gebhart/patrepeval huggingface dataset:
Invasive aspergillosis: clinical and pathological features of a new animal model (1989)

A new animal model of invasive aspergillosis is described in which female New Zealand White rabbits were immunosuppressed with corticosteroids and cyclophosphamide and were given an intratracheal inoculation of 4 × 104 conidia of <it>Aspergillus fumigatus</it>. Thirteen of 15 animals survived during a 10-day-period of observation. Most had clinical signs of a respiratory infection (dyspnoea) and at autopsy there was macroscopic and microscopic evidence of invasive pulmonary aspergillosis. Six control animals (infected but not immunosuppressed) showed no such signs. The extent of hyphal invasion was assessed histologically and quantified by calculating the number of colony forming units (c.f.u.) g-1 of tissue: in the experimental group the mean c.f.u. value for the lungs was 1·25 × 103 compared to 73·3 c.f.u. g-1 of lung for the control group (<it>P</it>=0·003). The infection was also quantified by a whole lung chitin assay: in the experimental group the mean chitin content (expressed as a glucosamine equivalent) was 3·05 μg g-1 lung tissue compared to a 0·53 μg g-1 lung tissue for the control group (<it>P</it>=0·01). We conclude that this model of invasive aspergillosis in rabbits reflects closely the pathological features of the disease in man and that it may prove useful for studies of the pathogenesis and the treatment of invasive aspergillosis.
High-Yield Passive Plasma Filtration from Human Finger Prick Blood (2018)

Whole-blood microsampling provides many benefits such as remote, patient-centric, and minimally invasive sampling. However, blood plasma, and not whole blood, is the prevailing matrix in clinical laboratory investigations. The challenge with plasma microsampling is to extract plasma volumes large enough to reliably detect low-concentration analytes from a small finger prick sample. Here we introduce a passive plasma filtration device that provides a high extraction yield of 65%, filtering 18 μL of plasma from 50 μL of undiluted human whole blood (hematocrit 45%) within less than 10 min. The enabling design element is a wedge-shaped connection between the blood filter and the hydrophilic bottom surface of a capillary channel. Using finger prick and venous blood samples from more than 10 healthy volunteers, we examined the filtration kinetics of the device over a hematocrit range of 35-55% and showed that 73 ± 8% of the total protein content was successfully recovered after filtration. The presented plasma filtration device tackles a major challenge toward patient-centric blood microsampling by providing high-yield plasma filtration, potentially allowing reliable detection of low-concentration analytes from a blood microsample.
Combinatorial Solution to the Partitioning of General Graphs (1975)

This paper reviews a dynamic programming procedure for the partitioning of connected graphs with integer-weighted nodes and positive valued edges. The upper bound on the number of feasible partitions generated using this technique is shown to grow factorially in the number of graph nodes. The use of graph properties is then introduced to reduce the number of feasible partitions generated in the determination of the optimal partition. Depending upon the structure of the graph, the use of these properties can cause a significant reduction in the computation time and storage space required to partition the graph.
Iodide Ions Control Seed-Mediated Growth of Anisotropic Gold Nanoparticles (2008)

There are now a variety of preparatory procedures for nanoscale gold rods, triangular prisms, and spheres. Many of these methods rely on seed-mediated approaches with cetyltrimethylammonium bromide (CTABr) as a surfactant. Interestingly, seemingly similar preparatory procedures yield very different morphologies, and although there have been a variety of proposals regarding the importance of different steps in shape control, there is no self-consistent procedure that allows one to take one batch of spherical seeds and grow either rods, prisms, or larger polyhedra in a controlled manner. In this report, it is shown that CTABr, depending upon supplier, has an iodide contaminant (at a significant but varying level), which acts as a key shape-directing element because it can strongly and selectively bind to the Au (111) facet and favor the formation of anisotropic structures. Furthermore, by starting with pure CTABr and deliberately adjusting iodide concentration, one can reproducibly drive the reaction to predominantly produce one of the three target morphologies.
Bovine Antigens and the Formation of Circulating Immune Complexes in Selective Immunoglobulin A Deficiency (1979)

