gebhart/patrepeval huggingface dataset:
Effect of antifungal agents on the adherence of Candida albicans to murine gastrointestinal mucosal surfaces (1990)

The in-vitro adherence of Candida albicans to murine gastrointestinal mucosal surfaces was investigated in the presence of sub-inhibitory concentrations of amphotericin B, ketoconazole and itraconazole. Each antifungal drug showed a significant ability to reduce the adherence of C. albicans to gastric and jejunal mucosa. However, the outcome of an adherence assay was dependent on pH, drug concentration and C. albicans strain. The type of mucosal surface and its cellular arrangement also had an important role to play. Sub-inhibitory concentrations of amphotericin B, ketoconazole and itraconazole significantly reduced the adherence of an azole sensitive strain C. albicans 3436. These effects were influenced by the type of mucosal surface and the concentration of the antifungal drug. Sub-inhibitory concentrations of amphotericin B inhibited the adherence of an azole resistant strain. C. albicans 3310, to stomach and jejunal mucosal surfaces while sub-inhibitory concentrations of ketoconazole only significantly reduced this strain's adherence to gastric mucosal explants. Sub-inhibitory concentrations of itraconazole had little effect. Amphotericin B reduced the adherence of C. albicans 3436 to gastric mucosal explants when assays were performed at physiological pH levels, an effect dependent on concentration. This drug also reduced the adherence of strain 3436 to jejunal mucosal cells and explants at physiological pH levels, though results obtained from assays involving jejunal mucosal explants, incubated at pH 8.0, were concentration dependent.
Label-Free Mass Spectrometry-Based Quantitative Proteomics to Evaluate the Effects of the Calcium-Sensing Receptor Agonist Cinacalcet on Protein Expression in Rat Brains and Livers (2022)

BACKGROUND Cinacalcet is a calcium-sensing receptor agonist that is clinically approved for the treatment of secondary hyperparathyroidism in chronic kidney disease and hypercalcemia in patients with parathyroid carcinoma. This study aimed to use quantitative mass spectrometry-based label-free proteomics to evaluate the effects of cinacalcet on protein expression in rat brains and livers. MATERIAL AND METHODS We randomly assigned 18 Wistar rats to 2 groups: an untreated control group (n=6) and a group treated with cinacalcet at a dose corresponding to the maximum dose used in humans (2 mg/kg/body weight, 5 days/week) divided into 7-day (n=6) and 21-day (n=6) treatment subgroups. A mass-spectrometry-based label-free quantitative proteomics approach using peptides peak area calculation was used to evaluate the changes in protein expression in examined tissues. Bioinformatics analysis of quantitative proteomics data was done using MaxQuant and Perseus environment. RESULTS No changes in protein expression were revealed in the 7-day treatment subgroup. We detected 10 upregulated and 3 downregulated proteins in the liver and 1 upregulated protein in the brain in the 21-day treatment subgroup compared to the control group. Based on Gene Ontology classification, all identified differentially expressed proteins were indicated as molecular functions involved in the enzyme regulator activity (36%), binding (31%), and catalytic activity (19%). CONCLUSIONS These findings indicate that long-term cinacalcet therapy can impair phase II of enzymatic detoxication and can cause disturbances in blood hemostasis, lipid metabolism, and inflammatory mediators or contribute to the acceleration of cognitive dysfunction; therefore, appropriate patient monitoring should be considered.
Towards Automatic Generation of Shareable Synthetic Clinical Notes Using\n Neural Language Models (2019)

Large-scale clinical data is invaluable to driving many computational\nscientific advances today. However, understandable concerns regarding patient\nprivacy hinder the open dissemination of such data and give rise to suboptimal\nsiloed research. De-identification methods attempt to address these concerns\nbut were shown to be susceptible to adversarial attacks. In this work, we focus\non the vast amounts of unstructured natural language data stored in clinical\nnotes and propose to automatically generate synthetic clinical notes that are\nmore amenable to sharing using generative models trained on real de-identified\nrecords. To evaluate the merit of such notes, we measure both their privacy\npreservation properties as well as utility in training clinical NLP models.\nExperiments using neural language models yield notes whose utility is close to\nthat of the real ones in some clinical NLP tasks, yet leave ample room for\nfuture improvements.\n
Resource Allocation for Autonomic Data Centers using Analytic Performance Models (2005)

