. Interesting immunomodulatory effects were detected when mice were given 10 mg of exopolysaccharide per kg of body weight; the proliferative responses of splenocytes to B-cell and T-cell mitogens were suppressed, the in vitro levels of production of gamma interferon and granulocyte-macrophage colony-stimulating factor by unstimulated and lipopolysaccharide-stimulated splenocytes were enhanced, and the levels of resistance to the intracellular pathogen Listeria monocytogenes was increased in mice. Also, the exopolysaccharide was able to induce lymphocyte proliferation in vitro. We conclude that P. jamilae produces an exopolysaccharide with interesting immunomodulatory properties.
The Role of RNA and Protein in Ribosome Function: A Review of Early Reconstitution Studies and Prospects for Future Studies (1987)

Although the major research effort of our laboratory during recent years has been on the genes for ribosomal components and the regulation of their expression, I have agreed to write an article reviewing the earlier work related to ribosome structure and function, based mostly on our own research on ribosome reconstitution from the late 1960s to the early 1970s, as well as studies on ribosome mutations in general.
Biological availability and nuclease resistance extend thein vitroactivity of a phosphorothioate-3′hydroxypropylamine oligonucleotide (1994)

Augmented biological activity in vitro has been demonstrated in oligonucleotides (oligos) modified to provide nuclease resistance, to enhance cellular uptake or to increase target affinity. How chemical modification affects the duration of effect of an oligo with potent activity has not been investigated directly. We postulated that modification with internucleotide phosphorothioates and 3' alkylamine provided additional nuclease protection which could significantly extend the biological activity of a 26 mer, (T2). We showed this analog, sT2a, could maximally inhibit interferon gamma-induced HLA-DR mRNA synthesis and surface expression in both HeLa and retinal pigmented epithelial cells and could continue to be effective, in the absence of oligo, 15 days following initial oligo treatment; an effect not observed with its 3'amine counterpart, T2a. In vitro stability studies confirmed that sT2a conferred the greatest stability to nucleases and that cellular accumulation of 32P-sT2a in both cell types was also greater than other T2 oligos. Using confocal microscopy, we revealed that the intracellular distribution of sT2a favored greater nuclear accumulation and release of oligo from cytoplasmic vesicles; a pattern not observed with T2a. These results suggest that phosphorothioate-3'amine modification could increase the duration of effect of T2 oligo by altering nuclease resistance as well as intracellular accumulation and distribution; factors known to affect biological availability.
T4 cell activation by immobilized phytohemagglutinin: differential capacity to induce IL-2 responsiveness and IL-2 production. (1988)

Soluble mitogens, such as PHA induce accessory cell (AC)-dependent T cell proliferation. One function of the AC is to create a stimulatory matrix. Therefore, experiments were carried out to determine whether PHA immobilized onto microtiter plates could stimulate T cells in the absence of AC. Peripheral blood T4 cells were cultured under limiting dilution conditions with either soluble or immobilized PHA with or without rIL-1 beta, rIL-2, r-TNF-alpha, an anti-CD28 mAb (9.3), or irradiated EBV-transformed B cells as AC. The frequency of proliferating T4 cells was assessed by examining wells microscopically, and the frequency of T4 cells producing IL-2 was assessed by examining the ability of supernatants to support CTLL-2 proliferation. The percentage of T4 cells growing and producing IL-2 was determined by a maximum likelihood procedure. Immobilized, but not soluble, PHA induced a mean of 20.0 +/- 2.6% of T4 cells to grow in the complete absence of AC in medium supplemented with rIL-2. Whereas rIL-1 beta, rTNF-alpha, and 9.3 were unable to support T4 cell growth in the absence of rIL-2, each enhanced the percentage of T4 cells responding to immobilized PHA in the presence of rIL-2. In contrast, both soluble and immobilized PHA were unable to induce T4 cell IL-2 production in the absence of AC, even when cultures were supplemented with rIL-1 beta or 9.3. In the presence of AC, a small percentage of T4 cells (5.4 to 11.7%) was stimulated to produce detectable amounts of IL-2 by either immobilized or soluble PHA. Moreover, in the presence of AC, a very small population (approximately 1%) of PHA-stimulated T4 cells proliferated without supplemental rIL-2. The data indicate that a matrix of immobilized PHA is sufficient for some T4 cells to be activated to respond to IL-2, whereas others require additional signals provided by rIL-1 beta, rTNF alpha, 9.3, or AC. In contrast, neither soluble nor immobilized PHA is sufficient to induce T cell IL-2 production. This response requires signals provided by intact AC.