We have shown that levels of circulating immune complexes are closely associated with the presence of precipitating antibodies to bovine milk proteins in individuals with selective immunoglobin (Ig)A deficiency. To test whether milk proteins are involved in immune complex formation, sera of seven IgA-deficient individuals were studied for the appearance of complexes after milk ingestion. In three of the seven, an initial fall in the level of complexes was followed by an increasing value, which peaked at 120-150 min. In another three, there was a tendency toward the formation of two peaks of complexes, the first at 30-60 min and the second at 120-150 min after drinking milk. One subject, who had had recent treatment for two separate neoplasms, had a steady level of complexes that did not change during the course of this test. After drinking milk, the molecular weight of the complexes found in the sera of one individual at the start of the milk test fell from >19S to 7-11S, and in vitro additions of progressively increasing amounts of a mixture of milk proteins or bovine gamma globulin, to sera that contained complexes produced a progressive reduction in the level of complexes detectable. We conclude that the circulating immune complexes found in some patients who lack IgA contain bovine milk proteins and that periodic fluctuation of the molecular weight of such complexes, depending upon antigen ingestion, appears likely. It remains uncertain what effect the chronic circulation of complexes has upon the clinical state of this group of patients.
Glatiramer in the treatment of multiple sclerosis-0 (2011)

Multiple sclerosis (MS) is a disease of the central nervous system with both an inflammatory and degenerative component. The disease primarily affects young adults and results in significant physical and cognitive disability. Several disease-modifying agents are currently used in the management of multiple sclerosis. Glatiramer acetate (GA, Copaxone, co-polymer 1) is a disease-modifying agent approved for the treatment of relapsing remitting multiple sclerosis. Apart from its unique mode of action, there is evidence pointing toward a possible neuroprotective role. This review will critically discuss GA's potential mechanisms of action, the results of clinical trials, safety profile, and future directions of treatment.
Del territorio minado al MediaPark (2010)

Cluster analysis of gene-wide expression data from DNA microarray hybridization studies has proved to be a useful tool for identifying biologically relevant groupings of genes and constructing gene regulatory networks. The motivation for considering mutual information is its capacity to measure a general dependence among gene random variables. We propose a novel clustering strategy based on minimizing mutual information among gene clusters. Simulated annealing is employed to solve the optimization problem. Bootstrap techniques are employed to get more accurate estimates of mutual information when the data sample size is small. Moreover, we propose to combine the mutual information criterion and traditional distance criteria such as the Euclidean distance and the fuzzy membership metric in designing the clustering algorithm. The performances of the new clustering methods are compared with those of some existing methods, using both synthesized data and experimental data. It is seen that the clustering algorithm based on a combined metric of mutual information and fuzzy membership achieves the best performance. The supplemental material is available at www.gspsnap.tamu.edu/gspweb/zxb/glioma_zxb.
Positional dependence of particles in microfludic impedance cytometry (2011)

Single cell impedance cytometry is a label-free electrical analysis method that requires minimal sample preparation and has been used to count and discriminate cells on the basis of their impedance properties. This paper shows experimental and numerically simulated impedance signals for test particles (6 μm diameter polystyrene) flowing through a microfluidic channel. The variation of impedance signal with particle position is mapped using numerical simulation and these results match closely with experimental data. We demonstrate that for a nominal 40 μm × 40 μm channel, the impedance signal is independent of position over the majority of the channel area, but shows large experimentally verifiable variation at extreme positions. The parabolic flow profile in the channel ensures that most of the sample flows through the area of uniform signal. At high flow rates inertial focusing is observed; the particles flow in equal numbers through two equilibrium positions reducing the coefficient of variance (CV) in the impedance signals to negligible values.
Whole-Genome Sequence Characterization of Primary Auxin-Responsive <I>Aux/IAA</I> Gene Family in Sorghum (<I>Sorghum bicolor</I> L.) (2010)

摘要：
Methanobactin and <scp>MmoD</scp> work in concert to act as the ‘copper‐switch’ in methanotrophs (2013)

