gebhart/patrepeval huggingface dataset:
Microbial diversity and complexity in hypersaline environments: A preliminary assessment (2002)

The microbial communities in solar salterns and a soda lake have been characterized using two techniques: BIOLOG, to estimate the metabolic potential, and amplicon length heterogeneity analysis, to estimate the molecular diversity of these communities. Both techniques demonstrated that the halophilic Bacteria and halophilic Archaea populations in the Eilat, Israel saltern are dynamic communities with extensive metabolic potentials and changing community structures. Halophilic Bacteria were detected in Mono Lake and the lower salinity ponds at the Shark Bay saltern in Western Australia, except when the crystallizer samples were stressed by exposure to Acid Green Dye #9899. At Shark Bay, halophilic Archaea were found only in the crystallizer samples. These data confirm both the metabolic diversity and the phylogenetic complexity of the microbial communities and assert the need to develop more versatile media for the cultivation of the diversity of bacteria in hypersaline environments.
Expression of a dominant negative TrkB receptor, T1, reveals a requirement for presynaptic signaling in BDNF-induced synaptic potentiation in cultured hippocampal neurons (1998)

We have developed a method to analyze the relative contributions of pre- and postsynaptic actions of a particular gene product in neurons in culture and potentially in slices using adenovirus-mediated gene transfer. A recombinant virus directed the expression of both a GFP reporter protein and TrkB.T1, a C-terminal truncated dominant negative TrkB neurotrophin receptor. When expressed in the presynaptic cell at synapses between embryonic hippocampal neurons in culture, the dominant negative TrkB.T1 inhibited two forms of synaptic potentiation induced by the neurotrophin brain-derived neurotrophic factor (BDNF): (i) greater evoked synaptic transmission and (ii) higher frequency of spontaneous miniature synaptic currents. These inhibition effects are not seen if the transgene is expressed only in the postsynaptic cell. We conclude that BDNF-TrkB signal transduction in the presynaptic terminal leads to both types of potentiation and is therefore the primary cause of synaptic enhancement by BDNF in these neurons.
A dowel inserter for anterior cervical interbody fusion (1984)

✓ The authors describe a new instrument for placement of bone dowels in procedures for anterior cervical interbody fusion.
Ellipsoid, geoid, gravity, geodesy, and geophysics (2001)

Abstract Geophysics uses gravity to learn about the density variations of the Earth's interior, whereas classical geodesy uses gravity to define the geoid. This difference in purpose has led to some confusion among geophysicists, and this tutorial attempts to clarify two points of the confusion. First, it is well known now that gravity anomalies after the “free-air” correction are still located at their original positions. However, the “free-air” reduction was thought historically to relocate gravity from its observation position to the geoid (mean sea level). Such an understanding is a geodetic fiction, invalid and unacceptable in geophysics. Second, in gravity corrections and gravity anomalies, the elevation has been used routinely. The main reason is that, before the emergence and widespread use of the Global Positioning System (GPS), height above the geoid was the only height measurement we could make accurately (i.e., by leveling). The GPS delivers a measurement of height above the ellipsoid. In principle, in the geophysical use of gravity, the ellipsoid height rather than the elevation should be used throughout because a combination of the latitude correction estimated by the International Gravity Formula and the height correction is designed to remove the gravity effects due to an ellipsoid of revolution. In practice, for minerals and petroleum exploration, use of the elevation rather than the ellipsoid height hardly introduces significant errors across the region of investigation because the geoid is very smooth. Furthermore, the gravity effects due to an ellipsoid actually can be calculated by a closed-form expression. However, its approximation, by the International Gravity Formula and the height correction including the second-order terms, is typically accurate enough worldwide.
Ein Fichtenbaum (1979) (2006)

