gebhart/patrepeval huggingface dataset:
EngineeredControl of Cell Morphology In Vivo Reveals Distinct Roles for Yeast andFilamentous Forms of Candida albicans duringInfection (2003)

It is widely assumed that the ability of Candida albicans to switch between different morphologies is required for pathogenesis. However, most virulence studies have used mutants that are permanently locked into either the yeast or filamentous forms which are avirulent but unsuitable for discerning the role of morphogenetic conversions at the various stages of the infectious process. We have constructed a strain in which this developmental transition can be externally modulated both in vitro and in vivo. This was achieved by placing one copy of the NRG1 gene (a negative regulator of filamentation) under the control of a tetracycline-regulatable promoter. This modified strain was then tested in an animal model of hematogenously disseminated candidiasis. Mice injected with this strain under conditions permitting hyphal development succumbed to the infection, whereas all of the animals injected under conditions that inhibited this transition survived. Importantly, fungal burdens were almost identical in both sets of animals, indicating that, whereas filament formation appears to be required for the mortality resulting from a deep-seated infection, yeast cells play an important role early in the infectious process by extravasating and disseminating to the target organs. Moreover, these infecting Candida yeast cells still retained their pathogenic potential, as demonstrated by allowing this developmental transition to occur at various time points postinfection. We demonstrate here the importance of morphogenetic conversions in C. albicans pathogenesis. This engineered strain should provide a useful tool in unraveling the individual contributions of the yeast and filamentous forms at various stages of the infectious process.
STEPS TOWARD UNMASKING SECURE COMMUNICATIONS (1994)

This work tests the level of security in secure communication systems based on nonlinear dynamics (NLD), or chaos. In these systems, a chaotic carrier signal is used in a type of spread-spectrum signaling system, with the added benefit that the hidden information signal is buried at something of the order of −30 dB with respect to the chaotic carrier. To investigate the level of security in such systems, an examination was conducted on a test set of chaotic carriers and hidden information signals prepared by the NLD research group at the Naval Research Lab. The hidden signals included a triangle wave, a period doubled signal, and a chaotic signal that was different from the chaotic carrier. The analysis process was to use NLD forecasting to predict the carrier dynamics, and then subtract away the predicted values to reveal the hidden signal or at least increase its signal-to-noise ratio with respect to the carrier. In each case, it was a simple task to determine the power spectrum of the hidden signal once the prediction of the carrier was removed. This was then used to create a “comb” filter to extract the correct frequencies from the FFT of the first two signals. When this was done, the hidden signals were recreated with almost perfect accuracy. In the third case, the hidden chaotic signal had a broadband component, so the spectrum was used to develop a Weiner filter which enabled the hidden signal to be reconstructed with only moderate accuracy, where the overall structure of the hidden chaotic signal was preserved, but the fine structure was lost. As a further test, the processing approach was applied to a voice signal hidden in one-dimensional Lorenz data at −35 dB. After subtracting away the carrier model, the voice signal was reconstructed with reasonable accuracy, and had the same characteristic structure. In this case, no secondary filtering was applied. The forecasting approach was then extended to allow for dynamic signal estimation using threshold detection, so that whenever a signal was detected, multiple predictions of the carrier behavior were made into the future. This was tested on a square wave embedded at −42 dB in Lorenz data. The extended approach was able to reveal the square wave with almost perfect precision, except in a few regions where it temporarily lost synchrony with the carrier. This allowed for the elimination of the secondary filtering requirement entirely. The final conclusion is that the secure communications systems based on chaotic carriers may be useful to increase privacy, but are not yet capable of providing a high level of security. The paper concludes with a discussion of measures which may be taken to improve the security of such systems so that they may be applicable to areas where higher security is required.
Control of IκB-α Proteolysis by Site-Specific, Signal-Induced Phosphorylation (1995)

