gebhart/patrepeval huggingface dataset:
Serotonin Regulates Macrophage-Mediated Angiogenesis in a Mouse Model of Colon Cancer Allografts (2008)

Serotonin, a neurotransmitter with numerous functions in the central nervous system (CNS), is emerging as an important signaling molecule in biological processes outside of the CNS. Recent advances have implicated serotonin as a regulator of inflammation, proliferation, regeneration, and repair. The role of serotonin in tumor biology in vivo has not been elucidated. Using a genetic model of serotonin deficiency (Tph1(-/-)) in mice, we show serotonin to be crucial for the growth of s.c. colon cancer allografts in vivo. Serotonin does not enhance tumor cell proliferation but acts as a regulator of angiogenesis by reducing the expression of matrix metalloproteinase 12 (MMP-12) in tumor-infiltrating macrophages, entailing lower levels of angiostatin-an endogenous inhibitor of angiogenesis. Accordingly, serotonin deficiency causes slower growth of s.c. tumors by reducing vascularity, thus increasing hypoxia and spontaneous necrosis. The biological relevance of these effects is underscored by the reconstitution of serotonin synthesis in Tph1(-/-) mice, which restores allograft phenotype in all aspects. In conclusion, we show how serotonin regulates angiogenesis in s.c. colon cancer allografts by influencing MMP-12 expression in tumor-infiltrating macrophages, thereby affecting the production of circulating angiostatin.
A single laser method for subtraction of cell autofluorescence in flow cytometry (1987)

In flow cytometry cell autofluorescence often interferes with efforts to measure low levels of bound fluorescent antibody. We have developed a way to correct for autofluorescence on a cell-by-cell basis. This results in improved estimates of real staining and better separation of the fluorescence histograms of stained and non-stained cells. Using a single laser, two-color fluorescence measurement system and two-color compensation electronics, autofluorescence and one fluorescent reagent are measured (rather than two fluorescent reagents). With fluorescein-conjugated antibodies the signal in the 515 to 555 nm range (green fluorescence) includes both fluorescein emission and part of the cellular autofluorescence. In the cases we have investigated, autofluorescence collected at wavelengths above 580 nm ("red") is well correlated with the green autofluorescence of the cells. A fraction of this red fluorescence is subtracted from the green fluorescence to produce an adjusted fluorescein output on which unstained cells have zero average signal. Use of this method facilitates the selection of rare cells transfected with surface antigen genes. Culture conditions affect the level of autofluorescence and the balance between red and green autofluorescence. When applied with fluorescein-conjugated reagents, the technique is compatible with the use of propidium iodide for live/dead cell discrimination.
It's not just a phase: crystallization and X-ray structure determination of bacteriorhodopsin in lipidic cubic phases (1998)

Utilization of lipidic cubic phases in the crystallization of bacteriorhodopsin (bR) has yielded long sought after crystals that diffract X-rays to 2 A resolution. The resulting structure provides new information on the protein conformation and the mechanism of proton translocation. Crystallization of bR via lipidic cubic phases may be a harbinger of new membrane protein crystallization strategies.
Geometry and Mechanics in the Opening of Chiral Seed Pods (2011)

We studied the mechanical process of seed pods opening in Bauhinia variegate and found a chirality-creating mechanism, which turns an initially flat pod valve into a helix. We studied conﬁgurations of strips cut from pod valve tissue and from composite elastic materials that mimic its structure. The experiments reveal various helical conﬁgurations with sharp morphological transitions between them. Using the mathematical framework of "incompatible elasticity," we modeled the pod as a thin strip with a flat intrinsic metric and a saddle-like intrinsic curvature. Our theoretical analysis quantitatively predicts all observed conﬁgurations, thus linking the pod's microscopic structure and macroscopic conformation. We suggest that this type of incompatible strip is likely to play a role in the self-assembly of chiral macromolecules and could be used for the engineering of synthetic self-shaping devices.
Angiotensin II type 2 receptor-coupled nitric oxide production modulates free radical availability and voltage-gated Ca2+currents in NTS neurons (2012)

