gebhart/patrepeval huggingface dataset:
Use of Telemetry and Plethysmography to Assess Respiratory Function in Conscious Rats with Bleomycin-Induced Lung Fibrosis (2019)

<b>Introduction:</b> IPF is characterised by irreversible lung function decline. This study assessed lung function in a repetitive bleomycin challenge model to better diagnose fibrosis in conscious rats. Respiratory parameters were determined using Intra-Pleural Pressure/Head-out Plethysmography and Whole Body Plethysmography. <b>Method:</b> Male telemetered rats were administered bleomycin on 5 occasions and treated with nintendanib (60 mg/kg, BID) or vehicle. Respiratory assessments were performed during Week 1 and 4. Lungs were scored for fibrosis. <b>Results:</b> Bleomycin-challenged animals developed fibrosis; fibrosis was reduced in nintedanib-treated animals. In the acute phase, bleomycin significantly changed respiratory rate, tidal volume, apnoea time and compliance; these parameters were improved with nintedanib treatment (Table). There were no significant differences in respiratory parameters in the established fibrosis phase. Acute phase respiratory rates and apnoea times were positively correlated with the extent of lung fibrosis on Day 29 (P&lt;0.01). <b>Conclusion:</b> Lung function assessment in concious rats detected early damage but did not diagnose the extent of fibrosis once established. These data will now be analysed using Attractor Reconstruction to determine whether fibrosis is better identified by novel parameters generated from the complete waveform.
Changes in Sugars and Volatiles of Ripening Erect Blackberry Fruit (1997)

Erect-fruited blackberries are often described as having a wild blackberry flavor. Flavor can be greatly affected by sugar and volatile composition, neither of which is known for erect-fruited blackberries. This study was done to characterize changes in sugar and volatile composition in ripening blackberries. Blackberries of `Navaho', `Arapaho', `Shawnee', and `Choctaw' were harvested at red, mottled, shiny, and dull black ripeness stages. Sucrose was found in small amounts (4% to 15%) in all stages of ripeness in all cultivars. Total sugars increased from ≈20–30 to 60–80 mg/g dry weight as fruit ripened from red to dull black. Fructose and glucose maintained a constant 1:1 ratio with ripeness stage and cultivar. Three of the four cultivars had a linear increase in total sugars with ripening; total sugars increased 4% to 40% as fruit ripened from shiny to dull black. Twenty to 25 volatile peaks were found by headspace gas chromatography in ripening blackberries. Six volatiles, tentatively identified as α-pinene, eugenol, limonene, p-cymene, α-terpinol, and gernaylacetone, appeared in all cultivars, but only in ripe (shiny and dull black) fruit. Few volatile peaks were observed in red (unripe) fruit. Data indicate that blackberries continue to increase in sugars in the latter stages of ripeness and that volatiles unique to ripe blackberries are produced during this period.
Genome Analysis of Moraxella catarrhalis Strain RH4, a Human Respiratory Tract Pathogen (2012)

__AUTHOR'S CORRECTION__ 

Volume 192, no. 14, pages 3574–3583, 2010. The genome sequence described is that of strain BBH18, isolated from sputum, and not of strain RH4, which was isolated from blood. Consequently, the title should read “Genome Analysis of Moraxella catarrhalis Strain BBH18, a Human Respiratory Tract Pathogen,” and the strain name RH4 should be replaced by BBH18 throughout the manuscript. Furthermore, in the abstract (page 3574, line 4), introduction (page 3574, column 2, line 27), and Materials and Methods (page 3575, column 1, lines 13 and 14), the phrase “isolated from blood of an infected patient (14)” should be changed to “isolated from sputum of a patient with COPD during an exacerbation (45).” The correct reference for strain BBH18 is reference 45 (A. Mollenkvist et al., J. Bacteriol. 185:2285–2295, 2003).
Invited Talk 2 (2009)