Biological oxidation of methane to methanol by aerobic bacteria is catalysed by two different enzymes, the cytoplasmic or soluble methane monooxygenase (sMMO) and the membrane-bound or particulate methane monooxygenase (pMMO). Expression of MMOs is controlled by a 'copper-switch', i.e. sMMO is only expressed at very low copper : biomass ratios, while pMMO expression increases as this ratio increases. Methanotrophs synthesize a chalkophore, methanobactin, for the binding and import of copper. Previous work suggested that methanobactin was formed from a polypeptide precursor. Here we report that deletion of the gene suspected to encode for this precursor, mbnA, in Methylosinus trichosporium OB3b, abolishes methanobactin production. Further, gene expression assays indicate that methanobactin, together with another polypeptide of previously unknown function, MmoD, play key roles in regulating expression of MMOs. Based on these data, we propose a general model explaining how expression of the MMO operons is regulated by copper, methanobactin and MmoD. The basis of the 'copper-switch' is MmoD, and methanobactin amplifies the magnitude of the switch. Bioinformatic analysis of bacterial genomes indicates that the production of methanobactin-like compounds is not confined to methanotrophs, suggesting that its use as a metal-binding agent and/or role in gene regulation may be widespread in nature.
An Eleven Parameter Axial Turbine Airfoil Geometry Model (1985)

The mathematical derivation, and FORTRAN code, of a comprehensive but easy to use geometry model for axial flow turbine nozzles and rotors is presented. To uniquely define an airfoil on a cylinder the aerodynamicist need only specify the number of blades, and at each radius of interest: the axial and tangential chord, throat, uncovered turning, leading and trailing edge radii, inlet and exit blade angles, and inlet wedge angle. Default values exist for six of these geometric variables, which proves useful when starting a design. Both the suction and the pressure surfaces are described entirely by analytical functions. Sample airfoils are included that demonstrate the effect of each parameter upon blade shape.
Hypertrophy of Neurons Within Cardiac Ganglia in Human, Canine, and Rat Heart Failure: The Potential Role of Nerve Growth Factor (2013)

Hypertrophied neurons are significantly less excitable than smaller ones; thus, hypertrophy of vagal postganglionic neurons in cardiac ganglia would help to explain the parasympathetic withdrawal that accompanies heart failure. Furthermore, our observations suggest that nerve growth factor, which is elevated in the failing human heart, causes hypertrophy of neurons in cardiac ganglia.
Cytokine Requirements for Production of a Novel Anti-CD8-Resistant CTL Population (1999)

A population of CD8+ CTL can be generated in vitro in the presence of anti-CD8 mAb. Due to their apparent high avidity characteristic, these anti-CD8-resistant CD8+ CTL may have important functional in vivo roles in graft rejection, and may be important in antiviral and antitumor responses. We have previously reported that this anti-CD8-resistant subset of CD8+ CTL demonstrates functional differences from anti-CD8-sensitive CD8+ CTL. One important difference between the subsets is the markedly greater dependence of anti-CD8-resistant CTL upon exogenous cytokines for their generation in vitro. In this study, we have investigated in detail the cytokine requirements for the generation of allospecific CD8+ CTL in vitro and have found that IL-4 can augment the generation of anti-CD8-sensitive but not anti-CD8-resistant CTL, whereas IL-2 or IL-12 can augment the generation of both anti-CD8-sensitive and anti-CD8-resistant CTL. However, anti-CD8-resistant CTL require at least 10-fold higher concentrations of IL-2 than do anti-CD8-sensitive CTL. This more stringent IL-2 requirement precludes the efficient generation of anti-CD8-resistant CTL in vitro in the absence of exogenous IL-2 because they cannot produce sufficient IL-2 to meet their needs, in contrast to anti-CD8-sensitive CTL. By providing exogenous cytokines to allospecific CTL generation cultures, we further demonstrate that anti-CD8-resistant CTL can be functionally skewed to the Tc1 subset, but differ from anti-CD8-sensitive conventional CTL in that they cannot be skewed to the Tc2 subset.
Laminin-1 promotes differentiation of fetal mouse pancreatic beta-cells. (1999)