The medial region of the nucleus tractus solitarius (mNTS) is a key brain stem site controlling cardiovascular function, wherein ANG II modulates neuronal L-type Ca(2+) currents via activation of ANG II type 1 receptors (AT(1)R) and production of reactive oxygen species (ROS). ANG II type 2 receptors (AT(2)R) induce production of nitric oxide (NO), which may interact with ROS and modulate AT(1)R signaling. We sought to determine whether AT(2)R-mediated NO production occurs in mNTS neurons and, if so, to elucidate the NO source and the functional interaction with AT(1)R-induced ROS or Ca(2+) influx. Electron microscopic (EM) immunolabeling showed that AT(2)R and neuronal NO synthase (nNOS) are coexpressed in neuronal somata and dendrites receiving synapses in the mNTS. In the presence of the AT(1)R antagonist losartan, ANG II increased NO production in isolated mNTS neurons, an effect blocked by the AT(2)R antagonist PD123319, but not the angiotensin (1-7) antagonist D-Ala. Studies in mNTS neurons of nNOS-null or endothelial NOS (eNOS)-null mice established nNOS as the source of NO. ANG II-induced ROS production was enhanced by PD123319, the NOS inhibitor N(G)-nitro-l-arginine (LNNA), or in nNOS-null mice. Moreover, in the presence of losartan, ANG II reduced voltage-gated L-type Ca(2+) current, an effect blocked by PD123319 or LNNA. We conclude that AT(2)R are closely associated and functionally coupled with nNOS in mNTS neurons. The resulting NO production antagonizes AT(1)R-mediated ROS and dampens L-type Ca(2+) currents. The ensuing signaling changes in the NTS may counteract the deleterious effects of AT(1)R on cardiovascular function.
Effect of daily iron supplementation on health in children aged 4–23 months: a systematic review and meta-analysis of randomised controlled trials (2013)

Victoria Fellowship (Government of Victoria, Australia); CRB Blackburn Scholarship (Royal Australasian College of Physicans); Overseas Research Experience Scholarship, University of Melbourne.
Parallel computers for graphics applications (1987)

Specialived computer architectures can provide better price~performance for executing image processing and graphics applications than general purpose designs. Two processors are presented that use parallel SIMD data paths to support common graphics data structures as primitive operands in arithmetic expressions. A variant of the C language has been implemented to allow high level language coding of user applications on these processors. High level programming support is designed into the processor architecture that implements parallel object data typing and parallel conditional evaluation in hardware.
Biorthogonal cosine-modulated filter banks without DC leakage (2002)

In this paper, we present a structure for implementing the polyphase filters of biorthogonal modulated filter banks that automatically guarantees perfect reconstruction (PR) of the filter bank and furthermore allows to specify the values of the filters' frequency responses at certain frequencies. Thus, modulated filter banks without DC leakage can be designed. The new structure is based on lifting schemes for the polyphase filters and DC leakage can be avoided very easily when reducing the number of lifting coefficients that can be freely chosen and used for filter optimization. The great advantage of the new method is that we do not have to take constraints into consideration when optimizing the prototype filter, but PR and specified zeros are structure inherent.
Critical Review of Burn Depth Assessment Techniques: Part I. Historical Review (2009)

The assessment of burn depth, and as such, the estimation of whether a burn wound is expected to heal on its own within 21 days, is one of the most important roles of the burn surgeon. A false-positive assessment and the patient faces needless surgery, a false-negative one and the patient faces increased length of stay, risks contracture, and hypertrophic scar formation. Although many clinical signs can aid in this determination, accurate assessment of burn depth is possible only 64 to 76% of the time, even for experienced burn surgeons. Through the years, a variety of tools have become available, all attempting to improve clinical accuracy. Part 1 of this two-part article reviews the literature supporting the different adjuvants to clinical decision making is, providing a historical perspective that serves as a framework for part 2, a critical assessment of laser Doppler imaging.
Engineering Pseudomonas protegens Pf-5 for Nitrogen Fixation and its Application to Improve Plant Growth under Nitrogen-Deficient Conditions (2013)

