gebhart/patrepeval huggingface dataset:
Comparison of Different Fluorescence Fluctuation Methods for their Use in FRET Assays: Monitoring a Protease Reaction (2005)

We compare the accuracy of a variety of Fluorescence Fluctuation Spectroscopy (FFS) methods for the study of Förster Resonance Energy Transfer (FRET) assays. As an example, the cleavage of a doubly labeled, FRET-active peptide substrate by the protease Trypsin is monitored and analyzed using methods based on fluorescence intensity, Fluorescence Correlation Spectroscopy (FCS) and Fluorescence Intensity Distribution Analysis (FIDA). The presented fluorescence data are compared to High-Pressure Liquid Chromatography (HPLC) data obtained from the same assay. The HPLC analysis discloses general disadvantages of the FRET approach, such as incomplete labeling and the need for aliquots. However, the simultaneous use of two photon detectors monitoring the fluorescence signal of both labels significantly improves the analysis. In particular, the two global analysis tools Two-Dimensional Fluorescence Intensity Distribution Analysis (2D-FIDA) and Two-Color Global Fluorescence Correlation Spectroscopy (2CG-FCS) highlight the potential of a combination of FFS and FRET. While conventional FIDA and FCS auto- or cross-correlation analysis leaves the user with drawbacks inherent in two-color and FRET applications, these effects are overcome by the global analysis on the molecular level. Furthermore, it is advantageous to analyze the unnormalized as opposed to the normalized correlation data when combining any fluorescence correlation method with FRET, since the analysis of the unnormalized data introduces more accuracy and is less sensitive to the experimental drawbacks.
Photoacoustic imaging beyond the acoustic diffraction-limit with dynamic speckle illumination and sparse joint support recovery (2017)

In deep tissue photoacoustic imaging the spatial resolution is inherently limited by the acoustic wavelength. Recently, it was demonstrated that it is possible to surpass the acoustic diffraction limit by analyzing fluctuations in a set of photoacoustic images obtained under unknown speckle illumination patterns. Here, we purpose an approach to boost reconstruction fidelity and resolution, while reducing the number of acquired images by utilizing a compressed sensing computational reconstruction framework. The approach takes into account prior knowledge of the system response and sparsity of the target structure. We provide proof of principle experiments of the approach and demonstrate that improved performance is obtained when both speckle fluctuations and object priors are used. We numerically study the expected performance as a function of the measurements signal to noise ratio and sample spatial-sparsity. The presented reconstruction framework can be applied to analyze existing photoacoustic experimental datasets containing dynamic fluctuations.
Cholera toxin inhibits signal transduction by several mitogens and the in vitro growth of human small-cell lung cancer. (1990)

Cholera toxin (CT) inhibited the in vitro growth of three of four human small-cell lung carcinoma (SCLC) cell lines with a 50% inhibitory concentration of 27-242 ng/ml. Loss of surface membrane ruffling and the capacity of [Tyr4]-bombesin, vasopressin, and fetal calf serum to stimulate increases in intracellular free calcium clearly preceded effects on cellular metabolic activity and cell growth. 125I-[Tyr4]-bombesin binding was unaffected by CT treatment but [Tyr4]-bombesin stimulated phospholipase C activity was decreased in membranes from CT-treated SCLC cells. CT stimulated a rapid but transient increase in intracellular cyclic AMP ([cAMP]i) in SCLC. The effects of CT on susceptible SCLC were not reproduced by elevations of [cAMP]i induced by forskolin or cyclic AMP analogues. GM1 ganglioside, the cellular binding site for CT, was highly expressed in the CT-sensitive but not the CT-resistant SCLC cell lines. In contrast, expression of guanine nucleotide binding protein substrates for ADP-ribosylation by CT was similar. These data demonstrate the existence of a CT-sensitive growth inhibitory pathway in SCLC-bearing GM1 ganglioside. Addition of CT results in decreased responsiveness to several mitogenic stimuli. These results suggest novel therapeutic approaches to human SCLC.
Supplementary Table from Unleashing Cell-Intrinsic Inflammation as a Strategy to Kill AML Blasts (2023)