Large data centers host several application environments (AEs) that are subject to workloads whose intensity varies widely and unpredictably. Therefore, the servers of the data center may need to be dynamically redeployed among the various AEs in order to optimize some global utility function. Previous approaches to solving this problem suffer from scalability limitations and cannot easily address the fact that there may be multiple classes of workloads executing on the same AE. This paper presents a solution that addresses these limitations. This solution is based on the use of analytic queuing network models combined with combinatorial search techniques. The paper demonstrates the effectiveness of the approach through simulation experiments. Both online and batch workloads are considered
Structure-based optimization of a PDZ-binding motif within a viral peptide stimulates neurite outgrowth (2019)

Protection of neuronal homeostasis is a major goal in the management of neurodegenerative diseases. Microtubule-associated Ser/Thr kinase 2 (MAST2) inhibits neurite outgrowth, and its inhibition therefore represents a potential therapeutic strategy. We previously reported that a viral protein (G-protein from rabies virus) capable of interfering with protein-protein interactions between the PDZ domain of MAST2 and the C-terminal moieties of its cellular partners counteracts MAST2-mediated suppression of neurite outgrowth. Here, we designed peptides derived from the native viral protein to increase the affinity of these peptides for the MAST2-PDZ domain. Our strategy involved modifying the length and flexibility of the noninteracting sequence linking the two subsites anchoring the peptide to the PDZ domain. Three peptides, Neurovita1 (NV1), NV2, and NV3, were selected, and we found that they all had increased affinities for the MAST2-PDZ domain, with <i>K<sub>d</sub></i> values decreasing from 1300 to 60 nm, while target selectivity was maintained. A parallel biological assay evaluating neurite extension and branching in cell cultures revealed that the NV peptides gradually improved neural activity, with the efficacies of these peptides for stimulating neurite outgrowth mirroring their affinities for MAST2-PDZ. We also show that NVs can be delivered into the cytoplasm of neurons as a gene or peptide. In summary, our findings indicate that virus-derived peptides targeted to MAST2-PDZ stimulate neurite outgrowth in several neuron types, opening up promising avenues for potentially using NVs in the management of neurodegenerative diseases.
Fibroblast Growth Factor Receptor Signaling Activates the Human Interstitial Collagenase Promoter via the Bipartite Ets-AP1 Element (1997)

Interstitial collagenases participate in the remodeling of skeletal matrix and are regulated by fibroblast growth factor (FGF). A 0.2-kb fragment of the proximal human interstitial collagenase [matrix metalloproteinase (MMP1)] promoter conveys 4- to 8-fold induction of a luciferase reporter in response to FGF2 in MC3T3-E1 osteoblasts. By 5′-deletion, this response maps to nucleotides− 100 to −50 relative to the transcription initiation site. The 63- bp MMP1 promoter fragment −123 to −61 confers this FGF2 response on the rous sarcoma virus minimal promoter. Intact Ets and AP1 cognates in this element are both required for responsiveness. The AP1 site supports basal and FGF-inducible promoter activity. The intact Ets cognate represses basal transcriptional activity in both heterologous and native promoter contexts and is also required for FGF activation. FGF2 up-regulates a DNA-binding activity that recognizes the MMP1 AP1 cognate and contains immunoreactive Fra1 and c-Jun. Both constitutive and FGF-inducible DNA-binding activities are present in MC3T3-E1 cells that recognize the MMP1 Ets cognate; prototypic Ets transcriptional activators are not present in these complexes. Inhibitors of protein kinase C, phosphatidyl inositol 3-OH kinase, and calmodulin-dependent protein kinase do not attenuate MMP1 promoter activation. FGF2 activates ERK1/ERK2 signaling in osteoblasts; however, 25 μm MAPK-ERK kinase (MEK) inhibitor PD98059 (inhibits by > 85% the phosphorylation of ERK1/ERK2) has no effect on MMP1 promoter activation by FGF2. Ligand-activated and constitutively active FGF receptors initiate MMP1 induction. Dominant negative Ras abrogates MMP1 induction by constitutively active FGFR2-ROS, but dominant negative Rho and Rac do not inhibit induction. The mitogen-activated protein kinase (MAPK) phosphatase MKP2[ inactivates extracellular regulated kinase (ERK) = Jun N-terminal kinase (JNK) > p38 MAPK] completely abrogates MMP1 activation, whereas PAC1 (inactivates ERK = p38 > JNK) attenuates but does not completely prevent induction. Thus, a Ras- and MKP2-regulated MAPK pathway, independent of ERK1/ERK2 MAPK activity, mediates FGF2 transcriptional activation of MMP1 in MC3T3-E1 osteoblasts, converging upon the bipartite Ets-AP1 element. The DNA-protein interactions and signal cascades mediating FGF induction of the MMP1 promoter are distinct from two other recently described FGF response elements: the MMP1 promoter (−123 to −61) represents a third FGF-activated transcriptional unit.
A 1 K/spl times/1 K high dynamic range CMOS image sensor with on-chip programmable region-of-interest readout (2002)

