gebhart/patrepeval huggingface dataset:
Artificial Light‐Gated Catalyst Systems (2010)

Having control over an entity or even an entire process is arguably the ultimate demonstration of its understanding and it will enable its potential to be fully exploited. With this in mind, chemists have not only been creating and optimizing a myriad of different catalysts for most (relevant) chemical reactions over the past decades, but have recently started to implement controlling elements into the catalyst design. These incorporated gates operate upon exposure to suitable control stimuli, and light represents perhaps the scientifically and technologically most attractive stimulus. In principle, irradiation can thereby induce activity and selectivity in a given catalyst system with high spatial and temporal control, leading to an overall localization and amplification of an optical signal and translation into chemical action. While nature has developed and utilized this concept, in particular in the processes of vision and photomovement, such artificial photocontrolled catalyst systems offer unique opportunities and have high potential for future applications. In this Review, we outline the general concept of light-gated catalysis based on photocaged and also photoswitchable systems, and discuss relevant examples of the past and recent literature.
D-SPECT: A new solid state camera for high speed molecular imaging (2006)

542 Objectives: For 50 years, physicists have been struggling with the inherent trade-off between spatial resolution and sensitivity associated with radionuclide imaging. A novel technology (D-SPECT) constituting a radical departure from the conventional Anger camera (A-SPECT) has been developed. The aim of this study was to demonstrate the order of magnitude increase in sensitivity and improved spatial resolution of D- SPECT ( Spectrum-Dynamics, Haifa, Israel), as compared to Anger camera SPECT (A-SPECT). Methods: The novel technology employs ten detector columns, tungsten collimators with large holes and an acceptance angle of nearly five times that of the standard parallel-hole collimator in front of cadmium zinc telluride (CZT) crystals. The detector columns rotate and concentrate on the object of interest viewing it from thousands of different angles. The acquired data are processed by innovative iterative algorithms. A NEMA phantom with three 2.7 mCi Co-57 line sources, each of 1 mm diameter and 20cm in length, was employed to demonstrate the inherent resolution of the two systems. With each system, time of acquisition and resolution was measured (FWHM). Mapping of the usable field of view (UFOV) was carried out by imaging a 2.7 mCi Co-57 point source of 1mm moved on a 30 x 29 x 12 cm grid in 150 x 145 x 60 mm steps throughout the UFOV by a robotic arm. Results: For the NEMA phantom, total scan time for D-SPECT was 128 seconds and a resolution of 7 mm in the x-axis and 6.5 mm in the y-axis was demonstrated for the central rod. Total scan time for A-SPECT (GE Millenium VG) with a high resolution collimator was 900 seconds and demonstrated a resolution of 12.6 mm in the x-axis and 13.6 mm in the y-axis for the central rod. Mapping of the UFOV demonstrated an average resolution of 8.4 mm, 7.9 mm and 5.8 mm (std. dev. 2.6mm, 2.7mm, 2.1mm) in the x,y,and z axis. The most centrally located point demonstrated a sensitivity of 1407 counts/µCi/min; as opposed to 160-240 counts/µCi/min range generally observed with standard cameras. Conclusions: D-SPECT has demonstrated an order of magnitude improvement in sensitivity and ~2-fold improvement in spatial resolution. The marked increase in sensitivity and spatial resolution could enable the use of low-dose radiopharmaceuticals, dynamic imaging with absolute measurements of tissue perfusion, as well as parametric representation of molecular function.
Isolation of biologically active nanomaterial (inclusion bodies) from bacterial cells (2010)

The study shows that among the three methods tested, homogenization is the most appropriate method for the isolation of active nanoparticles from bacterial cells.
Functional analysis of the polypyrimidine tract in pre-mRNA splicing (1997)