Supplementary Table from Unleashing Cell-Intrinsic Inflammation as a Strategy to Kill AML Blasts
Emicizumab improves the stability and structure of fibrin clot derived from factor VIII‐deficient plasma, similar to the addition of factor VIII (2020)

Emicizumab effectively improved fibrin clot stability and structure in FVIII-deficient plasma, and the physical properties of emicizumab-induced fibrin clots were similar to those with FVIII.
Optical interconnects (2007)

The speed and complexity of integrated circuits are increasing rapidly as integrated circuit technology advances from very-large-scale integrated (VLSI) circuits to ultra-large-scale integrated (ULSI) circuits. As the number of devices per chip, the number of chips per board, the modulation speed, and the degree of integration continue to increase, electrical interconnects are facing their fundamental bottlenecks, such as speed, packaging, fan-out, and power dissipation. In the quest for high-density packaging of electronic circuits, the construction of multichip modules (MCM), which decrease the surface area by removing package walls between chips, improved signal integrity by shortening interconnection distances and removing impedance problems and capacitances. The employment of copper and materials with lower dielectric constant materials can release the bottleneck in a chip level for the next several years. The International Technology Roadmap for Semiconductors (ITRS) expects that on-chip local clock speed will constantly increase to 10 GHz by the year 2011. Electrical interconnects operating at a high-frequency region have many problems to be solved, such as crosstalk, impedance matching, power dissipation, skew, and packing density. Optical interconnection has several advantages, such as immunity to the electromagnetic interference, independency to impedance mismatch, less power consumption, and high-speed operation. Although the optical interconnects have great advantages compared with the copper/low K interconnection, they still have some difficulties regarding packaging, multilayer technology, signal tapping, and reworkability. In this presentation, the progress of optical interconnect for intra and inter-board levels will be presented with both passive and active components suitable for system integration including thin film planar waveguides, vertical cavity surface emitting lasers (VCSELs), PIN photodiode array and silicon nano-photonic crystal waveguide modulators.
Electronic bracelet for monitoring of alcohol lifestyle (2016)

We demonstrate a wearable electronic bracelet for monitoring of alcohol lifestyle through the detection of ethyl glucuronide (EtG), a metabolite of ethanol associated with alcohol consumption, from human sweat. The device leverages disposable nanoporous polymer substrates that easily wick small volumes of sweat over the sensors electrodes. A gold working electrode fabricated on the flexible substrate is functionalized with EtG specific monocolonal antibodies using thiol based chemistry, as well as with a potassium ferricyanide redox molecule. When exposed to EtG in pooled human sweat, and sweat analog the binding of EtG to the sensing electrode results in chemiresistive changes to the electrode surface that can be quantified using square wave voltammetry (SWV). Varying doses of EtG was thus quantified and reported electronically by measuring changes in response peak currents. Detection of EtG was demonstrated in the range of 1–100 μg/mL in sweat analog. Similar dose discrimination was shown in the range of 1–10000 μg/L for human sweat, corresponding to one or more U.S. standard drinks. Validation of the EtG sensor performance was done using cyclic voltammetry and electrochemical impedance spectroscopy.
The Dense LDL Phenotype: Association with plasma lipoprotein levels, visceral obesity, and hyperinsulinemia in men (1996)

It thus appears that the high TG-low HDL cholesterol dyslipidemia frequently found in visceral obesity and in a hyperinsulinemic state is a strong correlate of the small dense LDL phenotype. Although associated with the dense LDL phenotype, visceral obesity and hyperinsulinemia were not independent predictors of an increased proportion of small dense LDL particles after controlling for TG and HDL cholesterol levels.
Research Note: A Rapid Method for the Detection of the Rous-Associated Endogenous Solitary Long Terminal Repeat, ev 15 (1993)