I kappa B-alpha inhibits transcription factor NF-kappa B by retaining it in the cytoplasm. Various stimuli, typically those associated with stress or pathogens, rapidly inactivate I kappa B-alpha. This liberates NF-kappa B to translocate to the nucleus and initiate transcription of genes important for the defense of the organism. Activation of NF-kappa B correlates with phosphorylation of I kappa B-alpha and requires the proteolysis of this inhibitor. When either serine-32 or serine-36 of I kappa B-alpha was mutated, the protein did not undergo signal-induced phosphorylation or degradation, and NF-kappa B could not be activated. These results suggest that phosphorylation at one or both of these residues is critical for activation of NF-kappa B.
The p75 Neurotrophin Receptor Promotes Amyloid-β(1-42)-Induced Neuritic DystrophyIn VitroandIn Vivo (2009)

Oligomeric forms of amyloid-beta (Abeta) are thought to play a causal role in Alzheimer's disease (AD), and the p75 neurotrophin receptor (p75(NTR)) has been implicated in Abeta-induced neurodegeneration. To further define the functions of p75(NTR) in AD, we examined the interaction of oligomeric Abeta(1-42) with p75(NTR), and the effects of that interaction on neurite integrity in neuron cultures and in a chronic AD mouse model. Atomic force microscopy was used to ascertain the aggregated state of Abeta, and fluorescence resonance energy transfer analysis revealed that Abeta oligomers interact with the extracellular domain of p75(NTR). In vitro studies of Abeta-induced death in neuron cultures isolated from wild-type and p75(NTR-/-) mice, in which the p75(NTR) extracellular domain is deleted, showed reduced sensitivity of mutant cells to Abeta-induced cell death. Interestingly, Abeta-induced neuritic dystrophy and activation of c-Jun, a known mediator of Abeta-induced deleterious signaling, were completely prevented in p75(NTR-/-) neuron cultures. Thy1-hAPP(Lond/Swe) x p75(NTR-/-) mice exhibited significantly diminished hippocampal neuritic dystrophy and complete reversal of basal forebrain cholinergic neurite degeneration relative to those expressing wild-type p75(NTR). Abeta levels were not affected, suggesting that removal of p75(NTR) extracellular domain reduced the ability of excess Abeta to promote neuritic degeneration. These findings indicate that although p75(NTR) likely does not mediate all Abeta effects, it does play a significant role in enabling Abeta-induced neurodegeneration in vitro and in vivo, establishing p75(NTR) as an important therapeutic target for AD.
Prosthetic-Joint Infections (2004)

Modern techniques have reduced the frequency of infections that are associated with prosthetic joints, but such infections continue to pose difficult problems in clinical management. Advances in understanding biofilms and the pathogenesis of microbial interactions with the implant have led to more rational approaches to therapy. This review offers guidance in establishing the diagnosis correctly and an algorithm summarizing the appropriate medical and surgical options.
24-HOUR RABBIT HEART STORAGE WITH UW SOLUTION (1989)

A new technique for 24-hr cardiac preservation is described utilizing very low flow perfusion (microperfusion) with a cold flush solution. Rabbit hearts were arrested with UW solution and then perfused with the same solution through the aortic root at 0 degrees C at a rate of 3-6 ml/gm heart weight/24 hr. When tested on an ex vivo working heart model, the cardiac output (CO) was 28.72 +/- 7.69 ml/g/min compared with fresh UW flushed controls of 26.48 +/- 2.25 ml/g/min. Both oxygenated highflow perfusion with a more conventional perfusate and 24-hr ice storage with UW led to inferior results. Omission of the colloid, hydroxyethyl starch (HES), from the UW solution or prolonged shelf storage were also significantly detrimental. When a previously untested colloid, polyethylene glycol 20,000, was substituted for HES for microperfusion, excellent cardiac function was obtained. In fact, the mean CO of this group, 31.91 +/- 5.70, was significantly above that of fresh HES-UW unstored controls. The suggestion that the UW solution might be improved by this substitution warrants further study.
Tyrosine-Phosphorylated Bacterial Proteins (2000)