Harry Mayer\nEin Fichtenbaum (1979)\ntext by Heinrich Heine, Poem 33 of Lyrisches Intermezzo (Buch der Lieder)
Fumonisin contamination of commercial corn-based human foodstuffs (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFumonisin contamination of commercial corn-based human foodstuffsEric W. Sydenham, Gordon S. Shephard, Pieter G. Thiel, Walter F. O. Marasas, and Sonja StockenstromCite this: J. Agric. Food Chem. 1991, 39, 11, 2014–2018Publication Date (Print):November 1, 1991Publication History Published online1 May 2002Published inissue 1 November 1991https://pubs.acs.org/doi/10.1021/jf00011a028https://doi.org/10.1021/jf00011a028research-articleACS PublicationsRequest reuse permissionsArticle Views319Altmetric-Citations221LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Networking in Containers and Container Clusters (2015)

Containers are becoming a popular way of deploying applications quickly, cheaply, and reliably. As with the early days of virtual machines, a variety of container networking configurations have been proposed to deal with the issues of discovery, flexibility and performance. Using Docker we present available networking configurations along with many of the popular networking setups, their uses, and their problems today. A second aspect we will explore are containers in clusters, as these systems rely even more heavily on the network. We use Kubernetes as an example of this type of system. We present the network setups of the core components of Kubernetes: pods and services.
Caffeoyl Shikimate Esterase (CSE) Is an Enzyme in the Lignin Biosynthetic Pathway in Arabidopsis (2013)

Lignin is a major component of plant secondary cell walls. Here we describe caffeoyl shikimate esterase (CSE) as an enzyme central to the lignin biosynthetic pathway. Arabidopsis thaliana cse mutants deposit less lignin than do wild-type plants, and the remaining lignin is enriched in p-hydroxyphenyl units. Phenolic metabolite profiling identified accumulation of the lignin pathway intermediate caffeoyl shikimate in cse mutants as compared to caffeoyl shikimate levels in the wild type, suggesting caffeoyl shikimate as a substrate for CSE. Accordingly, recombinant CSE hydrolyzed caffeoyl shikimate into caffeate. Associated with the changes in lignin, the conversion of cellulose to glucose in cse mutants increased up to fourfold as compared to that in the wild type upon saccharification without pretreatment. Collectively, these data necessitate the revision of currently accepted models of the lignin biosynthetic pathway.
2-Cyano-3,12-dioxooleana-1,9-dien-28-imidazolide (CDDO-Im) Directly Targets Mitochondrial Glutathione to Induce Apoptosis in Pancreatic Cancer (2005)

Surgical resection is the only curative strategy for pancreatic cancer (PC). Unfortunately, >80% of pancreatic cancer patients bear inoperable, locally advanced, chemoresistant tumors demonstrating the urgent need for development of novel therapeutic approaches to treat this disease. Here we report that the synthetic triterpenoid 2-cyano-3,12 dioxooleana-1,9 dien-28-imidazolide (CDDO-Im) antagonizes PC cell growth by inducing apoptosis at submicromolar concentrations. Notably, we demonstrate for the first time that the cytotoxicity of CDDO-Im is accompanied by the rapid and selective depletion of mitochondrial glutathione that results in accumulation of reactive oxygen species, oxidation of the cellular glutathione pool, loss of mitochondrial membrane potential, and phosphatidylserine externalization. The parent compound CDDO as well as the methyl ester of CDDO also depleted mitochondrial glutathione, demonstrating that this effect is mediated by the triterpenoid nucleus of these agents. Co-treatment with sulfhydryl nucleophiles completely prevented apoptosis and loss of viability induced by CDDO-Im, whereas alkylation of intracellular thiols by diethylmaleate or co-treatment with dithiothreitol decreased the accumulation of a biotinylated derivative of CDDO, TP-301, in PC cells, suggesting that intracellular reduced thiols are functional targets of the electrophilic triterpenoid nucleus of CDDO and its derivatives. In conclusion, our report is the first to identify mitochondrial glutathione as a target of CDDO and its derivatives and demonstrates that depletion of this antioxidant in the mitochondria is an effective strategy to induce cell death in PC cells. These results suggest that CDDO and its derivatives may offer a clinical benefit for the treatment of PC.
Generation of longer 3' cDNA fragments from massively parallel signature sequencing tags (2004)