Nitrogen is the second most critical factor for crop production after water. In this study, the beneficial rhizobacterium Pseudomonas protegens Pf-5 was genetically modified to fix nitrogen using the genes encoding the nitrogenase of Pseudomonas stutzeri A1501 via the X940 cosmid. Pf-5 X940 was able to grow in L medium without nitrogen, displayed high nitrogenase activity and released significant quantities of ammonium to the medium. Pf-5 X940 also showed constitutive expression and enzymatic activity of nitrogenase in ammonium medium or in nitrogen-free medium, suggesting a constitutive nitrogen fixation. Similar to Pseudomonas protegens Pf-5, Pseudomonas putida, Pseudomonas veronii and Pseudomonas taetrolens but not Pseudomonas balearica and Pseudomonas stutzeri transformed with cosmid X940 showed constitutive nitrogenase activity and high ammonium production, suggesting that this phenotype depends on the genome context and that this technology to obtain nitrogen-fixing bacteria is not restricted to Pf-5. Interestingly, inoculation of Arabidopsis, alfalfa, tall fescue and maize with Pf-5 X940 increased the ammonium concentration in soil and plant productivity under nitrogen-deficient conditions. In conclusion, these results open the way to the production of effective recombinant inoculants for nitrogen fixation on a wide range of crops.
Morphological characteristics of the external carotid artery (2013)

Abstract The morphological characteristics at the level of the bifurcation of the common carotid artery were studied on 46 cases, finding that the most frequent, in 52.17% of cases, the common carotid bifurcation appear as the letter “V”, with two possible variations: a wide “V”, in 43.48% of cases and narrow “V” in 8.7% of cases. In 30.43% of cases, the two carotids showed an ascending traject, united for 1-2 cm up to their crossing; in 13,04% of the cases the two arteries were superimposed, the external located anteriorly. In only in two cases on the right side (4.35% of cases and 8.33% of right samples) we found a peculiar aspect of a “U” shaped bifurcation. Regarding the caliber of the external carotid artery, we found that in 43.33% of the cases the external carotid artery had a similar diameter to the internal carotid, also in 43.33% of the external carotid artery have a higher caliber than internal one and the remaining 13.33% of the cases, the external carotid artery had a smaller diameter than the internal one, with all cases on the left (16.67% of left carotid arteries). The caliber of the right external carotid artery was between 4 to 5.6 mm and the one of the left was between 3.6 to 5 mm. When the external carotid was more voluminous than the internal, the differences were 0.5 to 1.2 mm and when the internal carotid was more voluminous than the external, the differences were smaller, 0.2 to 0.8 mm. In relation to the common carotid, the external carotid had a smaller caliber from 0.6 to 1.1 mm. Regarding the external carotid traject, most commonly, from the bifurcation of the common carotid, the external carotid artery showed a vertical trajectory, in 50% of cases; in 40% of cases, the traject was oblique superomedially and in 6.67% of cases the external carotid artery described a curve with the convexity facing laterally, with all cases on the right (11.76% of right carotid arteries); in 3.33% of cases, both on the left (7.69% of the left carotid arteries), the external carotid artery traject described an inverted italic “S”
Programming transparency and portable hardware interfacing: towards general-purpose reconfigurable computing (2004)

Despite enabling significant performance improvements, reconfigurable computing systems have not gained widespread acceptance: most reconfigurable computing paradigms lack (1) a unified and transparent programming model, and (2) a standard interface for integration of hardware accelerators. Ideally, programmers should code algorithms and designers should write hardware accelerators independently of any detail of the underlying platform. We argue that achieving portability and uniform programming with only limited loss of performance is one of the main issues that hinder the widespread acceptance of reconfigurable computing. To make reconfigurable computing globally more attractive, we suggest a transparent, portable, and hardware agnostic programming paradigm. For achieving software code and hardware design portability, platform-specific tasks are delegated to a system-level virtualisation layer that supports a chosen programming model-much in the same way platform details are hidden from users in general-purpose computers. Although an additional abstraction inherently brings overheads, we show that the involvement of the virtualisation layer exposes potential optimisations that compensate the overheads and bring additional speedups. As a case-study, we present a real design and implementation of a number of building blocks of such system and discuss the challenges involved in materialising the others.
Cancer immunotherapy using recombinantListeria monocytogenes: Transition from bench to clinic (2011)