The polypyrimidine tract is one of the important cis-acting sequence elements directing intron removal in pre-mRNA splicing. Progressive deletions of the polypyrimidine tract have been found to abolish correct lariat formation, spliceosome assembly and splicing. In addition, the polypyrimidine tract can alter 3'-splice site selection by promoting alternative branch site selection. However, there appears to be great flexibility in the specific sequence of a given tract. Not only the optimal composition of the polypyrimidine tract, but also the role of the tract in introns with no apparent polypyrimidine tracts or where changes in the tract are apparently harmless are uncertain. Accordingly, we have designed a series of cis-competition splicing constructs to test the functional competitive efficiency of a variety of systematically mutated polypyrimidine tracts. An RT/PCR assay was used to detect spliced product formation as a result of differential branch point selection dependent on direct competition between two opposing polypyrimidine tracts. We found that pyrimidine tracts containing 11 continuous uridines are the strongest pyrimidine tracts. In such cases, the position of the uridine stretch between the branch point and 3'-splice site AG is unimportant. In contrast, decreasing the continuous uridine stretch to five or six residues requires that the tract be located immediately adjacent to the AG for optimal competitive efficiency. The block to splicing with decreasing polypyrimidine tract strength is primarily prior to the first step of splicing. While lengthy continuous uridine tracts are the most competitive, tracts with decreased numbers of consecutive uridines and even tracts with alternating purine/pyrimidine residues can still function to promote branch point selection, but are far less effective competitors in 3'-splice site selection assays.
Systems Biology Approach in Chlamydomonas Reveals Connections between Copper Nutrition and Multiple Metabolic Steps (2011)

In this work, we query the Chlamydomonas reinhardtii copper regulon at a whole-genome level. Our RNA-Seq data simulation and analysis pipeline validated a 2-fold cutoff and 10 RPKM (reads per kilobase of mappable length per million mapped reads) (~1 mRNA per cell) to reveal 63 CRR1 targets plus another 86 copper-responsive genes. Proteomic and immunoblot analyses captured 25% of the corresponding proteins, whose abundance was also dependent on copper nutrition, validating transcriptional regulation as a major control mechanism for copper signaling in Chlamydomonas. The impact of copper deficiency on the expression of several O₂-dependent enzymes included steps in lipid modification pathways. Quantitative lipid profiles indicated increased polyunsaturation of fatty acids on thylakoid membrane digalactosyldiglycerides, indicating a global impact of copper deficiency on the photosynthetic apparatus. Discovery of a putative plastid copper chaperone and a membrane protease in the thylakoid suggest a mechanism for blocking copper utilization in the chloroplast. We also found an example of copper sparing in the N assimilation pathway: the replacement of copper amine oxidase by a flavin-dependent backup enzyme. Forty percent of the targets are previously uncharacterized proteins, indicating considerable potential for new discovery in the biology of copper.
Sampling the Egg Population (1993)

Mosquito eggs are found in many different habitats, e.g. small pools, large marshes, rock pools, tree-holes, plant axils, flower bracts, fallen leaves, fruit husks, empty snail shells, bromeliads and a variety of man-made containers. While some species lay their eggs singly, others lay them in egg rafts or in sticky masses glued to the undersides of floating leaves. Many species deposit their eggs on the water surface, but a few lay them on the upper surface of floating vegetation, and a large number oviposit not on the water surface but at varying distances from the water’s edge amongst leaf litter, mud and debris or on the walls of man-made containers, plants, tree-holes and bamboo.
Human IgE receptor alpha-chain IgG chimera blocks passive cutaneous anaphylaxis reaction in vivo. (1993)