Massively Parallel Signature Sequencing (MPSS) is a powerful technique for genome-wide gene expression analysis, which, similar to SAGE, relies on the production of short tags proximal to the 3'end of transcripts. A single MPSS experiment can generate over 10(7) tags, providing a 10-fold coverage of the transcripts expressed in a human cell. A significant fraction of MPSS tags cannot be assigned to known transcripts (orphan tags) and are likely to be derived from transcripts expressed at very low levels (approximately 1 copy per cell). In order to explore the potential of MPSS for the characterization of the human transcriptome, we have adapted the GLGI protocol (Generation of Longer cDNA fragments from SAGE tags for Gene Identification) to convert MPSS tags into their corresponding 3' cDNA fragments. GLGI-MPSS was applied to 83 orphan tags and 41 cDNA fragments were obtained. The analysis of these 41 fragments allowed the identification of novel transcripts, alternative tags generated from polymorphic and alternatively spliced transcripts, as well as the detection of artefactual MPSS tags. A systematic large-scale analysis of the genome by MPSS, in combination with the use of GLGI-MPSS protocol, will certainly provide a complementary approach to generate the complete catalog of human transcripts.
Muscle regeneration in the prolonged absence of myostatin (2005)

Myostatin is an endogenous inhibitor of muscle conserved across diverse species. In the absence of myostatin, there is massive muscle growth in mice, cattle, and humans. Previous studies in the mdx mouse model of muscular dystrophy demonstrate that inhibiting myostatin attenuates several features of dystrophic muscle. These findings have encouraged the development of human therapies to block myostatin. However, little is known of the long-term effects on muscle of myostatin blockade. To evaluate potential sequelae from the prolonged absence of myostatin, senescent myostatin null (mstn-/-) mice were studied. Senescent mstn-/- mice continue to have normal muscle with increased mass and strength relative to controls. Muscles of senescent mstn-/- mice regenerate robustly from both chronic and acute injury. Early markers of regeneration are enhanced in the absence of myostatin, suggesting a mechanism for the attenuation of dystrophic features found in mdx mice lacking myostatin.
Lipopolysaccharide regions involved in the activation of Escherichia coli outer membrane protease OmpT (2002)

OmpT is an integral outer membrane protease of Escherichia coli. Overexpression of OmpT in E. coli and subsequent in vitro folding of the produced inclusion bodies yielded protein with a native-like structure. However, enzymatically active protease was only obtained after addition of the outer membrane lipid lipopolysaccharide (LPS). OmpT is the first example of an enzyme that requires LPS for activity. In this study, we investigated the nature of this activation. Circular dichroism analysis showed that binding of LPS did not lead to large structural changes. Titration of OmpT with LPS and determining the resulting OmpT activity with a fluorimetric assay yielded a dissociation constant of 10-4 m for E. coli K-12 LPS. Determining the dissociation constants for different LPS chemotypes revealed that a fully acylated lipid A part is minimally required for activation of OmpT. The heptose-bound phosphates in the inner core region were also important for activation. The affinity for LPS was not dependent on the concentration of substrate, neither was affinity for the substrate influenced by the concentration of LPS. This indicated that LPS most likely does not act at the level of substrate binding. We hypothesize that LPS induces a subtle conformational change in the protein that is required for obtaining a native active site geometry.
MemTracker (2009)