Extracellular factors that regulate the growth and differentiation of cell lineages in the pancreatic primordia are poorly understood. Identification of these factors for pancreatic islet beta-cells could open new avenues for the treatment of insulin-dependent diabetes. We developed a low cell density serum-free culture system for dissociated pancreatic cells from the 13.5-day mouse fetus and investigated the effects of extracellular matrix proteins on differentiation of islet cells. After 4 days in culture, total cell number decreased by two-thirds, but insulin-positive beta-cell number increased 10-fold. Both of collagens I and IV inhibited cell survival (by >50%), whereas fibronectin had no effect. In the presence of soluble laminin-1, however, the number of beta-cells increased linearly by 60-fold without an increase in the total cell number; glucagon-positive cell number was unchanged, and somatostatin and pancreatic polypeptide-positive cells were not detected. The effect of laminin-1 was completely blocked by a monoclonal rat anti-laminin-1 antibody. In the presence of laminin-1, the thymidine analogue, BrdU, was incorporated into only 2.5% of cells, which were mainly insulin-negative at days 1-3. Laminin-1 appeared, therefore, to induce differentiation of beta-cells from precursor cells in day-13.5 fetal pancreas. Laminin-1 was shown to be expressed in the epithelial basement membrane of the 13.5- to 17.5-day fetal pancreas. These findings provide the first evidence of a role for laminin-1 to promote differentiation of pancreatic beta-cells.
Iodine-Zinc Exchange Reactions Mediated by<i> i</i>-Pr<sub>2</sub>Zn. A New Preparation of Secondary Zinc Reagents (1997)

By treatment with i-Pr2Zn, functionalized secondary alkyl iodides undergo a smooth iodine-zinc exchange reaction leading to polyfunctional secondary dialkylzinc derivatives. Remarkably, i-Pr2Zn generated in situ from i-PrMgBr and ZnBr2 undergoes this exchange reaction almost 200 times faster than salt free i-Pr2Zn and constitutes a practical source of i-Pr2Zn for the performance of exchange reactions.
Analysis of the proteins and<i>cis</i>-acting elements regulating the stress-induced phage shock protein operon (1995)

The phage shock protein operon (pspABCE) of Escherichia coli is strongly induced by adverse environmental conditions. Expression is controlled principally at the transcriptional level, and transcription is directed by the sigma factor sigma 54. PspB and PspC are required for high-level psp expression during osmotic shock, ethanol treatment and f1 infection, but heat-induced expression is independent of these proteins. We report here that the promoter region contains an upstream activation sequence (UAS) that is required for psp induction and has the enhancer-like ability to activate at a distance. A DNA-binding activity is detected in crude protein extracts that is dependent on the UAS and induced by heat shock. We further show that integration host factor (IHF) binds in vitro to a site between the UAS and sigma 54 recognition sequence. In bacteria lacking IHF, psp expression is substantially reduced in response to high temperature and ethanol. During osmotic shock in contrast, psp expression is only weakly stimulated by IHF, and IHF mutants can strongly induce the operon. The dependence of psp expression on IHF varies with the inducing condition, but does not correlate with dependence on PspB and PspC, indicating distinct, agent-specific activation mechanisms.
High-power-density fault-current limiting devices using superconducting YBa2Cu3O7 films and high-resistivity alloy shunt layers (2004)

Switching of superconducting thin-film resistive fault-current limiting devices with alloy shunt layers was studied. Au–Ag alloy thin films, whose room-temperature resistivity is about six times higher than that of pure gold, were sputter deposited on YBa2Cu3O7 films on sapphire substrates with high critical current density of Jc=3.05±0.05MA∕cm2. A small sample, 5mm wide and 40mm long, had the capacity of a rated current of 32Arms in normal operation and withstood a high voltage of 107Vrms for 0.1s after switching, resulting in a very high switching power density of ∼1.7kVA∕cm2, which is more than four times higher than conventional devices using gold shunt layers.
Hypertonic saline-dextran improves intestinal perfusion and survival in porcine endotoxin shock (2000)

Small-volume HSD resuscitation is much more effective than ISD resuscitation. Variables that were improved include cardiac output, portal blood flow, and intestinal mucosal blood flow in ET shock, all of which improve survival. Such beneficial effects of HSD on splanchnic perfusion may be of value in treating critically ill septic patients in the intensive care unit.
Transcriptional regulation of lysosomal acid lipase in differentiating monocytes is mediated by transcription factors Sp1 and AP-2 (1998)