For over a century, since the discovery by Roux and Yersin that sterile culture supernatants of Corynebacterium diphtheriae contained a potent toxin able to reproduce the lesions caused by diphtheria ([1][1]), most pathogenic bacteria have been considered to be microorganisms able to intoxicate
Linearly precoded or coded OFDM against wireless channel fades? (2002)

Orthogonal frequency division multiplexing (OFDM) converts a dispersive channel into parallel subchannels and thus facilitates equalization. But when the channel has nulls close to or on the FFT grid, OFDM faces serious symbol recovery problems. As an alternative to various error-control coding techniques that have been proposed to ameliorate the problem, we linearly precode (LP) symbols before they are multiplexed. We identify the maximum achievable diversity order for iid or correlated Rayleigh fading channels and also provide design rules for achieving maximum diversity gains with LP-OFDM. Simulated performance comparisons of LP-OFDM with existing block and convolutionally coded OFDM alternatives favor LP-OFDM in a HiperLan2 experiment.
Program for physicists (1970)

Share Icon Share Twitter Facebook Reddit LinkedIn Reprints and Permissions Cite Icon Cite Search Site Citation Richard L. Smith; Program for physicists. Physics Today 1 August 1970; 23 (8): 13. https://doi.org/10.1063/1.3022275 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentPhysics Today Search Advanced Search
The HTK hidden Markov model toolkit: design and philosophy (1993)

ion. However, they are not actually abstract data types. Far from it, all HTK data types are very concrete. The full definition of each type is visible outside of the module that defines it and the program which uses that type is free to manipulate its innards. Thus, from a software engineering perspective, the construction of HTK is unsafe since it is all too easy for an external agent to corrupt the internal operation of a module. Furthermore, it is necessary for an external agent to have a detailed understanding of each library module data type in order to use it effectively. Again, the HMMDef type provides a good example since this type represents a large hierarchical structure which HTK tools need to traverse and manipulate. To do this they have to access and manipulate the structure directly and since it is complex, this kind of operation will be prone to error. There are several reasons why HTK has been constructed like this. Firstly, and perhaps most importantly, it is very har...
Electrophilic Fluorination−Nucleophilic Addition Reaction Mediated by Selectfluor: Mechanistic Studies and New Applications (1999)

The electrophilic fluorination-nucleophilic addition reaction with Selectfluor-type reagents upon glycals has been studied and optimized. This reaction leads to selective fluorination at the 2-position with concomitant nucleophilic addition to the anomeric center. To understand the stereochemical outcome of this process, a mechanistic study has led to the discovery that, in the fucose series, Selectfluor adds specifically in a <i>syn</i> manner, yielding a 1-[TEDA-CH<sub>2</sub>Cl]-2-fluoro saccharide that anomerizes slowly to a more stable intermediate. The anomeric α/β distribution was studied as a function of reactants and conditions, and it was found that a judicious choice of protective group strategy can improve the stereoselectivity of both fluorination and nucleophilic addition. Furthermore, a hypersensitive radical probe was used to probe the reaction, and no product characteristic of a radical process was isolated, suggesting that no single electron transfer occurs during the attack of the glycal on Selectfluor. The importance of solvent effect, Selectfluor counterion, and stepwise procedure has also been discussed. This study has brought an important improvement of yields and a broader range of allowed nucleophiles such as secondary alcohols of carbohydrates, amino acids, phosphates, or phosphonates. This optimized process was further applied to the modification of important bioactive molecules, including the synthesis of fluorinated daunomycin and oleandrin analogues and the oxidation of thioglycosides to the corresponding sulfoxides.
Catechol‐O‐methyltransferase and Its Inhibitors in Parkinson's Disease (2007)