Memory bugs are a broad class of bugs that is becoming increasingly common with increasing software complexity, and many of these bugs are also security vulnerabilities. Existing software and hardware approaches for finding and identifying memory bugs have a number of drawbacks including considerable performance overheads, target only a specific type of bug, implementation cost, and inefficient use of computational resources. This article describes MemTracker, a new hardware support mechanism that can be configured to perform different kinds of memory access monitoring tasks. MemTracker associates each word of data in memory with a few bits of state, and uses a programmable state transition table to react to different events that can affect this state. The number of state bits per word, the events to which MemTracker reacts, and the transition table are all fully programmable. MemTracker's rich set of states, events, and transitions can be used to implement different monitoring and debugging checkers with minimal performance overheads, even when frequent state updates are needed. To evaluate MemTracker, we map three different checkers onto it, as well as a checker that combines all three. For the most demanding (combined) checker with 8 bits state per memory word, we observe performance overheads of only around 3%, on average, and 14.5% worst-case across different benchmark suites. Such low overheads allow continuous (always-on) use of MemTracker-enabled checkers, even in production runs.
Antigen Receptor Signaling to NF- B via CARMA1, BCL10, and MALT1 (2010)

The signaling pathway controlling antigen receptor-induced regulation of the transcription factor NF-kappaB plays a key role in lymphocyte activation and development and the generation of lymphomas. Work of the past decade has led to dramatic progress in the identification and characterization of new players in the pathway. Moreover, novel enzymatic activities relevant for this pathway have been discovered, which represent interesting drug targets for immuno-suppression or lymphoma treatment. Here, we summarize these findings and give an outlook on interesting open issues that need to be addressed in the future.
Phosphorylation-Dephosphorylation of Enzymes (1979)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Memory effect in the current–voltage characteristic of a low-band gap conjugated polymer (2001)

Diodes formed by electrodeposition of the low-band gap polymer poly(4-dicyano methylene-4H-cyclopenta[2,1-b:3,4-b′]dithiophene), onto glass slides coated with indium tin oxide (ITO) and furnished with evaporated aluminum counterelectrodes exhibit a reversible bistability in their current–voltage (I–V) characteristics. Applying +5 V to the ITO electrode induces a “high” conductance state while applying −5 V induces a “low” conductance state. The effect is identical in most respects to recent observations in diodes formed from thin films of chromium-doped SrZrO3 sandwiched between SrRuO3 and gold electrodes. A number of mechanisms are discussed but the evidence points to the controlling influence of an interfacial depletion layer at the ITO–polymer interface. It is also shown that the high capacitances associated with such layers can lead to higher than expected displacement currents being generated during the automated collection of I–V data. The presence of such currents distorts the I–V characteristics in the low-bias low-current regime.
Tracking Motion and Intensity Variations Using Hierarchical 2-D Mesh Modeling for Synthetic Object Transfiguration (1996)

We propose a method for tracking the motion and intensity variations of a 2-D mildly deformable image object using a hierarchical 2-D mesh model. The proposed method is applied to synthetic object transfiguration, namely, replacing an object in a real video clip with another synthetic or natural object via digital postprocessing. Successful transfiguration requires accurate tracking of both motion and intensity (contrast and brightness) variations of the object-to-be-replaced so that the replacement object can be rendered in exactly the same way from a single still picture. The proposed method is capable of tracking image regions corresponding to scene objects with nonplanar and/or mildly deforming surfaces, accounting for intensity variations, and is shown to be effective with real image sequences.
A New, Simple Procedure for the Synthesis of Formyl Amides (2004)

A simple and mild method for the N-formylation of amines and α-amino esters is described via reaction with 2-chloro-4,6-dimethoxy[1,3,5]triazine and formic acid. The reaction can be accelerated under microwave irradiation and yields the N-formyl species in high yields and without racemization in the case of optically active α-amino esters.
Observation of Two-Photon “Ghost” Interference and Diffraction (1995)