Hardware security is essential to the prevention of cloning, theft of service and tampering. Effective hardware security starts with secure key storage. The level of security provided by a key is dependent upon the effort an attacker needs to expend to compromise the key. The sophistication of the tools that are used to carry out such attacks has increased significantly over the years, compromising the protection of traditional key-storage approaches. A radically new approach is needed to counter this increased threat. Rather than trying harder to conceal the key in the hardware, a revolutionary approach has emerged in which the key is simply not stored. This new approach to hardware security relies on the unique electronic "fingerprint" inherent in every semiconductor device and is known as Hardware Intrinsic Security (HIS).
Regulation of pancreatic β-cell mass and proliferation by SOCS-3 (2005)

Growth hormone and prolactin are important growth factors for pancreatic beta-cells. The effects exerted by these hormones on proliferation and on insulin synthesis and secretion in beta-cells are largely mediated through the Janus kinase (JAK)/signal transducer and activator of transcription (STAT) signaling pathway. Suppressors of cytokine signaling (SOCS) proteins are specific inhibitors of the JAK/STAT pathway acting through a negative-feedback loop. To investigate in vivo effects of SOCS-3 in growth hormone (GH)/prolactin signaling in beta-cells we generated transgenic mice with beta-cell-specific overexpression of SOCS-3. The relative beta-cell proliferation and volume in the mice were measured by morphometry. Beta-cell volume of transgenic female mice was reduced by over 30% compared with beta-cell volume in wild-type female mice. Stimulation of transgenic islets in vitro with GH showed a reduced tyrosine phosphorylation of STAT-5 when compared with wild-type islets. Transduction of primary islet cultures with adenoviruses expressing various SOCS proteins followed by stimulation with GH or glucagon-like peptide-1 (GLP-1) revealed that SOCS-3 inhibited GH- but not GLP-1-mediated islet cell proliferation, indicating that the decreased beta-cell volume observed in female transgenic mice could be caused by an inhibition of GH-induced beta-cell proliferation by SOCS-3. In spite of the reduced beta-cell volume the transgenic female mice exhibited enhanced glucose tolerance compared with wild-type littermates following an oral glucose-tolerance test. Together these data suggest that SOCS-3 modulates cytokine signaling in pancreatic beta-cells and therefore potentially could be a candidate target for development of new treatment strategies for diabetes.
PRESAS: Block‐structured preconditioning of iterative solvers within a primal active‐set method for fast model predictive control (2020)

Summary Model predictive control (MPC) for linear dynamical systems requires solving an optimal control structured quadratic program (QP) at each sampling instant. This article proposes a primal active‐set strategy, called PRESAS , for the efficient solution of such block‐sparse QPs, based on a preconditioned iterative solver to compute the search direction in each iteration. Rank‐one factorization updates of the preconditioner result in a per‐iteration computational complexity of , where m denotes the number of state and control variables and N the number of control intervals. Three different block‐structured preconditioning techniques are presented and their numerical properties are studied further. In addition, an augmented Lagrangian based implementation is proposed to avoid a costly initialization procedure to find a primal feasible starting point. Based on a standalone C code implementation, we illustrate the computational performance of PRESAS against current state of the art QP solvers for multiple linear and nonlinear MPC case studies. We also show that the solver is real‐time feasible on a dSPACE MicroAutoBox‐II rapid prototyping unit for vehicle control applications, and numerical reliability is illustrated based on experimental results from a testbench of small‐scale autonomous vehicles.
Glycosphingolipids of the model fungus Aspergillus nidulans (2003)

