gebhart/patrepeval huggingface dataset:
Description and Interpretation of Adaptive Evolution of Escherichia coli K-12 MG1655 by Using a Genome-Scale In Silico Metabolic Model (2003)

Genome-scale in silico metabolic networks of Escherichia coli have been reconstructed. By using a constraint-based in silico model of a reconstructed network, the range of phenotypes exhibited by E. coli under different growth conditions can be computed, and optimal growth phenotypes can be predicted. We hypothesized that the end point of adaptive evolution of E. coli could be accurately described a priori by our in silico model since adaptive evolution should lead to an optimal phenotype. Adaptive evolution of E. coli during prolonged exponential growth was performed with M9 minimal medium supplemented with 2 g of alpha-ketoglutarate per liter, 2 g of lactate per liter, or 2 g of pyruvate per liter at both 30 and 37 degrees C, which produced seven distinct strains. The growth rates, substrate uptake rates, oxygen uptake rates, by-product secretion patterns, and growth rates on alternative substrates were measured for each strain as a function of evolutionary time. Three major conclusions were drawn from the experimental results. First, adaptive evolution leads to a phenotype characterized by maximized growth rates that may not correspond to the highest biomass yield. Second, metabolic phenotypes resulting from adaptive evolution can be described and predicted computationally. Third, adaptive evolution on a single substrate leads to changes in growth characteristics on other substrates that could signify parallel or opposing growth objectives. Together, the results show that genome-scale in silico metabolic models can describe the end point of adaptive evolution a priori and can be used to gain insight into the adaptive evolutionary process for E. coli.
Common Mechanisms Of Transformation By Small DNA Tumor Viruses (1989)

Based on a 1989 conference in Newport Beach, California. Contributors, mostly from the US and France, present 17 papers that give overviews of common paths to transformation and present mechanisms of transformation and early gene function, the molecular basis for regulation of early gene expression,
Tissue Sealing Concept in Minimally Invasive Surgery in Children (2001)

Background: The Adjustable Minimally Invasive Surgery Applicator (AMISA) is an innovative instrument used for tissue gluing; e.g., for sealing larger defects in parenchymal organs. After the applicator is loaded with an approx. 5 × 10-cm self-adhesive collagen fleece (TachoCombv®), the AMISA can be introduced into the relevant body cavity with the aid of a conventional 10/12-mm trocar. The fleece roll is positioned over the tissue defect and rolled out like a carpet thanks to the rotary applicator head. Methods and Results: Preliminary studies of selective leak closure (SLC) demonstrated that fleece-bound tissue sealing with a ready-to-use collagen fleece coated with tissue glue is efficient. In vitro studies of SLC of porcine pleura demonstrated significantly higher adhesive stability than with liquid gluing methods employing various fleece materials. The main indications are larger-area leakages of parenchymal organs of various origins that cannot be controlled or cannot be taken care of quickly enough with conventional minimally invasive pediatric surgery (MIPS) devices (staplers, high-frequency energy, laser, piezoelectric). Conclusion: Sealing with AMISA expands the range of application for MIPS and simplifies complication management (bleeding, rupture, leakage, secretion). Further economic advantages (decrease in drainage time, reduction in treatment time) are consistent with the principles of minimally invasive therapy in pediatric surgery.
A Rubberlike Stretchable Active Matrix Using Elastic Conductors (2008)

By using an ionic liquid of 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide, we uniformly dispersed single-walled carbon nanotubes (SWNTs) as chemically stable dopants in a vinylidene fluoride-hexafluoropropylene copolymer matrix to form a composite film. We found that the SWNT content can be increased up to 20 weight percent without reducing the mechanical flexibility or softness of the copolymer. The SWNT composite film was coated with dimethyl-siloxane-based rubber, which exhibited a conductivity of 57 siemens per centimeter and a stretchability of 134%. Further, the elastic conductor was integrated with printed organic transistors to fabricate a rubberlike active matrix with an effective area of 20 by 20 square centimeters. The active matrix sheet can be uniaxially and biaxially stretched by 70% without mechanical or electrical damage. The elastic conductor allows for the construction of electronic integrated circuits, which can be mounted anywhere, including arbitrary curved surfaces and movable parts, such as the joints of a robot's arm.
Nobody's Perfect: Billy Wilder and the Postwar American Cinema (2003)