A rapid method has been developed for the detection of the solitary long terminal repeat ev15, a member of the avian leukosis virus (ALV) family of endogenous viral elements (ev genes) in chickens. Detection is accomplished by a polymerase chain reaction (PCR) assay that can be performed on purified genomic DNA samples or crude preparations of partially purified whole blood lysates. The test discriminates unambiguously between birds that are homozygous ev15-, homozygous ev15+, or heterozygous ev15-/ev15+. The incorporation of a modified touchdown amplification profile significantly improved the specificity of the PCR assay. Small-scale screening of birds from a variety of chicken breeds has revealed that ev15 is present in populations of both egg-strain birds and broilers.
Distributed effects of a gap in power/ground planes (2003)

A signal line running between two PCB power/ground planes, with one of the planes having a gap (split), was analyzed using full-wave electromagnetic tools. The gap inductance and the mutual coupling caused by the gap were examined, and distributed effects were observed. As a conclusion, a gap should always be AC-shorted, preferably in the immediate vicinity of critical signal lines.
Modified cryptochrome in vivo absorption in dim photosporulation mutants of Trichoderma (1985)

Mutants of Trichoderma harzianum that are defective in blue-light-induced sporulation were induced by nutritional stresses as an alternative to light. These mutants may be modified in the putative photoreceptor pigment "cryptochrome" or in an early transduction component. dim (dimsighted) mutants induced by a short transient stress were mapped into four complementation groups and were chosen for study of pigment deficiencies by in vivo absorption spectroscopy. Mutants rib(-)10 and lys(-)44 in the dimY complementation group had altered in vivo absorption spectra in the blue region. Difference spectra obtained by subtracting dimY spectra from that of the wild type had difference bands with peaks at 455 and 480 nm. The similarity between the in vivo difference spectra and the action spectrum for sporulation in wild-type Trichoderma suggests that the mutants lack cryptochrome or have a defective cryptochrome. The decrease in photoresponse as well as the modification of the action spectrum near 480 nm in a dimY mutant support these suggestions. Both dimY mutants pleiotropically accumulate a yellow water-soluble pigment absorbing at wavelengths lower than the blue maxima of cryptochrome; this yellow pigment may be related to cryptochrome.
A Novel Lid Seal Evaluation (2014)

Light emanating from between "closed" lids during the Korb-Blackie lid-light evaluation is associated with symptoms of ocular discomfort on awakening. These symptoms of discomfort may be linked to the inability of the lids to achieve an adequate seal to prevent subtle ocular surface desiccation during sleeping.
Re‐evaluating the Role of Sterics and Electronic Coupling in Determining the Open‐Circuit Voltage of Organic Solar Cells (2013)

The effects of sterics and molecular orientation on the open-circuit voltage and absorbance properties of charge-transfer states are explored in model bilayer organic photovoltaics. It is shown that the open-circuit voltage correlates linearly with the charge-transfer state energy and is not significantly influenced by electronic coupling.
A local renal renin&ndash;angiotensin system activation via renal uptake of prorenin and angiotensinogen in diabetic rats (2016)

The mechanism of activation of local renal renin-angiotensin system (RAS) has not been clarified in diabetes mellitus (DM). We hypothesized that the local renal RAS will be activated via increased glomerular filtration and tubular uptake of prorenin and angiotensinogen in diabetic kidney with microalbuminuria. Streptozotocin (STZ)-induced DM and control rats were injected with human prorenin and subsequently with human angiotensinogen. Human prorenin uptake was increased in podocytes, proximal tubules, macula densa, and cortical collecting ducts of DM rats where prorenin receptor (PRR) was expressed. Co-immunoprecipitation of kidney homogenates in DM rats revealed binding of human prorenin to the PRR and to megalin. The renal uptake of human angiotensinogen was increased in DM rats at the same nephron sites as prorenin. Angiotensin-converting enzyme was increased in podocytes, but decreased in the proximal tubules in DM rats, which may have contributed to unchanged renal levels of angiotensin despite increased angiotensinogen. The systolic blood pressure increased more after the injection of 20 μg of angiotensinogen in DM rats than in controls, accompanied by an increased uptake of human angiotensinogen in the vascular endothelium. In conclusion, endocytic uptake of prorenin and angiotensinogen in the kidney and vasculature in DM rats was contributed to increased tissue RAS and their pressor response to angiotensinogen.
Age-Related Distribution of Neuropathologic Changes in the Cerebral Cortex of Patients With Down's Syndrome (1995)