Abstract Cross-linking of the high affinity IgE receptor (Fc epsilon RI) expressed on mast cells and basophils is essential for triggering anaphylaxis in vivo. Previously, other investigators have tried to produce competitive inhibitors using IgE peptide analogues and anti-IgE antibodies with limited success. To create a novel specific inhibitor of IgE that can block binding of IgE to Fc epsilon RI without the capacity to stimulate degranulation, we made an Fc epsilon RI-IgG immunoadhesin. The Fc epsilon RI-IgG was constructed by gene fusion of the extracellular portion of the human alpha-chain of Fc epsilon RI, which contains the high affinity binding site for IgE, with a truncated human IgG1 H chain C region. The Fc epsilon RI-IgG recognizes both human and murine IgE. Coincubation of Fc epsilon RI-IgG with murine IgE prevented sensitization of RBL-2H3 cells and the subsequent histamine release in response to anti-IgE. Similarly, when the Fc epsilon RI-IgG was preincubated with equimolar concentrations of either hyperimmune mouse sera or purified mouse IgE, it completely blocked the passive cutaneous anaphylaxis reaction in rats. Furthermore, i.v. administration of Fc epsilon RI-IgG following intracutaneous injection of serum from DNP-immunized mice was able to block the passive cutaneous anaphylaxis reaction in a time-dependent fashion. These results demonstrate that Fc epsilon RI-IgG is a potent inhibitor of IgE binding to intracutaneous mast cells in vivo and may prove clinically useful for the treatment of IgE-mediated disease.
Markedly prolonged incubation period of hepatitis B in a chimpanzee passively immunized with a human monoclonal antibody to the a determinant of hepatitis B surface antigen. (1993)

The protective efficacy of a human monoclonal antibody directed against the a determinant of hepatitis B virus (HBV) surface antigen was studied in a chimpanzee. A single high dose of 5 mg/kg (body weight) of monoclonal antibody SDZ OST 577 was intravenously administered to a chimpanzee, followed by intravenous challenge with 10(3.5) chimpanzee infectious doses of a wild-type HBV, the MS-2 strain (ayw subtype). The passively acquired antibody to HBV surface antigen could be detected for 40 weeks. Serum HBV DNA tested by a "nested" polymerase chain reaction assay was negative through the 36th week after virus challenge but became positive by the 38th week. The chimpanzee subsequently developed acute hepatitis B approximately 1 year after challenge. The nucleotide sequence of the a determinant of the surface gene of the replicated virus was identical with that of the inoculated wild-type virus. Thus, a human monoclonal antibody directed against the a determinant of HBV surface antigen delayed but did not prevent experimental infection of HBV and hepatitis in the chimpanzee. Our results indicate an incomplete ability of this antibody to protect against HBV infection in vivo after a single infusion.
Fabrication of high-density nanostructures by electron beam lithography (1998)

We demonstrate a fabrication method to define high-density, uniform nanostructures by electron beam lithography at conventional beam voltages (&amp;lt;40 kV). Here we optimize the exposure and development conditions needed to generate such nanostructure arrays using polymethylmethacrylate as positive resist and isopropyl alcohol as a developer. Arrays of 12 nm dots with 25 nm period and 20 nm lines with 40 nm period were fabricated to show the resolution of this optimized process.
Thermoregulatory and soporific effects of very low dose melatonin injection (1999)

The effect of a rapid increase in circulating melatonin on body temperatures and sleepiness was investigated in eight young adults at 1000. Melatonin administered intravenously at 10- and 30-microgram doses, but not 3 microgram, resulted in elevated plasma and saliva levels consistent with endogenous levels measured in adults at night. Melatonin at 10 and 30 microgram significantly attenuated the daytime increase in rectal core temperature (P < 0.05 for both). The mean maximum rectal core temperature differences between saline and melatonin treatment were 0.11 +/- 0.03 degreesC, 0.16 +/- 0.04 degreesC, and 0.18 +/- 0.04 degreesC after the 3-, 10-, and 30-microgram melatonin doses, respectively. All three doses significantly increased hand temperature compared with saline (P < 0. 05) within 30 min. The mean maximum hand temperature differences were 0.72 +/- 0.12 degreesC (3 microgram), 0.95 +/- 0.15 degreesC (10 microgram), and 0.65 +/- 0.11 degreesC (30 microgram). Foot temperature and subjective sleepiness measures did not change at any melatonin dose. The results suggest that daytime intravenous injection of melatonin to achieve normal nocturnal levels in young adults may produce significant thermoregulatory changes without soporific effects.
Cardiac disease detection from echocardiogram using edge filtered scale-invariant motion features (2010)