Billy Wilder's reputation as filmmaker is built on his tight, cynical and witty sceenplays. But where is Billy Wilder, the director? In this study of scenes from four films Double Indemnity, Sunset Blvd, Some Like It Hot and The Apartment William Rothman looks for his signature.
Research Notes : United States : A method of isolating poly(A)-containing RNA from soybean suspension culture cells for cDNA synthesis and cloning (1984)

Our laboratories are interested in using recombinant DNA techniques to study the genetics of amino acid metabolism in soybeans. An especially useful technique used to study gene regulation is the in vitro synthesis of DNA com-plementary to mRNA; this cDNA can be used directly as a hybridization probe, or cloned and amplified in a suitable host. The protocol described here was developed for isolating total cellular poly{A)-containing RNA from soybean suspension culture cells of sufficient purity for use as a template for cDNA synthesis.
Tissue‐specific and time‐coordinated hormone regulation of plasminogen‐activator‐inhibitor type I and tissue‐type plasminogen activator in the rat ovary during gonadotropin‐induced ovulation (1991)

The plasminogen-activator system provides proteolytic activity in many biological processes. The regulation of plasminogen activation may occur at many levels including the synthesis and secretion of plasminogen activators (PA) and the specific inhibition of PA activity by inhibitors. PA-inhibitor type-1 (PAI-1) is an efficient inhibitor of tissue-type PA (tPA) and urokinase-type PA (uPA) that may therefore be instrumental for the control of plasminogen activation. To investigate if coordinated regulation of PA and PA inhibitors take place in vivo in response to physiological signals, we have examined the regulation of PAI-1 and tPA in the ovary during gonadotropin-induced ovulation. We found that PAI-1, as well as tPA activity and mRNA levels, were coordinately regulated by gonadotropins in a time-dependent and cell-specific manner, such that a surge of PA-activity was obtained just prior to ovulation. Both theca-interstitial and granulosa cells synthesized PAI-1, but their maximal PAI-1 expression occurred at different times during the periovulatory period, ensuring inhibition of proteolytic activity in ovarian extra cellular compartments both before and after ovulation. The coordinated regulation of tPA and PAI-1 in the ovary may fine-tune the peak of PA activity which may be important for the regulation of the ovulatory process.
On the performance of wide-area thin-client computing (2006)

While many application service providers have proposed using thin-client computing to deliver computational services over the Internet, little work has been done to evaluate the effectiveness of thin-client computing in a wide-area network. To assess the potential of thin-client computing in the context of future commodity high-bandwidth Internet access, we have used a novel, noninvasive slow-motion benchmarking technique to evaluate the performance of several popular thin-client computing platforms in delivering computational services cross-country over Internet2. Our results show that using thin-client computing in a wide-area network environment can deliver acceptable performance over Internet2, even when client and server are located thousands of miles apart on opposite ends of the country. However, performance varies widely among thin-client platforms and not all platforms are suitable for this environment. While many thin-client systems are touted as being bandwidth efficient, we show that network latency is often the key factor in limiting wide-area thin-client performance. Furthermore, we show that the same techniques used to improve bandwidth efficiency often result in worse overall performance in wide-area networks. We characterize and analyze the different design choices in the various thin-client platforms and explain which of these choices should be selected for supporting wide-area computing services.
Antigenic, morphologic, and molecular characterization of new Ehrlichia risticii isolates (1994)

Ehrlichia risticii causes an acute infectious disease in horses called Potomac horse fever. To investigate the biological diversity of E. risticii organisms, nine E. risticii isolates derived from the peripheral blood monocytes of clinically sick horses in Ohio and Kentucky during the summers of 1991 and 1993 were compared with Illinois and Virginia isolates originally obtained from horses in Maryland in 1984. Seven of the nine isolates (081, 606, 380, 679, As, Co, and Ov) formed large morulae (tightly packed inclusions of ehrlichial organisms). The remaining isolates, including 1984 isolates, were individually dispersed or formed small morulae in the cytoplasm of P388D1 cells. In Western blot (immunoblot) analysis with four equine and one rabbit polyclonal anti-E. risticii sera, these recent E. risticii isolates showed patterns of antigenic proteins distinct from those of the 1984 isolates and could be divided into three groups: (i) 081; (ii) 606, 022, 067, 380, and 679; and (iii) As, Co, and Ov. By indirect fluorescent antibody labeling with two panels of murine anti-E. risticii (Illinois and Maryland isolates) monoclonal antibodies, isolate 081 was not labeled with any of 20 monoclonal antibodies tested. The remaining isolates were not labeled with several monoclonal antibodies. The digestion pattern with one of the restriction enzymes, AvaII, of the PCR-amplified partial 16S rRNA gene of E. risticii from all Kentucky isolates (As, Co, and Ov) was different from that of Illinois, Virginia, and six Ohio isolates. These results indicate the presence of distinct variants of E. risticii which vary significantly in morphology, antigenic composition, and the base sequence of the 16S rRNA gene.
Delivery of foreign antigens by engineered outer membrane vesicle vaccines (2010)