These results indicate that the development of pathologic changes in patients with Down's syndrome does not parallel that observed in elderly individuals and patients with Alzheimer's disease in all respects. However, the comparable development patterns of neurofibrillary tangle formation suggest that detailed analysis of patients with Down's syndrome may be useful to further our knowledge of the mechanisms underlying the installation of the neuropathologic alterations leading to the demonstrated loss of select neuronal populations in Alzheimer's disease.
120 W, 4 μJ from a purely Kerr-lens mode-locked Yb:YAG thin-disk oscillator (2013)

We report on a pure hard-aperture Kerr-lens mode-locked Yb:YAG thin-disk oscillator delivering 120-W, 4-μJ, 350-fs in air. This is, to our knowledge, the highest average power and pulse energy achieved from KLM oscillators so far.
Recovery Act - Demonstration of Sodium Ion Battery for Grid Level Applications (2012)

Aquion Energy received a $5.179 million cooperative research agreement under the Department of Energy's Smart Grid Demonstration Program Demonstration of Promising Energy Storage Technologies (Program Area 2.5) of FOA DE-FOE-0000036. The main objective of this project was to demonstrate Aquion's low cost, grid-scale, ambient temperature sodium ion energy storage device. The centerpiece of the technology is a novel hybrid energy storage chemistry that has been proven in a laboratory environment. The objective was to translate these groundbreaking results from the small-batch, small-cell test environment to the pilot scale to enable significant numbers of multiple ampere-hour cells to be manufactured and assembled into test batteries. Aquion developed a proof of concept demonstration unit that showed similar performance and major cost improvement over existing technologies. Beyond minimizing cell and system cost, Aquion built a technology that is safe, environmentally benign and durable over many thousands of cycles as used in a variety of grid support roles.
A first step towards practical single cell proteomics: a microfluidic antibody capture chip with TIRF detection (2011)

We have developed a generic platform to undertake the analysis of protein copy number from single cells. The approach described here is 'all-optical' whereby single cells are manipulated into separate analysis chambers using an optical trap; single cells are lysed by a shock wave caused by laser-induced microcavitation, and the protein released from a single cell is measured by total internal reflection microscopy as it is bound to micro-printed antibody spots within the device. The platform was tested using GFP transfected cells and the relative precision of the measurement method was determined to be 88%. Single cell measurements were also made on a breast cancer cell line to measure the relative levels of unlabelled human tumour suppressor protein p53 using a chip incorporating an antibody sandwich assay format. These results suggest that this is a viable method for measuring relative protein levels in single cells.
Skin cancer detection by spectroscopic oblique-incidence reflectometry: classification and physiological origins (2004)

Data obtained from 102 skin lesions in vivo by spectroscopic oblique-incidence reflectometry were analyzed. The participating physicians initially divided the skin lesions into two visually distinguishable groups based on the lesions' melanocytic conditions. Group 1 consisted of the following two cancerous and benign subgroups: (1) basal cell carcinomas and squamous cell carcinomas and (2) benign actinic keratoses, seborrheic keratoses, and warts. Group 2 consisted of (1) dysplastic nevi and (2) benign common nevi. For each group, a bootstrap-based Bayes classifier was designed to separate the benign from the dysplastic or cancerous tissues. A genetic algorithm was then used to obtain the most effective combination of spatiospectral features for each classifier. The classifiers, tested with prospective blind studies, reached statistical accuracies of 100% and 95% for groups 1 and 2, respectively. Properties that related to cell-nuclear size, to the concentration of oxyhemoglobin, and to the concentration of deoxyhemoglobin as well as the derived concentration of total hemoglobin and oxygen saturation were defined to explain the origins of the classification outcomes.
Assessing climate governance of Tainan City through stakeholder networks and text mining (2020)