Echocardiography provides important morphological and functional details of the heart which can be used for the diagnosis of various cardiac diseases. Most of the existing automatic cardiac disease recognition systems that use echocardiograms are either based on unreliable anatomical region detection (e.g. left ventricle) or require extensive manual labeling of training data which renders such systems unscalable. In this paper we present a novel system for automatic cardiac disease detection from echocardiogram videos which overcomes these limitations and exploits cues from both cardiac structure and motion. In our framework, diseases are modeled using a configuration of novel salient features which are located at the scale-invariant points in the edge filtered motion magnitude images and are encoded using local spatial, textural and motion information. To demonstrate the effectiveness of this technique, we present experimental results for automatic cardiac Hypokinesia detection and show that our method outperforms the existing state-of-the-art method for this task.
A Novel Glutathione Containing Eicosanoid (FOG7) Chemotactic for Human Granulocytes (2000)

A biologically active glutathione adduct of the eicosanoid 5-oxo-eicosatetraenoic acid has been observed as a product formed within the murine peritoneal macrophage. This five-oxo glutathione adduct (FOG(7)) was structurally characterized using electrospray tandem mass spectrometry as a 1,4 Michael addition product 5-oxo-7-glutathionyl-8,11,14-eicosatrienoic acid. FOG(7) was found to be highly potent in stimulating eosinophil as well as neutrophil chemotaxis, also capable of initiating actin polymerization, without elevating intracellular free calcium ion concentration within either the eosinophil or polymorphonuclear leukocyte. These biological responses suggest that either FOG(7) activates a subset of receptors mediating the broader biological activity of the parent eicosanoid 5-oxo-6,8,11,14-eicosatetraenoic acid (5-oxo-ETE) or that a receptor not activated by 5-oxo-ETE participates in the chemotactic activity of FOG(7). The only other known biologically active glutathione adduct has been leukotriene C(4) (LTC(4)), another eicosanoid that exerts potent effects through the Cys-LT receptor. The biochemical parallel between the formation of LTC(4) and FOG(7) suggests an interesting mechanism by which biologically active eicosanoids derived from electrophilic intermediates may have unique distribution and prolonged efficacy in vivo.
Evaluation of the Abbott m 2000 RealTi m e Human Immunodeficiency Virus Type 1 (HIV-1) Assay for HIV Load Monitoring in South Africa Compared to the Roche Cobas AmpliPrep-Cobas Amplicor, Roche Cobas AmpliPrep-Cobas TaqMan HIV-1, and BioMerieux NucliSENS EasyQ HIV-1 Assays (2009)

The implementation of antiretroviral therapy demands the need for increased access to viral load (VL) monitoring. Newer real-time VL testing technologies are faster and have larger dynamic ranges and fully automated extraction to benefit higher throughputs in resource-poor environments. The Abbott RealTime human immunodeficiency virus type 1 (HIV-1) assay was evaluated as a new option for testing for HIV-1 subtype C in South Africa, and its performance was compared to the performance of existing assays (the Cobas AmpliPrep-Cobas TaqMan HIV-1, version 1, assay; the AmpliPrep-Cobas Monitor standard HIV-1 assay; and the NucliSENS EasyQ-EasyMag HIV-1 assay) in a high-throughput laboratory. The total precision of the RealTime HIV-1 assay was acceptable over all viral load ranges. This assay compared most favorably with the Cobas AmpliPrep-Cobas TaqMan HIV-1 assay (R(2) = 0.904), with a low standard deviation of difference being detected (0.323 copies/ml). The bias against comparator assays ranged from -0.001 copies/ml to -0.228 copies/ml. Variability in the reporting of VLs for a 20-member subtype panel compared to the variability of other assays was noted with subtypes G and CRF02-AG. The RealTime HIV-1 assay can test 93 samples per day with minimal manual preparation, less staff, and the minimization of contamination through automation. This assay is suitable for HIV-1 subtype C VL quantification in South Africa.
Autoimmune mechanisms in psoriasis. (1991)

