gebhart/patrepeval huggingface dataset:
High speed two-dimensional imaging with an analog interface (2023)

A quantitative pulse count (event detection) algorithm with linearity to high count rates is accomplished by combining a high-speed, high frame rate camera with simple logic code run on a massively parallel processor such as a GPU. The parallel processor elements examine frames from the camera pixel by pixel to find and tag events or count pulses. The tagged events are combined to form a combined quantitative event image.
Deep tissue imaging of microfracture and non-displaced fracture of bone using the second and third near-infrared therapeutic windows (2014)

Near-infrared (NIR) light in the wavelengths of 700 nm to 2,000 nm has three NIR optical, or therapeutic, windows, which allow for deeper depth penetration in scattering tissue media. Microfractures secondary to repetitive stress, particularly in the lower extremities, are an important problem for military recruits and athletes. They also frequently occur in the elderly, or in patients taking bisphosphonates or denosumab. Microfractures can be early predictors of a major bone fracture. Using the second and third NIR therapeutic windows, we investigated the results from images of chicken bone and human tibial bone with microfractures and non-displaced fractures with and without overlying tissues of various thicknesses. Images of bone with microfractures and non-displaced fractures with tissue show scattering photons in the third NIR window with wavelengths between 1,650 nm and 1,870 nm are diminished and absorption is increased slightly from and second NIR windows. Results from images of fractured bones show the attenuation length of light through tissue in the third optical window to be larger than in the second therapeutic window. Use of these windows may aid in the detection of bone microfractures, and thus reduce the incidence of major bone fracture in susceptible groups.
Interaction of Hepatitis B virus (HBV) with p53 family-induced apoptosis signaling pathways is involved in viral clearance (2009)

One major risk factor for development of hepatocellular carcinoma (HCC) is chronic infection with hepatitis B virus (HBV). We have previously shown in vivo that a functional p53 pathway and an intact CD95-apoptosis signaling pathway are essential for clearance of HBV infection. In addition, we have described a central role of the p53/p63/p73 network for tumor development, treatment response and prognosis of HCC. Upregulation of the antiapoptotic, dominant negative isoform of p73, ΔNp73, in patients with HCC correlated with reduced survival. Our data indicate that ΔNp73 is an important gene in hepatocarcinogenesis. Thus, we hypothesized if antiapoptotic, oncogenic ΔN isoforms of the p53 family would interfere with p53-, p63- and/or p73-induced apoptosis of HBV-infected liver cells.
THE INWARD H+ PATHWAY IN BACTERIORHODOPSIN: THE ROLE OF M412 AND P(N)560 INTERMEDIATES (1984)

Abstract In purple bacteriorhodopsin sheets adsorbed onto the phospholipid‐impregnated collodion film, electrogenic stages are identified correlating with decays of the M and N(P)‐type intermediates. It is concluded that both M N and N bR transitions are electrogenic. The M decay is shown to be of a complex kinetics. In purple sheets, the lower the light intensity, the higher the rate of “slow M” decay. Such a dependence, which is absent from monomeric bacteriorhodopsin in proteoliposomes and from Triton X‐100‐solubilized protein, may be explained by the inhibiting effect of a light‐induced conformation change in a bacteriorhodopsin molecule upon the M decay in some other bacteriorhodopsin molecules within the same sheet. The light intensity‐independent “slow M” decay in solubilized bacteriorhodopsin is shown to correlate with the decay of the N intermediate and H + uptake after the flash. In contrast to “fast M”, “slow M” is pH dependent, closely resembling in this respect the N intermediate. It is suggested that there is a fast light‐independent equilibration between M and N so that “slow M” represents the portion of the M pool that monitors the N concentration. The M N equilibrium is assumed to be involved in the effect of the light‐induced electric field on the M decay. No direct effect of light on the equilibrium was found.
Novel High Molecular Weight Levelers Extending Gap Fill to Smaller Features (2009)

It has been recently demonstrated that a high molecular weight leveler can improve gap fill, in addition to minimizing the overburden (1). An analysis of this phenomenon and a quantitative model explaining the effect are presented here. The penetration of the high molecular weight leveler into the via is restricted due to its large size and slow diffusion, leading to preferential passivation of the wafer top surface. Since the leveler is a strong inhibitor, the applied current is therefore preferentially directed into the vias. Because the side walls are passivated by PEG, the majority of this current is directed to the via bottom, improving bottom-up fill. The process conditions and the distribution of features on the wafer affect this improvement. The model has been quantified using a computer implemented simulation combining empirical and analytical methods. Requirements for suitable additives for this application are specified, identifying polyethylenimine as one such additive.
Ultrafast Förster resonance energy transfer between tyrosine and tryptophan: potential contributions to protein–water dynamics measurements (2022)