Urban governance is recognized as a vital component of the human response to climate change. However, a diverse urban ecosystem and the associated climate hazards impose great challenges on an urban climate response and assessment. Tainan, a city in southern Taiwan, experiences these challenges and is the focus of the present chapter. We apply social network analysis (SNA) and text mining techniques to comprehend the complexity of the social ecosystem and assess its stakeholder interactions with the goal of offering suggestions for Tainan’s climate governance as part of the Taiwan Climate Change Adaptation Technology (TaiCCAT) program. Stakeholders were identified and categorized into seven actors: central government, municipal government, district office, private sector, NGOs, academic experts, and individual citizens. Analysis in this chapter reveals three findings: first, that a municipality-led style of governance is prominent in Tainan; second, that the central and municipal governments, district offices, and expert sectors acted cohesively in resource exchange and cooperation networks; and third, that the actions of municipality and district level offices are strongly impacted by network inertia resulting in ineffectual responses to natural hazards over the long term. We conclude that NGOs can and should play a much more supportive role in the planning and execution of water disaster prevention and recovery in Tainan.
Electron beam dynamics in Pasotron microwave sources (2003)

The Pasotron is a high efficiency (∼50%), plasma-assisted microwave generator in which the beam electrons exhibit two-dimensional motion in the slow wave structure. The electron beam propagates in the ion-focusing regime (Bennett pinch regime) because there is no applied magnetic field. Since initially only the neutral gas is present in the vacuum system and the ions in the neutralizing plasma channel are produced only due to the beam impact ionization, the beam dynamics in Pasotrons is inherently a nonstationary process, and important for efficient operation. The present paper contains results of experimental studies of stationary and nonstationary effects in the beam dynamics in Pasotrons and their theoretical interpretation.
Nano-scale fault tolerant machine learning for cognitive radio (2008)

We introduce a machine learning based channel state classifier for cognitive radio, designed for nano-scale implementation. The system uses analog computation, and consists of cyclostationary feature extraction and a radial basis function network for classification. The description of the system is partially abstract, but our design choices are motivated by domain knowledge and we believe the system will be feasible for future nanotechnology implementation. We describe an error model for the system, and simulate experimental performance and fault tolerance of the system in recognizing WLAN signals, under different levels of input noise and computational errors. The system performs well under the expected non-ideal manufacturing and operating conditions.
Stratification Requirements for Seed Dormancy Alleviation in a Wetland Weed (2013)

Echinochloaoryzicola(syn.E. phyllopogon) is an exotic weed of California rice paddies that has evolved resistance to multiple herbicides. Elimination of seedlingsthroughcertain weed control methods can limit the spread of this weed, but is contingent on accurate predictions of germination and emergence timing, which are influenced by seed dormancy levels.In summer annuals, dormancy can often be relieved through stratification, a period of prolonged exposure to cold and moist conditions.We used population-based threshold models to quantify the effects of stratification on seed germination of four E. Oryzicola populations at a range of water potential (Ψ) and oxygen levels. We also determined how stratification temperatures, moisture levels and durations contributed to dormancy release. Stratification released dormancy by decreasing base Ψ and hydrotimerequired for germination and by eliminating any germination sensitivity to oxygen. Stratification also increased average germination rates (GR), which were used as a proxy for relative dormancy levels. Alternating temperatures nearly doubled GR in all populations, indicating that seeds could be partially dormant despite achieving high final germination percentages. Stratification at Ψ = 0 MPa increased GR compared to stratification at lower water potentials, demonstrating that Ψ contributed to regulating dormancy release. Maximum GR occurred after 2-4 weeks of stratification at 0 MPa; GR were often more rapid for herbicide-resistant than for herbicide-susceptible seeds, implying greater dormancy in the latter. Manipulation of field conditions to promote dormancy alleviation of E. oryzicola seeds might improve the rate and uniformity of germination for seed bank depletion through seedling weed control. Our results suggest field soil saturation in winter would contribute towards E. oryzicola dormancy release and decrease the time to seedling emergence.