As new disease threats arise and existing pathogens grow resistant to conventional interventions, attention increasingly focuses on the development of vaccines to induce protective immune responses. Given their admirable safety records, protein subunit vaccines are attractive for widespread immunization, but their disadvantages include poor immunogenicity and expensive manufacture. We show here that engineered Escherichia coli outer membrane vesicles (OMVs) are an easily purified vaccine-delivery system capable of greatly enhancing the immunogenicity of a low-immunogenicity protein antigen without added adjuvants. Using green-fluorescent protein (GFP) as the model subunit antigen, genetic fusion of GFP with the bacterial hemolysin ClyA resulted in a chimeric protein that elicited strong anti-GFP antibody titers in immunized mice, whereas immunization with GFP alone did not elicit such titers. Harnessing the specific secretion of ClyA to OMVs, the ClyA-GFP fusion was found localized in OMVs, resulting in engineered recombinant OMVs. The anti-GFP humoral response in mice immunized with the engineered OMV formulations was indistinguishable from the response to the purified ClyA-GFP fusion protein alone and equal to purified proteins absorbed to aluminum hydroxide, a standard adjuvant. In a major improvement over current practice, engineered OMVs containing ClyA-GFP were easily isolated by ultracentrifugation, effectively eliminating the need for laborious antigen purification from cell-culture expression systems. With the diverse collection of heterologous proteins that can be functionally localized with OMVs when fused with ClyA, this work signals the possibility of OMVs as a robust and tunable technology platform for a new generation of prophylactic and therapeutic vaccines.
In vivo effects of the anti–interleukin‐6 receptor inhibitor tocilizumab on the B cell compartment (2011)

Tocilizumab induced a significant reduction in the frequency of peripheral preswitch and postswitch memory B cells. In addition, the number of IgG+ and IgA+ B cells declined and correlated well with reduced serum immunoglobulin levels. The data indicate that IL-6 blockade affects the B cell hyperreactivity in RA patients.
Analgesic Effect of Delta‐9‐Tetrahydrocannabinol (1975)

A preliminary trial of oral delta-9-tetrahydrocannabinol (THC) demonstrated an analgesic effect of the drug in patients experiencing cancer pain. Placebo and 5, 10, 15, and 20 mg THC were administered double blind to ten patients. Pain relief significantly superior to placebo was demonstrated at high dose levels (15 and 20 mg). At these levels, substantial sedation and mental clouding were reported.
Synthesis of Metal-Oxide Matrix with Embedded Nickel Nanoparticles by a Bottom-up Chemical Process (2003)

Here we describe a new chemical route for obtaining highly dispersed nanometric Ni particles embedded in different matrices based on Al2O3, MgO, and TiO2 and in the heterogeneous matrices CeO2-doped Al2O3 and MgO-doped Al2O3. The synthesis method is based on a modification of the polymeric precursor method. The Ni nanoparticles (particles in the range of 1-40 nm) were obtained in a single process, without the use of an external reducing agent (hydrogen atmosphere).
Possible mechanism for the influence of weak magnetic fields on biological systems (1991)

A physical mechanism is suggested for a resonant interaction of weak magnetic fields with biological systems. An ion inside a Ca(2+)-binding protein is approximated by a charged oscillator. A shift in the probability of ion transition between different vibrational energy levels occurs when a combination of static and alternating magnetic fields is applied. This in turn affects the interaction of the ion with the surrounding ligands. The effect reaches its maximum when the frequency of the alternating field is equal to the cyclotron frequency of this ion or to some of its harmonics or sub-harmonics. A resonant response of the biosystem to the magnetic field results. The proposed theory permits a quantitative explanation for the main characteristics of experimentally observed effects.
Clinical Ascertainment of Health Outcomes Among Adults Treated for Childhood Cancer (2013)