An integrated 1024/spl times/1024 CMOS image sensor with programmable region-of-interest (ROI) readout and multiexposure technique has been developed and successfully tested. Size and position of the ROI is programmed based on multiples of a minimum readout kernel of 32/spl times/32 pixels. Since the dynamic range of the irradiance normally exceeds the electrical dynamic range of the imager that can be covered using a single integration time, a multiexposure technique has been implemented in the imager. Subsequent sensor images are acquired using different integration times and recomputed to form a single composite image. A newly developed algorithm performing the recomputation is presented. The chip has been realized in a 0.5-/spl mu/m n-well standard CMOS process. The pixel pitch is 10 /spl mu/m/sup 2/ and the total chip area is 164 mm/sup 2/.
Optical properties of a single type of optically active center inSi∕Si:Ernanostructures (2004)

We present the results of high-resolution photoluminescence and magneto-optical spectroscopy of selectively doped $\mathrm{Si}∕\mathrm{Si}:\mathrm{Er}$ nanolayer structures grown by sublimation molecular beam epitaxy method. We show that the annealing of such samples results in a preferential formation of a single type of optically active $\mathrm{Er}$-related center. Detailed information on the microscopic structure of this center has been revealed from the investigation of the Zeeman effect. Its symmetry is found to be orthorhombic $I$ $({C}_{2v})$ and several $g$-tensors of the ground and excited states are determined. The consequences of current findings for the microscopic model of the $\mathrm{Er}$-related center preferentially generated in $\mathrm{Si}∕\mathrm{Si}:\mathrm{Er}$ nanolayers are discussed.
High Numerical Aperture Aberration Compensation Enabled by an Artificial Neural Network (2019)

The determination of phase aberrations is essential to ensure diffraction limited performance in optical imaging and three-dimensional laser fabrication [1]. It is especially crucial as the photonics community transitions from microscopy to nanoscopy and from microfabrication to nanofabrication. However, the determination of phase aberrations is often a highly parallel and nonlinear problem that necessitates specialist equipment, intensive computation, or prolonged iteration.
Laboratory evidence for an asymmetric accretion structure upon slanted matter impact in young stars (2020)