Psoriasis is a chronic papulosquamous skin disorder affecting 1% to 3% of the general population. There is increasing evidence that immunologic mechanisms are involved in the pathogenesis of psoriasis, and that a link between psoriasis and autoimmunity may exist. A variety of autoantibodies has been observed in psoriasis including antinuclear antibodies, antibodies to small nuclear and cytoplasmic ribonucleoproteins, and antibodies to epidermal cells. UV light treatment of psoriasis may play a role in inducing these autoantibodies in some individuals. Recent evidence that activated T cells in psoriatic plaques may produce interferon-gamma leading to the appearance of ectopic class II major histocompatibility products on the surface of keratinocytes also supports the idea of a link between psoriasis and disordered immunoregulation. The immunologic abnormalities in psoriasis and the association of psoriasis with particular types of autoantibodies raise the possibility that a common etiology may underlie both psoriasis and autoimmunity in some patients, but the different responses of the two diseases to UV light treatment and certain pharmacological agents suggest that psoriasis may not have an autoimmune pathogenesis.
The autophagic tumor stroma model of cancer (2010)

A loss of stromal Cav-1 in the tumor fibroblast compartment is associated with early tumor recurrence, lymph-node metastasis, and tamoxifen-resistance, resulting in poor clinical outcome in breast cancer patients. Here, we have used Cav-1 (-/-) null mice as a pre-clinical model for this "lethal tumor micro-environment." Metabolic profiling of Cav-1 (-/-) mammary fat pads revealed the upregulation of numerous metabolites (nearly 100), indicative of a major catabolic phenotype. Our results are consistent with the induction of oxidative stress, mitochondrial dysfunction, and autophagy/mitophagy. The two most prominent metabolites that emerged from this analysis were ADMA (asymmetric dimethyl arginine) and BHB (beta-hydroxybutyrate; a ketone body), which are markers of oxidative stress and mitochondrial dysfunction, respectively. Transcriptional profiling of Cav-1 (-/-) stromal cells and human tumor stroma from breast cancer patients directly supported an association with oxidative stress, mitochondrial dysfunction, and autophagy/mitophagy, as well as ADMA and ketone production. MircoRNA profiling of Cav-1 (-/-) stromal cells revealed the upregulation of two key cancer-related miR's, namely miR-31 and miR-34c. Consistent with our metabolic findings, these miR's are associated with oxidative stress (miR-34c) or activation of the hypoxic response/HIF1a (miR-31), which is sufficient to drive authophagy/mitophagy. Thus, via an unbiased comprehensive analysis of a lethal tumor micro-environment, we have identified a number of candidate biomarkers (ADMA, ketones, and miR-31/34c) that could be used to identify high-risk cancer patients at diagnosis, for treatment stratification and/or for evaluating therapeutic efficacy during anti-cancer therapy. We propose that the levels of these key biomarkers (ADMA, ketones/BHB, miR-31, and miR-34c) could be (1) assayed using serum or plasma from cancer patients, or (2) performed directly on excised tumor tissue. Importantly, induction of oxidative stress and autophagy/mitophagy in the tumor stromal compartment provides a means by which epithelial cancer cells can directly "feed off" of stromal-derived essential nutrients, chemical building blocks (amino acids, nucleotides), and energy-rich metabolites (glutamine, pyruvate, ketones/BHB), driving tumor progression and metastasis. Essentially, aggressive cancer cells are "eating" the cancer-associated fibroblasts via autophagy/mitophagy in the tumor micro-environment. Lastly, we discuss that this "Autophagic Tumor Stroma Model of Cancer Metabolism" provides a viable solution to the "Autophagy Paradox" in cancer etiology and chemo-therapy.
Fecal DNA Biomarkers for the Detection of Colorectal Neoplasia: Attractive, but Is It Feasible? (2005)

Because of the high mortality associated with advanced disease, accessibility to direct visual examination, extensive research, and recognition of the genetic mechanisms associated with its carcinogenesis, the colon and rectum have emerged as an important model for the introduction of innovative and effective cancer screening and early detection tools for large populations.