Among adult survivors of childhood cancer, the prevalence of adverse health outcomes was high, and a systematic risk-based medical assessment identified a substantial number of previously undiagnosed problems that are more prevalent in an older population. These findings underscore the importance of ongoing health monitoring for adults who survive childhood cancer.
Efectividad de un gel de polihexanida al 0,1% (2008)

Durante los ultimos anos han aumentado los estudios sobre la infeccion de las heridas cronicas, dando lugar a nuevos terminos como el de colonizacion critica o biofilms bacterianos que, junto con las condiciones de base del paciente, estan intimamente relacionados con el proceso de cicatrizacion, especialmente con el estancamiento o retroceso del mismo. Por ello se evalua la efectividad de un producto de polihexanida 0,1% (Prontosan Gel®) frente a las recomendaciones sobre la limpieza de heridas del GNEAUPP y la AHCPR (Agency for Health Care Policy and Research) en el control de la carga bacteriana de las heridas cronicas. 
Los datos obtenidos en la valoracion final de las lesiones han sido: reversion de cultivos positivos (p=0,004); mejora en el estancamiento del proceso de cicatrizacion (p=0,000); disminucion de la superficie de la lesion (p=0,013); mejora del porcentaje de tejido de granulacion (p=0,001), del porcentaje de esfacelos en el lecho de la herida (p=0,002), de la presencia de exudado (p=0,008), de exudado purulento (p=0,005), del estado de la piel perilesional (p=0,021); control del dolor (p=0,049), del eritema de la piel perilesional (p=0,004), del edema de la piel perilesional (p=0,000), del calor de la piel perilesional (p=0,004) y del olor (p=0,029). 
La utilizacion de este producto propicia la limpieza del lecho de la herida de esfacelos desvitalizados; favorece el control bacteriano y la reduccion de los biofilms y el manejo de la infeccion local de las lesiones; estimula la granulacion, favoreciendo el control de las ulceras estancadas, sin evolucion, en su proceso de cicatrizacion, sin efectos toxicos sobre el tejido de neoformado; beneficia la cicatrizacion de las lesiones disminuyendo el tiempo de cierre; aumenta la calidad al controlar el dolor, olor y el estado de los tejidos circundantes (edema, eritema, maceracion...).
Relationship between gene polymorphisms of mannose‐binding lectin (MBL) and two molecular forms of MBL (2003)

Mannose-binding lectin (MBL) activates complement through MBL-associated serine proteases (MASP). A deficiency in MBL due to mutations at exon 1 of the human MBL gene is reported to cause vulnerability to infection. We examined sera of known MBL genotype by gel filtration and assessed their elution patterns using an ELISA for MBL and identified two MBL forms, a high-molecular-mass form and a lower-molecular-mass form. By the identification of either or both forms in individual sera, three types of patterns emerged: type 1 consisted of a high-molecular form; type 2, of a low-molecular form; and type 3, of both forms. Types 1, 2 and 3 corresponded, respectively, to a wild type (A/A), a homozygous mutation at codon 54 (B/B) and their heterozygote (A/B). One exception was a heterozygous LXPA/LYPB phenotype that exhibited the type-2 pattern. Binding to mannan and MASP-1/3 occurred exclusively with the high-molecular form. An apparent MBL deficiency does not in fact representa deficiency in MBL molecules but rather the presence of circulating oligomeric mutant MBL with impaired function.
Ontogeny of human mannan‐binding protein, a lectin of the innate immune system (1995)

Mannan-binding protein (MBP) is a member of the collectins. These lectins are composed of polypeptide chains which contains a collagen-like region and a calcium dependent carbohydrate recognition domain (named a C-type CRD). MBP binds via the CRD to carbohydrate structures on microorganisms. MBP can activate the complement system when bound to carbohydrate. MBP is thus thought to play a role in the defence against microorganisms. The present report describes the ontogeny of MBP. The level of MBP increase during the first 3 months of life, at which time a stable level is reached, comparable to that seen in adults. On average, the level of MBP at term was 37% of the post 3-month level. Measurements on infants born prematurely showed a 3-fold increase in MBP concentration from the time of birth at around 30 weeks from conception to the 10th week of life.
Marked acceleration of exogenous fatty acid incorporation into cellular triglycerides by fetuin. (1990)