Aims. Investigating the process of matter accretion onto forming stars through scaled experiments in the laboratory is important in order to better understand star and planetary system formation and evolution. Such experiments can indeed complement observations by providing access to the processes with spatial and temporal resolution. A previous investigation revealed the existence of a two-component stream: a hot shell surrounding a cooler inner stream. The shell was formed by matter laterally ejected upon impact and refocused by the local magnetic field. That laboratory investigation was limited to normal incidence impacts. However, in young stellar objects, the complex structure of magnetic fields causes variability of the incident angles of the accretion columns. This led us to undertake an investigation, using laboratory plasmas, of the consequence of having a slanted accretion impacting a young star. Methods. Here, we used high power laser interactions and strong magnetic field generation in the laboratory, complemented by numerical simulations, to study the asymmetry induced upon accretion structures when columns of matter impact the surface of young stars with an oblique angle. Results. Compared to the scenario where matter accretes perpendicularly to the star surface, we observe a strongly asymmetric plasma structure, strong lateral ejecta of matter, poor confinement of the accreted material, and reduced heating compared to the normal incidence case. Thus, slanted accretion is a configuration that seems to be capable of inducing perturbations of the chromosphere and hence possibly influencing the level of activity of the corona.
High-resolution dual comb spectroscopy using a free-running, bidirectional ring titanium sapphire laser (2022)

We report the first measurement of resolved molecular absorption lines with dual-comb spectroscopy using a Kerr-lens mode-locked bidirectional Ti:sapphire ring laser cavity. A 3 nm broad spectrum has been recorded in 5.3 ms with a spectral resolution of ≈ 1 GHz (0.05 cm-1) corresponding to a relative spectral resolution of 2.5 × 10<sup>-6</sup>. The measurement of spectrally resolved molecular absorption lines have been demonstrated on the oxygen A-band at 394 THz (760 nm, 13 000 cm<sup>-1</sup>) and was obtained with two free-running 100 fs Ti:sapphire trains of pulses without the need for active phase stabilization protocol nor real-time or post-processing correction. This work demonstrates that the bidirectional laser configuration enables a sufficient level of absolute and mutual coherence for dual-comb spectroscopy of resolved molecular absorption lines. Considering the high versatility of Ti:sapphire emission spectral range (from 600 to 1100 nm) with high-peak powers, the here reported results pave the way for Dual-Comb spectroscopy in the UV range at mW average output power using a standalone set-up, in the aim to extend its applicability for atmospheric remote-sensing.
Pore surface grafting of porous low-k dielectrics by selective polymers (2017)

Polymer grafting of pore sidewalls is studied as a protecting agent against processing damage. Polymethyl-methacrylate (PMMA), an improved polystyrene (PS-pro), and a tailored plasma damage management polymer (PDM) are considered as potential candidates. PMMA and PS-pro show nonhomogeneous grafting properties, while PDM coat the pore sidewalls uniformly through the bulk of the porous low-k film. A k ∼ 2.2 porous spin-on glass is used as a vehicle for processing damage study. Approximately one monolayer is grafted on the pore walls, leading to a k-value increase up to Δk ∼ 0.2. Using grafted PDM, the porous low-k chemical stability in 0.5% diluted hydrofluoric acid is significantly improved. Concerning plasma damage, at constant etch depth methyl depletion is decreased, mainly in capacitive coupled plasma discharge showing high polymerizing character, leading to similar damage depth as found for a reference organo-silicate glass 2.7 low-k. However, moisture uptake is not improved, leading to significant drift in the dielectric constant.
Interhemispheric Transfer Time Asymmetry of Visual Information Depends on Eye Dominance: An Electrophysiological Study (2018)

The interhemispheric transfer of information is a fundamental process in the human brain. When a visual stimulus appears eccentrically in one visual-hemifield, it will first activate the contralateral hemisphere but also the ipsilateral one with a slight delay due to the interhemispheric transfer. This interhemispheric transfer of visual information is believed to be faster from the right to the left hemisphere in right-handers. Such an asymmetry is considered as a relevant fact in the context of the lateralization of the human brain. We show here using current source density (CSD) analyses of visually evoked potential (VEP) that, in right-handers and, to a lesser extent in left-handers, this asymmetry is in fact dependent on the sighting eye dominance, the tendency we have to prefer one eye for monocular tasks. Indeed, in right-handers, a faster interhemispheric transfer of visual information from the right to left hemisphere was observed only in participants with a right dominant eye (DE). Right-handers with a left DE showed the opposite pattern, with a faster transfer from the left to the right hemisphere. In left-handers, albeit a smaller number of participants has been tested and hence confirmation is required, only those with a right DE showed an asymmetrical interhemispheric transfer with a faster transfer from the right to the left hemisphere. As a whole these results demonstrate that eye dominance is a fundamental determinant of asymmetries in interhemispheric transfer of visual information and suggest that it is an important factor of brain lateralization.
Sources of construction vibration, such as pile driving, dynamic compaction, blasting and operation of heavy construction equipment, may harmfully affect surrounding buildings and its effect ranges from serious disturbances of working conditions for sensitive devices and people to visible structural damage. (2004)