Cancer immunotherapy has developed into a field of intense study as aspects of the immune system involved in the eradication of cancer have become delineated. Listeria monocytogenes is a gram-positive, facultative intracellular bacterium which infects antigen presenting cells (APC), and is being used as a cancer vaccine to deliver tumor antigens directly to the APC. This results in the generation of a strong immune response towards the tumor associated antigen and direct targeting of the tumor by the immune system. Advances in this field have led to the development of a series of L. monocytogenes-based cancer vaccines, which are currently in clinical trials. A phase I study has shown these vaccines can be safely administered and well-tolerated in terminal stage cancer patients and an efficacy signal was observed in patients who did not respond to other therapies. Additional data on the efficacy of these vaccines is expected in the near-term.
Systemic activation of the vascular endothelial growth factor receptor KDR/flk-1 selectively triggers endothelial cells with an angiogenic phenotype. (1997)

The hypothesis that tumor growth is angiogenesis dependent has been documented by a considerable body of direct and indirect experimental data. A prerequisite for the development of novel anti-angiogenic agents is the design of drugs that would be active only on those endothelial cells with an angiogenic phenotype. We took advantage of the anti-idiotypic strategy to obtain circulating agonists specific for the vascular endothelial growth factor receptor KDR/flk-1 (J-IgG). They induced in the absence of VEGF cell proliferation in vitro and angiogenesis in the corneal pocket assay either through local or systemic delivery. Intraperitoneal injections of J-IgG in nude mice grafted with a prostatic adenocarcinoma led to tumor enlargement associated with an increase in both tumor vascularization and proliferation. In contrast KDR/flk-1 overstimulation had no detectable effect on normal tissues. These data underline that KDR/flk-1 is a functional marker of the angiogenic phenotype of endothelial cells.
Analysis and comparison of plasmid profiles of Borrelia burgdorferi sensu lato strains (1995)

The relationship between plasmid profiles and genospecies of the Lyme disease borreliae was investigated by using 40 strains from diverse biological and geographical sources. The genospecies of the strains were determined by examination of rRNA gene restriction patterns with cDNA probes complementary to the 16S and 23S rRNAs of Escherichia coli. Plasmid profiles were obtained by pulsed-field gel electrophoresis. The number of plasmids per strain and the size of these plasmids ranged from 4 to 10 and from 13.3 to 57.7 kb, respectively. The strains all contained a single large plasmid of 50 to 57.7 kb, with the exception of two Borrelia garinii strains that contained two or three of the large plasmids. The large plasmids of Borrelia burgdorferi sensu stricto strains ranged in size from 51.4 to 52.7 kb and were consistently smaller than the 54.0- to 57.7-kb plasmids present in B. garinii and Borrelia afzelii. The exceptions of this observation were the two B. garinii strains with multiple large plasmids; in this case the large plasmids were 50.6 to 53 kb. Although a large degree of heterogeneity in the sizes and frequencies of occurrence of smaller plasmids was observed, there were some differences among the three genospecies. The differences in plasmids were further studied by using two BamHI DNA fragments from a 28.7-kb plasmid of B. burgdorferi sensu stricto 297 as probes. Both probes hybridized with the 27- to 29-kb plasmids of B. burgdorferi sensu stricto strains. In contrast, two patterns of hybridization were observed with B. garinii and B. afzelii. One pattern was the hybridization of both probes, with each probe hybridizing with a different plasmid. The other pattern was the hybridization of a plasmid of a strain with only one of the two probes. some strains of the three genospecies did not hybridize with either probe. Our results suggest that the plasmid profiles of B. burgdorferi sensu lato have genospecies characteristics and that the hybridization patterns of similar-sized plasmids are different for the three genospecies.
A graph based framework for the definition of tools dealing with sparse and irregular distributed data structures (2002)