Human lysosomal acid lipase (LAL) is a hydrolase required for the cleavage of cholesteryl esters and triglycerides derived from plasma lipoproteins. It is shown here that during monocyte to macrophage differentiation, the expression of LAL-mRNA is induced. This induction is dependent on protein kinase C activity and protein synthesis. The cell type-specific increase in LAL expression is further investigated in the THP-1 cell line with respect to transcriptional regulation. The human monocytic leukemia cell line THP-1 differentiates into macrophage-like cells when treated with phorbol esters. In order to determine the cis-acting elements necessary for both basal and phorbol 12-myristate-13 acetate (PMA)-enhanced promoter activity, we performed deletion analysis and reporter gene assays. A PMA responsive element has been identified between -182 bp and -107 bp upstream of the major transcription start site. Gel mobility shift assays demonstrated that binding of Sp1 and AP-2 to the LAL promoter is increased by PMA in THP-1 cells. Co-transfections with expression plasmids for Sp1 and AP-2 further emphasized the important role of these transcription factors in both basal and PMA-enhanced LAL expression. Our data suggest that differentiation dependent increase of lysosomal acid lipase (LAL) expression in THP-1 cells is mediated by a concerted action of Sp1 and AP-2.
Triazene metabolism. IV. Derivatives of hydroxymethyltriazenes: potential prodrugs for the active metabolites of the anti-tumour triazene, DTIC. (1985)

A series of derivatives of the anti-tumour hydroxymethyltriazenes have been investigated for activity in vivo and in vitro. Acetoxymethyltriazenes are active in vivo against the TLX5, P388 and PC6 tumours in mice, and inhibit the growth of TLX5, Np and Li cells in vitro without metabolic activation. The acetoxymethyltriazenes are comparable with the hydroxymethyltriazenes and monomethyltriazenes in their spectrum of activity and thus appear to be prodrugs for these species. On the other hand, a methoxymethyltriazene was found to be active on the TLX5 tumour in vivo, but did not inhibit the growth of Np cells in vitro. This latter observation is consistent with the anticipated chemical stability of the methoxymethyltriazene and the requirement for metabolic O-demethylation to generate an active species. Acetoxymethyltriazenes do not require metabolic intervention and break down chemically in phosphate buffer to the hydroxymethyltriazene, which in turn loses formaldehyde to give the incipient methylating agent, the monomethyltriazene.
Cost enforcement and deadline monitoring in the real-time specification for Java (2004)

Modem real-time programming languages and operating systems provide support for monitoring the amount of CPU time a thread consumes. However, no system in widespread use fully integrates this monitoring with the scheduling facilities. The real-time specification for Java (RTSJ) provides an integrated approach to scheduling periodic threads and monitoring their CPU execution time. It supports a cost enforcement model whereby a periodic thread is suspended when it consumes more time than it requested. Version 1.0 of the RTSJ is under specified and it is difficult to understand the full model. This paper clarifies the position and defines the conditions under which a real-time thread is resumed. The model presented is the one that is fully defined in version 1.0.1 of the RTSJ. Unfortunately, version 1.0.1 of the specification will not have a general model for handling cost enforcement and deadline monitoring for all schedulable objects. This paper proposes extensions to the RTSJ that allow the cost enforcement model and deadline monitoring model to be consistently applied across all schedulable objects, and for it to be fully integrated with scheduling
Mapping the human retina (1998)

The new therapeutic method of scotoma-based photocoagulation (SBP) developed at the Vienna Eye Clinic for diagnosis and treatment of age-related macular degeneration requires retinal maps from scanning laser ophthalmoscope images. This paper describes in detail all necessary image analysis steps for map generation. A prototype software system for fully automatic map generation has been implemented and tested on a representative dataset selected from a clinical study with 50 patients. The map required for the SBP treatment can be reliably extracted in all cases. Thus, algorithms presented in this paper should be directly applicable in daily clinical routine without major modifications.
Rapid synthesis of diketopiperazine macroarrays via Ugi four-component reactions on planar solid supports (2006)

Libraries of diketopiperazines have been generated in high purity using the small molecule macroarray synthesis platform.