Parkinson's disease (PD) is a neurological disorder characterized by the degeneration of dopaminergic neurons, with consequent reduction in striatal dopamine levels leading to characteristic motor symptoms. The most effective treatment for this disease continues to be the dopamine replacement therapy with levodopa together with an inhibitor of aromatic amino acid decarboxylase (AADC). The efficacy of this therapy, however, decreases with time and most patients develop fluctuating responses and dyskinesias. The last decade showed that the use of catechol-O-methyltransferase inhibitors as adjuvants to the levodopa/AADC inhibitor therapy, significantly improves the clinical benefits of this therapy. The purpose of this article is to review the current knowledge on the enzyme catechol-O-methyltransferase (COMT) and the role of COMT inhibitors in PD as a new therapeutic approach to PD involving conversion of levodopa to dopamine at the target region in the brain and facilitation of the continuous action of this amine at the receptor sites. A historical overview of the discovery and development of COMT inhibitors is presented with a special emphasis on nebicapone, presently under clinical development, as well as entacapone and tolcapone, which are already approved as adjuncts in the therapy of PD. This article reviews human pharmacokinetic and pharmacodynamic properties of these drugs as well as their clinical efficacy and safety.
Fast deconvolution of multichannel systems using regularization (1998)

A very fast deconvolution method, which is based on the fast Fourier transform (FFT), can be used to control the outputs from a multichannel plant comprising any number of control sources and error sensors. The result is a matrix of causal finite impulse response filters whose performance is optimized at a large number of discrete frequencies. The paper is particularly aimed at multichannel sound reproduction and more specifically reproducing the sound field from a set of loudspeakers.
ANGPTL3 Decreases Very Low Density Lipoprotein Triglyceride Clearance by Inhibition of Lipoprotein Lipase (2002)

KK/San is a mutant mouse strain established in our laboratory from KK obese mice. KK/San mice show low plasma lipid levels compared with wild-type KK mice despite showing signs of hyperglycemia and hyperinsulinemia. Recently, we identified a mutation in the gene encoding angiopoietin-like protein 3 (Angptl3) in KK/San mice, and injection of adenoviruses encoding Angptl3 or recombinant ANGPTL3 protein to mutant KK/San mice raised plasma lipid levels. To elucidate the regulatory mechanism of ANGPTL3 on lipid metabolism, we focused on the metabolic pathways of triglyceride in the present study. Overexpression of Angptl3 in KK/San mice resulted in a marked increase of triglyceride-enriched very low density lipoprotein (VLDL). In vivo studies using Triton WR1339 revealed that there is no significant difference between mutant and wild-type KK mice in the hepatic VLDL triglyceride secretion rate. However, turnover studies using radiolabeled VLDL revealed that the clearance of (3)H-triglyceride-labeled VLDL was significantly enhanced in KK/San mice, whereas the clearance of (125)I-labeled VLDL was only slightly enhanced. In vitro analysis of recombinant protein revealed that ANGPTL3 directly inhibits LPL activity. These data strongly support the hypothesis that ANGPTL3 is a new class of lipid metabolism modulator, which regulates VLDL triglyceride levels through the inhibition of LPL activity.
A scheme of private key agreement based on the channel characteristics in OFDM land mobile radio (2005)

Abstract As a measure for preventing eavesdropping on land‐mobile communication, this paper studies an application of a private key agreement based on the propagation characteristics of channel to a practical system without key delivery. The paper proposes a private key agreement based on the time‐varying frequency characteristics suitable for OFDM. In the proposed method, the time‐varying frequency characteristics are alternately measured on the basis of the channel reciprocity and generation of the key and key agreement is attempted. Also, in the proposed method, for prevention of errors in key generation, measurement time difference compensation of the channel, noise reduction by the synchronous addition process, and key disagreement correction by an algebraic decoding method are applied. Further, in order to evaluate the safety of the key, a method for evaluation of independence of the key is discussed. As a system mode for evaluation of the performance of the proposed method, a model is constructed for study that is based on the specification of the IEEE802.11a wireless LAN using the OFDM, so that verification of an operation can be carried out in a more realistic environment. Numerical simulation indicates that it is possible to share the private key in a realistic setting with an SN ratio of 15 dB by means of various measures for prevention of key disagreement. Also, an evaluation confirms that independence is sufficiently maintained. © 2005 Wiley Periodicals, Inc. Electron Comm Jpn Pt 3, 88(9): 1–10, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/ecjc.20167
Cloning and sequencing of Pseudomonas genes encoding vanillate demethylase (1988)