Industrial applications use specific problem oriented implementations of large sparse and irregular data structures. Hence there is a need for tools that make it possible for developers to visualize their applications in terms of these data, their structure, and the operations that are applied to them, whatever their effective implementation and their distribution are. We present both a framework which we have setup to support the development of such tools, and prototypes which we have developed. The resulting environment is composed of two layers: the first layer is a model that we have defined and implemented as high level libraries that make it possible to efficiently abstract from the implementation; the second layer offers prototype tools built on top of these libraries. These tools are integrated within a graphical environment called Visit (T. Brandes et al., 1996) which is part of the HPFIT research effort (T. Brandes et al., 1996). HPFIT is a joint project involving three research laboratories: LIP in Lyon, France, LaBRI in Bordeaux, France, and GMD/SCAI in Bonn, Germany. Its aim is to provide an integrated HPF development environment that supports sparse and irregular data structures.
Synthesis of Ultralong and High Percentage of Semiconducting Single-walled Carbon Nanotubes (2002)

Two main results are reported here for single-walled carbon nanotubes (SWNTs) synthesized from well-controlled isolated catalytic Fe2O3 nanoparticles. The first is patterned growth of ultralong SWNTs (lengths up to 0.6 millimeters) by using a mixed methane and ethylene carbon source in chemical vapor deposition (CVD). Interesting loop and closed ring structures similar to those of fullerene “crop circles” are observed on these as-grown ultralong tubes. Second, surveying the electronic properties of individual SWNTs by transport measurements reveals that approximately 70% of individual SWNTs grown from isolated nanoparticles are semiconductors exhibiting field effect transistor (FET) characteristics. The distribution of CVD-grown SWNT chirality is elucidated for the first time, and implications to array-based nanotube electronics and sensors are discussed.
A Genetic Algorithm Approach for Discovering Diagnostic Patterns in Molecular Measurement Data (2005)

The objective of this work is the development of an algorithm that, after training, will be able to discriminate between disease classes in molecular data. The system proposed uses a genetic algorithm (GA) to achieve this discrimination. We apply our method to three publicly available data sets. Two of the data sets are based on microarray data that allow the simultaneous measurement of the expression levels of genes under different disease states. The third data set is based on serum proteomic pattern diagnostics of ovarian cancer using high-resolution mass spectrometry to extract a set of biomarker classifiers. We show how our methodology finds an abundance of different feature models, automatically selecting a subset of discriminatory features, whose classification accuracy is comparable to other approaches considered. This raises questions about how to choose among the many competing models, while simultaneously estimating the prediction accuracy of the chosen models.
Evaluation of Dextromethorphan Metabolism Using Hepatocytes from CYP2D6 Poor and Extensive Metabolizers (2005)

It is important to estimate the defective metabolism caused by genetic polymorphism of drug metabolizing enzymes before the clinical stage. We evaluated the utility of cryopreserved human hepatocytes of CYP2D6 poor metabolizer (PM) for the estimation of the metabolism in PM using dextromethorphan (DEX) as the probe drug for CYP2D6 substrate. The results of low formations of dextrorphan (DXO) and 3-hydroxymorphinan (3-HM) in CYP2D6 PM hepatocytes incubated with dextromethorphan reflected the clinical data. Formation of 3-methoxymorphinan (3-MEM) normalized by CYP3A4/5 activity in the PM hepatocytes reached about 2.8-fold higher than that in CYP2D6 extensive metabolizer (EM) hepatocytes, which clearly showed the compensatory metabolic pathway of O-demethylation catalyzed by CYP2D6 as seen in clinical study. On the contrary, in the condition of the EM hepatocytes with CYP2D6 inhibitors, the enhancement of 3-MEM formation was not observed. In phase II reaction, the glucuronide formation rate of DXO in the PM hepatocytes was lower than that in the EM hepatocytes, which was consistent with clinical data of DXO-glucuronide (DXO-glu) concentration. These results would suggest that CYP2D6 PM hepatocytes could be a good in vitro tool for estimating CYP2D6 PM pharmacokinetics.