Aspergillus nidulans is a well-established nonpathogenic laboratory model for the opportunistic mycopathogen, A. fumigatus. Some recent studies have focused on possible functional roles of glycosphingolipids (GSLs) in these fungi. It has been demonstrated that biosynthesis of glycosylinositol phosphorylceramides (GIPCs) is required for normal cell cycle progression and polarized growth in A. nidulans (Cheng, J., T.-S. Park, A. S. Fischl, and X. S. Ye. 2001. Mol. Cell Biol. 21: 6198-6209); however, the structures of A. nidulans GIPCs were not addressed in that study, nor were the functional significance of individual structural variants and the downstream steps in their biosynthesis. To initiate such studies, acidic GSL components (designated An-2, -3, and -5) were isolated from A. nidulans and subjected to structural characterization by a combination of one-dimensional (1-D) and 2-D NMR spectroscopy, electrospray ionization-mass spectrometry (ESI-MS), ESI-MS/collision-induced decomposition-MS (MS/CID-MS), ESI-pseudo-[CID-MS]2, and gas chromatography-MS methods. All three were determined to be GIPCs, with mannose as the only monosaccharide present in the headgroup glycans; An-2 and An-3 were identified as di- and trimannosyl inositol phosphorylceramides (IPCs) with the structures Man alpha 1-->3Man alpha 1-->2Ins1-P-1Cer and Man alpha 1-->3(Man alpha 1-->6)Man alpha 1-->2Ins1-P-1Cer, respectively (where Ins = myo-inositol, P = phosphodiester, and Cer = ceramide). An-5 was partially characterized, and is proposed to be a pentamannosyl IPC, based on the trimannosyl core structure of An-3.
Chemoprevention of Cigarette Smoke–Induced Alterations of MicroRNA Expression in Rat Lungs (2010)

We previously showed that exposure to environmental cigarette smoke (ECS) for 28 days causes extensive downregulation of microRNA expression in the lungs of rats, resulting in the overexpression of multiple genes and proteins. In the present study, we evaluated by microarray the expression of 484 microRNAs in the lungs of either ECS-free or ECS-exposed rats treated with the orally administered chemopreventive agents N-acetylcysteine, oltipraz, indole-3-carbinol, 5,6-benzoflavone, and phenethyl isothiocyanate (as single agents or in combinations). This is the first study of microRNA modulation by chemopreventive agents in nonmalignant tissues. Scatterplot, hierarchical cluster, and principal component analyses of microarray and quantitative PCR data showed that none of the above chemopreventive regimens appreciably affected the baseline microRNA expression, indicating potential safety. On the other hand, all of them attenuated ECS-induced alterations but to a variable extent and with different patterns, indicating potential preventive efficacy. The main ECS-altered functions that were modulated by chemopreventive agents included cell proliferation, apoptosis, differentiation, Ras activation, P53 functions, NF-kappaB pathway, transforming growth factor-related stress response, and angiogenesis. Some microRNAs known to be polymorphic in humans were downregulated by ECS and were protected by chemopreventive agents. This study provides proof-of-concept and validation of technology that we are further refining to screen and prioritize potential agents for continued development and to help elucidate their biological effects and mechanisms. Therefore, microRNA analysis may provide a new tool for predicting at early carcinogenesis stages both the potential safety and efficacy of cancer chemopreventive agents.
Improving Activity of Salt-Lyophilized Enzymes in Organic Media (2007)

Lyophilization with salts has been identified as an important method of activating enzymes in organic media. Using salt-activated enzymes to transform molecules tethered to solid surfaces in organic phase requires solubilization of enzymes in the solvents. Methods of improving performance of salt-lyophilized enzymes, further, via chemical modification, and use of surfactants and surfactants to create fine emulsions prior to lyophilization are investigated. The reaction system used is transesterification of N-acetyl phenylalanine ethyl ester with methanol or propanol. Initial rate of formation of amino acid esters by subtilisin Carlsberg (SC) was studied and found to increase two to sevenfold by either chemical modification or addition of surfactants in certain solvents, relative to the salt (only)-lyophilized enzyme. The method to prepare highly dispersed enzymes in a salt-surfactant milieu also improved activity by two to threefold. To test the effect of chemical modification on derivatization of drug molecules, acylation of bergenin was investigated using chemically modified SC.
eMeeting: the implementation of H.263 based embedded video communication (2006)