Summary: Construction-induced vibrations may be detrimental to adjacent structures and sensitive electronics operating nearby. Construction vibration sources have a wide range of energy and velocity, as a function of time, transmitted on the ground. Analysis of existing methods for predicting ground and structure vibrations shows that empirical equations provide calculations only of amplitudes of vertical soil vibrations with insufficient accuracy. This paper presents the application of the impulse response function concept to solve the geotechnical problem of predicting ground and structure vibrations before installation of vibration sources. Impulse response functions reflect real behavior of soil and structures without the investigation of soil and structure properties. A procedure is presented to compute predicted ground and structure vibrations. Good agreement is found between predicted and measured records.
Center-Shift Method for the Characterization of Dielectric Charging in RF MEMS Capacitive Switches (2008)

Radio frequency (RF) micro-electro-mechanical systems (MEMS) capacitive switches show great promise for use in wireless communication devices such as mobile phones, but for the successful application of these switches their reliability needs to be demonstrated. One of the main factors that limits the reliability is charge injection in the dielectric layer (SiN) which can cause irreversible stiction of the moving part of the switch. We present a way to characterize charge injection. By stressing the dielectric with electric fields on the order of 1 MV/cm, we inject charge in the dielectric and measure the effects it has on the CV curve. Instead of conventionally measuring the change of the pull-in voltage, the presented center shift method measures the change of the voltage at which the capacitance is minimal. This way, the measurement method does not influence the charge injected by the stress voltage. Another advantage is that the measurement of the amount of injected charge is not influenced by changes in the width of the CV curve. These two advantages make it possible to test RF-MEMS capacitive switches in a more accurate way.
Superhelical Architecture of the Myosin Filament-Linking Protein Myomesin with Unusual Elastic Properties (2012)

Active muscles generate substantial mechanical forces by the contraction/relaxation cycle, and, to maintain an ordered state, they require molecular structures of extraordinary stability. These forces are sensed and buffered by unusually long and elastic filament proteins with highly repetitive domain arrays. Members of the myomesin protein family function as molecular bridges that connect major filament systems in the central M-band of muscle sarcomeres, which is a central locus of passive stress sensing. To unravel the mechanism of molecular elasticity in such filament-connecting proteins, we have determined the overall architecture of the complete C-terminal immunoglobulin domain array of myomesin by X-ray crystallography, electron microscopy, solution X-ray scattering, and atomic force microscopy. Our data reveal a dimeric tail-to-tail filament structure of about 360 Å in length, which is folded into an irregular superhelical coil arrangement of almost identical α-helix/domain modules. The myomesin filament can be stretched to about 2.5-fold its original length by reversible unfolding of these linkers, a mechanism that to our knowledge has not been observed previously. Our data explain how myomesin could act as a highly elastic ribbon to maintain the overall structural organization of the sarcomeric M-band. In general terms, our data demonstrate how repetitive domain modules such as those found in myomesin could generate highly elastic protein structures in highly organized cell systems such as muscle sarcomeres.
Flexible GaN LED on a polyimide substrate for display applications (2011)

The flexible GaN-based light emitting diode (LED) has been fabricated on a plastic substrate for flexible display applications. The epitaxial structures of the GaN LED arrays are transferred onto a flexible substrate using standard soft lithography technology and connected to a source-meter by metal lines. To verify the mechanically and optically stable characteristics of the GaN LEDs on the flexible substrates, the electrical properties are characterized during 2000 bending cycles at various bending radius. A white light-emitting phosphor-coated GaN LED shows its potential as a next-generation flexible light source.