Fetuin belongs to a group of fetal glycoproteins whose specific function is not known. In this study we investigated the effect of bovine fetuin on exogenous fatty acid incorporation into lipid classes by fetal rabbit aortic smooth muscle cells (SMC) and human fetal skin fibroblasts. When compared with albumin, the addition of fetuin to the culture medium caused a dramatic increase in labeled fatty acid incorporation (nanomoles/mg of protein) by SMC into triglycerides (albumin (control) 2.8 +/- 0.3 + fetuin 178.3 +/- 13.7). This effect was noted at a wide range of fetuin concentrations (0.2-5%) at oleate:fetuin molar ratios of 3.3-0.13, respectively. Similar effects were noted using human fetal skin fibroblasts with both labeled oleic and arachidonic acids (0.1 mM) as substrates (arachidonic acid incorporation into triglycerides, albumin (control) 76.9 +/- 16.2 + fetuin 684.6 +/- 64.1). Stimulation of fatty acid incorporation into di- and monoglycerides was also noted. Although the amount of unbound fatty acid in the presence of fetuin was greater than with albumin, experiments done under conditions that create identical unbound oleate levels (by varying fatty acid concentration) still showed increased fatty acid incorporation into triglycerides by SMC when exposed to fetuin. This marked effect of fetuin on triglyceride accumulation in cells was confirmed by lipid analysis, strong positive staining with oil red O, and transmission of electron microscopy. Furthermore, the potential physiological role of fetuin in terms of fatty acid and transport was attested by (a) the presence of significant amounts of free fatty acids associated with fetuin; and (b) by the stimulatory effect of fetuin, even when added to culture media containing other fatty acid carriers. These results show that (a) fetuin is far more efficient than albumin in incorporating fatty acids into cells; and (b) this might represent a novel function for fetuin during development.
A specific inhibitor of phosphatidylinositol 3-kinase, 2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one (LY294002). (1994)

Phosphatidylinositol (PtdIns) 3-kinase is an enzyme implicated in growth factor signal transduction by associating with receptor and nonreceptor tyrosine kinases, including the platelet-derived growth factor receptor. Inhibitors of PtdIns 3-kinase could potentially give a better understanding of the function and regulatory mechanisms of the enzyme. Quercetin, a naturally occurring bioflavinoid, was previously shown to inhibit PtdIns 3-kinase with an IC50 of 1.3 microgram/ml (3.8 microM); inhibition appeared to be directed at the ATP-binding site of the kinase. Analogs of quercetin were investigated as PtdIns 3-kinase inhibitors, with the most potent ones exhibiting IC50 values in the range of 1.7-8.4 micrograms/ml. In contrast, genistein, a potent tyrosine kinase inhibitor of the isoflavone class, did not inhibit PtdIns 3-kinase significantly (IC50 > 30 micrograms/ml). Since quercetin has also been shown to inhibit other PtdIns and protein kinases, other chromones were evaluated as inhibitors of PtdIns 3-kinase without affecting PtdIns 4-kinase or selected protein kinases. One such compound, 2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one (also known as 2-(4-morpholinyl)-8-phenylchromone, LY294002), completely and specifically abolished PtdIns 3-kinase activity (IC50 = 0.43 microgram/ml; 1.40 microM) but did not inhibit PtdIns 4-kinase or tested protein and lipid kinases. Analogs of LY294002 demonstrated a very selective structure-activity relationship, with slight changes in structure causing marked decreases in inhibition. LY294002 was shown to completely abolish PtdIns 3-kinase activity in fMet-Leu-Phe-stimulated human neutrophils, as well as inhibit proliferation of smooth muscle cells in cultured rabbit aortic segments. Since PtdIns 3-kinase appears to be centrally involved with growth factor signal transduction, the development of specific inhibitors against the kinase may be beneficial in the treatment of proliferative diseases as well as in elucidating the biological role of the kinase in cellular proliferation and growth factor response.