Video communication on the mobile devices will be very popular in the near future, but the limited resource of the current embedded processors can not support the complex video codec. In this paper we present the eMeeting prototype system which can implement the H.263 video encode and decode and bidirection communication on one XScale PXA255 general embedded processor. Experiment results show that the eMeeting system can achieve the frame rate up to 8fps under the circumstances that the encoding, decoding, network communication, video capturing and other modules are ongoing simultaneously
Time-Variant Haptic Simulator Based on Fine and Fast Real-Time Discretization Using FDTD Method (2019)

This paper proposes fine and fast discretization, which is based on the Finite Difference Time Domain (FDTD) method without a matrix exponential function. The proposed method is more accurate than the conventional discretization based on the first-order Pade approximation. Moreover, compared with that of the conventional method, the computational cost of the proposed method is very small. Although the Pade approximation is impossible to realize broadband real-time control, the FDTD method achieves the broadband real-time control. The proposed method and the conventional Pade approximation are analyzed by the Taylor expansion in a symbolic expression. According to the theorical analysis, the error of the FDTD discretization method is smaller than that of the conventional method. Numerical simulations also compare the errors and computational cost associated with the proposed and conventional methods. The FDTD discretization method is applied in admittance control for rendering the time-variant haptic sensation. In the case of the conventional method, owing to the limitation due to computation cost, the parameter update is not completed within the sampling period. On the other hand, the FDTD method completes the discretization within the sampling period. The gain and phase characteristics of the proposed method are close to the ideal responses. The validity of the method is verified by an experiment involving linear motor systems.
Cloning and expression of cytokine genes (1995)

Abstract Cytokines are proteins secreted by a cell into the extracellular fluid where they exert their effects on the same cells (autocrine activity) or on neighbouring cells (paracrine activity) by interacting with specific receptors. Most cytokine proteins have, on a molar basis, very high biological activities (for instance, colony stimulating factors are active at 10™11 to 10™13 M concentrations) which usually can be assayed in rapid, sensitive and fairly specific in vitro test systems. These fast and simple detection systems have played a crucial role in the cloning of the corresponding cytokine genes by providing tools for either purification of the protein, the mRNA, or the direct detection of biologically active clones in cDNA expression libraries. Other cytokines, such as the strongly inducible chemokine family (the mRNA for these molecules can represent 1% of the total poly(A)+ RNA after stimulation), act in much higher concentrations (10™3 to 10™9 M) and have often been cloned by different techniques such as induction-specific differential hybridization or subtracted libraries. An important factor in a successful cloning procedure is the presence of an abundant source of protein and mRNA. The expression level of the desired gene in this source determines the frequency with which the genes will be found in the cDNA libraries.
Indium Compounds (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Monolithically-Integrated Dual-Wavelength Laser Diodes for Optical Pickups. (2002)

780 nm-band AlGaAs and 650 nm-band AlGaInP laser diodes are monolithically integrated on a GaAs substrate as the light source in DVD/CD optical pickups. In order to reduce internal losses for improved characteristics and to ensure better flexibility of device design, real-refractive index-guided self-aligned (RISA) structure is employed for both 780 nm and 650 nm-band LDs. As a result, low noise characteristics due to self-sustained pulsation in the both wavelength bands have been achieved. A dual-wavelength laser with a high power ( > 100 mW) 780 nm-band LD has also been developed for recording of CD-R/RW disks.
Thiol–Ene Click Reaction for Fine Polarity Tuning of Polymeric Binders in Solution-Processed All-Solid-State Batteries (2018)

Recent studies of all-solid-state batteries (ASSBs) have identified sulfide-based electrolytes with comparable ionic conductivities as those of liquid counterparts. Nevertheless, solution-based manufacturing is unestablished, since it is challenging to find adhesive polymeric binders that can be dispersed in common solvents with sulfide electrolytes. Currently available binders exhibit insufficient electrode adhesion due to their low polarity and are compromised by the chemical stability of a slurry. Here, we report a thiol–ene click reaction used to graft styrene–butadiene-block-copolymer with carboxylic acid at an optimal concentration. With polarity tuning, the click binder results in a uniform electrode slurry without ruining the structure of the sulfide electrolytes, while enabling electrode adhesion 1.4 times as high as that of commercial lithium-ion battery electrodes. The click binder also allows ASSBs to deliver decent electrochemical performance, implying that fine polarity tuning of functional binders can constitute an important step forward in advancing ASSBs to a real scalable technology.
Polar codes with mixed kernels (2011)