A 2,598-base-pair (bp) SalI-HincII DNA fragment has been cloned which codes for vanillate demethylase, the enzyme responsible for the demethylation of vanillate (3-methoxy-4-hydroxybenzoate) to protocatechuate (3,4-dihydroxybenzoate). Complementation and insertional inactivation experiments have shown that this fragment carries two genes (vanA and vanB) which are predominantly cotranscribed from a promoter upstream of vanA. Nucleotide sequencing of the SalI-HincII fragment confirmed the genetic data: two open reading frames of 987 and 942 bp were present in the transcribed orientation. These had a very high G + C content in the third base of each codon, which is characteristic of Pseudomonas chromosomal genes. Expression of the genes in Escherichia coli with the T7 RNA polymerase-promoter system gave rise to two polypeptides of 36 and 33 kilodaltons which could be identified by deletion analysis as the products of vanA and vanB, respectively. A search of the protein sequence data bank indicated that the vanB gene product was related to the ferredoxin family.
Elevated Levels of Interleukin-8 in Donor Lungs is Associated with Early Graft Failure after Lung Transplantation (2001)

Increased levels of the neutrophil chemokine interleukin (IL)-8 in the lungs of severe trauma patients can predict subsequent development of acute respiratory distress syndrome. Because the lungs of brain-dead organ donors can contain high levels of IL-8, we hypothesized that this may predispose to early graft failure in the recipient after lung transplantation. Twenty-six organ donors prospectively satisfying clinical criteria for lung donation underwent bronchoalveolar lavage and lung biopsy to determine the effect of neutrophil infiltration and IL-8 expression in the donor lung on graft function and survival in 26 respective recipients after lung transplantation. Nine recipients developed severe graft dysfunction, of whom six subsequently died (median survival: 24 d [range: 5 to 39 d]); all others survived beyond 6 mo. The IL-8 signal in the donor lung correlated with the percent neutrophils in bronchoalveolar lavage fluid (BALF) before implantation (42.4 +/- 7.24 [mean +/- SE]%, p = 0.03) and with the degree of impairment in graft oxygenation after implantation (p = 0.01). An increased level of IL-8 in the donor BALF was associated with the development of severe early graft dysfunction (p = 0.027) and with early recipient mortality (p = 0.0034). Use of donor lungs with high IL-8 levels is associated with a poor prognosis after lung transplantation. Attenuating the donor's inflammatory response before organ retrieval may improve early outcome after lung transplantation, and help maximize lung use from the existing donor pool.
Functional Properties and Lineage Relationship of CD8+ T Cell Subsets Identified by Expression of IL-7 Receptor α and CD62L (2005)

Three major subsets of Ag-experienced CD8+ T cells have been identified according to their expression of CD62L and CD127. These markers are associated with central memory T cells (CD62L+ CD127+), effector memory T cells (CD162L- CD127+), and effector T cells (CD62L- CD127-). In this study we characterized the development of these three populations during acute and chronic viral infections and after immunization with virus-like particles and determined their lineage relation and functional and protective properties. We found that the balance between the three subsets was critically regulated by the availability of Ag and time. After initial down-regulation of CD127, the responding CD8+ T cell population down-regulated CD62L and re-expressed CD127. Dependent on Ag availability, the cells then further differentiated into CD62L- CD127- effector cells or, in the absence of Ag, re-expressed CD62L to become central memory T cells. Although all three populations efficiently produced effector cytokines such as IFN-gamma, CD62L- CD127- effector cells exhibited the highest ex vivo lytic potential. In contrast, CD62L+ CD127+ central memory T cells most efficiently produced IL-2 and proliferated extensively in vitro and in vivo upon antigenic restimulation. Strikingly, only effector and effector memory, but not central memory, T cells were able to protect against peripheral infection with vaccinia virus, whereas central memory T cells were most potent at protecting against systemic infection with lymphocytic choriomeningitis virus, indicating that the antiviral protective capacities of specific CD8+ T cell subsets are closely related to the nature of the challenging pathogen.