Observations of unusual diffraction and interference by two-photon correlation measurements are reported. The signal and idler beams produced by spontaneous parametric down-conversion are sent in different directions, and detected by two distant pointlike photon counting detectors. A double slit or a single slit is inserted into the signal beam. Interference-diffraction patterns are observed in coincidences by scanning the detector in the idler beam.
Cysteine Mapping in Conformationally Distinct Kinase Nucleotide Binding Sites: Application to the Design of Selective Covalent Inhibitors (2011)

Kinases have emerged as one of the most prolific therapeutic targets. An important criterion in the therapeutic success of inhibitors targeting the nucleotide binding pocket of kinases is the inhibitor residence time. Recently, covalent kinase inhibitors have attracted attention since they confer terminal inhibition and should thus be more effective than reversible inhibitors with transient inhibition. The most robust approach to design irreversible inhibitors is to capitalize on the nucleophilicity of a cysteine thiol group present in the target protein. Herein, we report a systematic analysis of cysteine residues present in the nucleotide binding site of kinases, which could be harnessed for irreversible inhibition, taking into consideration the different kinase conformations. We demonstrate the predictive power of this analysis with the design and validation of an irreversible inhibitor of KIT/PDGFR kinases. This is the first example of a covalent kinase inhibitor that combines a pharmacophore addressing the DFG-out conformation with a covalent trap.
Controlling cellular reactive responses around neural prosthetic devices using peripheral and local intervention strategies (2003)

While chronic use of indwelling micromachined neural prosthetic devices has great potential, the development of reactive responses around them results in a decrease in electrode function over time. Since the cellular events responsible for these responses may be anti-inflammatory in nature, we have tested the effectiveness of dexamethasone and cyclosporin A as potential drugs for developing intervention strategies following insertion of single-shank micromachined silicon devices. Peripheral injection of dexamethasone was effective in attenuating increased expression of glial fibrillary acidic protein and astrocyte hyperplasia observed during both initial- and sustained-reactive responses observed at one and six weeks post insertion, respectively. Peripheral injection of cyclosporin A had no positive effect. If anything, application of this drug increased the early reactive response. Effectiveness of local release of dexamethasone in rat neocortex was tested by inserting ribbons of poly (ethyl-vinyl) acetate containing 35% (w/w) dexamethasone. Initial concentrations of dexamethasone were similar to those obtained by peripheral injection. Local drug release provided continued control of cellular reactive responses during the six-week study period. These results demonstrate that peripheral delivery of dexamethasone can be used to control reactive responses and that local drug delivery by slow-release from biocompatible polymers may be a more effective method of drug intervention. Incorporating these strategies on micromachined devices may provide an intervention strategy that will insure the chronic functioning of electrodes on intracortical neuroprosthetic devices.
The proteolytic activity of the HtrA (DegP) protein from Escherichia coli at low temperatures (2008)

The HtrA (DegP) protein from Escherichia coli is a periplasmic protease whose function is to protect cells from the deleterious effects of various stress conditions. At temperatures below 28 degrees C the proteolytic activity of HtrA was regarded as negligible and it was believed that the protein mainly plays the role of a chaperone. In the present work we provide evidence that HtrA can in fact act as a protease at low temperatures. Under folding stress, caused by disturbances in the disulfide bond formation, the lack of proteolytic activity of HtrA lowered the survival rates of mutant strains deprived of a functional DsbA/DsbB oxidoreductase system. HtrA degraded efficiently the unfolded, reduced alkaline phosphatase at 20 degrees C, both in vivo and in vitro. The cleavage was most efficient in the case of HtrA deprived of its internal S-S bond; therefore we expect that the reduction of HtrA may play a regulatory role in proteolysis.
Validation of a Novel Point-of-Care Nerve Conduction Device for the Detection of Diabetic Sensorimotor Polyneuropathy (2006)

A novel point-of-care device has excellent diagnostic accuracy for detecting electrophysiological abnormality in the sural nerve of patients who have diabetes. This automated device represents an alternative to conventional nerve conduction studies for the diagnosis of diabetic sensorimotor polyneuropathy.