A generalization of the polar coding scheme is proposed. It exploits several homogeneous kernels over alphabets of different sizes. An analysis of the introduced scheme is undertaken. Specifically, asymptotic properties of the polarization are shown to be strongly related to the ones of the constituent kernels.
Melanization ofCryptococcus neoformansandHistoplasma capsulatumReduces Their Susceptibilities to Amphotericin B and Caspofungin (2002)

The fungal pathogens Cryptococcus neoformans and Histoplasma capsulatum produce melanin-like pigments in the presence of L-dopa in vitro and during mammalian infection. We investigated whether melanization affected the susceptibilities of the fungi to amphotericin B, caspofungin, fluconazole, itraconazole, or flucytosine (5FC). Using the standard macrodilution MIC protocol (the M27A protocol) of the National Committee for Clinical Laboratory Standards for yeast, we found no difference in the susceptibilities of melanized and nonmelanized C. neoformans and H. capsulatum isolates. Killing assays demonstrated that melanization reduced the susceptibilities of both fungi to amphotericin B and caspofungin. Laccase-deficient C. neoformans cells grown with L-dopa were significantly more susceptible than congenic melanin-producing yeast to killing by amphotericin B or caspofungin. Preincubation of amphotericin B or caspofungin with melanins decreased their antifungal activities. Elemental analysis of melanins incubated with amphotericin B or caspofungin revealed an alteration in the C:N ratios of the melanins, which indicated binding of these drugs by the melanins. In contrast, incubation of fluconazole, itraconazole, or 5FC with melanins did not significantly affect the antifungal efficacies of the drugs or the chemical composition of the melanins. The results suggest a potential explanation for the inefficacy of caspofungin against C. neoformans in vivo, despite activity in vitro. Furthermore, the results indicate that fungal melanins protect C. neoformans and H. capsulatum from the activities of amphotericin B and caspofungin and that this protection is not demonstrable by standard broth macrodilution assays.
Factors Affecting the Relative and Absolute Rates of β-Scission of Alkoxythiocarbonyl Radicals and Alkoxycarbonyl Radicals (2006)

High-level ab initio calculations demonstrate that alkoxy-thiocarbonyl radicals (ROC*=S) undergo beta-scission significantly faster than alkoxycarbonyl radicals (ROC*=O) despite having similar exothermicities. The relatively low reactivity of the ROC*=O radicals is reduced further by electron-donating R groups and arises from the large polarization of the C*-O bonds of the reactant radicals. The results suggest that the generation of alkyl radicals from ROC*=S should be particularly efficient when the R group bears radical-stabilizing and/or electron-accepting groups, such as CN.
Time-dependent photon migration using path integrals (1995)

We present an approach to the problem of light propagation in turbid media based on the path integral formalism. The method of analysis provides solutions to the time-dependent equation of radiative transfer for a number of cases for which known approximations, including the diffusion approximation, are not applicable. The theory and experiments show that trajectories of photon traversing a turbid medium cluster around a well defined, time-resolved path called a classical path. This concept is a powerful tool, and it provides physical insight into optical propagation in turbid media.
Buffer sizing at a host in an ATM network (1992)

The authors develop a queuing model of a buffer that collects cells for reassembly into packets for a protocol layer above the asynchronous transfer mode (ATM) layer. Whenever the buffer fills with all packets incomplete, a packet must be sacrificed to make room for others. The queuing model estimates the equilibrium fraction of packets sacrificed. Applications to sizing the buffer for a prescribed loss probability are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>