Ultrafast Förster Resonance Energy Transfer (FRET) between Tyrosine (Tyr, Y) and Tryptophan (Trp, W) in the model peptides Trp-(Pro)<sub><i>n</i></sub>-Tyr (WP<i>n</i>Y) has been investigated using a femtosecond up-conversion spectrophotofluorometer. The ultrafast energy transfer process (<100 ps) in short peptides (WY, WPY and WP2Y) has been resolved. In fact, this FRET rate is found to be mixed with the rates of solvent relaxation (SR), ultrafast population decay (QSSQ) and other lifetime components. To further dissect and analyze the FRET, a spectral working model is constructed, and the contribution of a FRET lifetime is separated by reconciling the shapes of decay associated spectra (DAS). Surprisingly, FRET efficiency did not decrease monotonically with the growth of the peptide chain (as expected) but increased first and then decreased. The highest FRET efficiency occurred in peptide WPY. The kinetic results have been accompanied with molecular dynamics simulations that reconcile and explain this strange phenomenon: due to the strong interaction between amino acids, the distance between the donor and receptor in peptide WPY is actually closest, resulting in the fastest FRET. In addition, the FRET lifetimes (<i>τ</i><sub>cal</sub>) were estimated within the molecular dynamics simulations, and they were consistent with the lifetimes (<i>τ</i><sub>exp</sub>) separated out by the experimental measurements and the DAS working model. This benchmark study has implications for both previous and future studies of protein ultrafast dynamics. The approach taken can be generalized for the study of proximate tyrosine and tryptophan in proteins and it suggests spectral strategies for extracting mixed rates in other complex FRET problems.
Electrostatics of PEGylated Micelles and Liposomes Containing Charged and Neutral Lipopolymers (2005)

The electrostatics of large unilamellar vesicles (LUVs) of various lipid compositions were determined and correlated with steric stabilization. The compositional variables studied include (a) degree of saturation, comparing the unsaturated egg phosphatidylcholine (EPC) and the fully hydrogenated soy phosphatidylcholine (HSPC) as liposome-forming lipids; (b) the effect of 40 mol % cholesterol; (c) the effect of mole % of three methyl poly(ethylene glycol) (mPEG)-lipids (the negatively charged mPEG-distearoyl phosphoethanolamine (DSPE) and two uncharged lipopolymers, mPEG-distearoyl glycerol (DSG) and mPEG-oxycarbonyl-3-amino-1,2-propanediol distearoyl ester (DS)); and (d) the negatively charged phosphatidyl glycerol (PG). The lipid phases were as follows: liquid disordered (LD) for the EPC-containing LUV, solid ordered (SO) for the HSPC-containing LUV, and liquid ordered (LO) for either of those LUV with the addition of 40 mol % cholesterol. The LUV zeta potential and electrical surface potential (psi(0)) were determined. It was found that progressive addition of mPEG(2k)-DSPE to liposomes increases negative surface potential and reduces surface pH to a similar extent as the addition of PG. However, due to the "hidden charge effect", zeta potential was more negative for liposomes containing PG than for those containing mPEG(2k)-DSPE. Replacing mPEG-DSPE with mPEG(2k)-DS or mPEG-DSG had no effect on surface pH and surface potential, and zeta potential was approximately zero. Addition of low concentrations of cationic peptides (protamine sulfate and melittin) to PG- or mPEG-DSPE-containing liposomes neutralized the liposome negative surface potential to a similar extent. However, only in liposomes containing PG, did liposome aggregation occur. Replacing the negatively charged lipopolymer mPEG-DSPE with the neutral lipopolymers mPEG-DS or mPEG-DSG eliminates or reduces such interactions. The relevance of this effect to the liposome performance in vivo is discussed.
Wireless packet scheduling for integrated services of real-time and non-real-time applications in mobile broadband wireless access system (2006)

This paper considers an opportunistic packet scheduling algorithm to support both RT and NRT service in mobile broadband wireless access system. The design objective of our proposed packet scheduler is to determine the optimal number of RT and NRT users based on the service charges (which differ depending on the type of services) in order to maximize the revenue, while at the same time satisfying their individual QoS requirements, i.e., the maximum allowable packet loss rate for RT traffic and the minimum reserved bit rate for NRT traffic. It takes an urgency of RT users into account only when their head-of-line (HOL) packet delays exceed the given threshold, which allows for maximizing the system capacity of NRT users. Evaluating the proposed approach in orthogonal frequency division multiple access/frequency division duplex (OFDMA/FDD)based mobile access system, it has been shown that, in terms of the number of RT and NRT service users, system capacity can be significantly improved.
Constitutive Notch Activation Upregulates Pax7 and Promotes the Self-Renewal of Skeletal Muscle Satellite Cells (2012)

Notch signaling is a conserved cell fate regulator during development and postnatal tissue regeneration. Using skeletal muscle satellite cells as a model and through myogenic cell lineage-specific NICD(OE) (overexpression of constitutively activated Notch 1 intracellular domain), here we investigate how Notch signaling regulates the cell fate choice of muscle stem cells. We show that in addition to inhibiting MyoD and myogenic differentiation, NICD(OE) upregulates Pax7 and promotes the self-renewal of satellite cell-derived primary myoblasts in culture. Using MyoD(-/-) myoblasts, we further show that NICD(OE) upregulates Pax7 independently of MyoD inhibition. In striking contrast to previous observations, NICD(OE) also inhibits S-phase entry and Ki67 expression and thus reduces the proliferation of primary myoblasts. Overexpression of canonical Notch target genes mimics the inhibitory effects of NICD(OE) on MyoD and Ki67 but not the stimulatory effect on Pax7. Instead, NICD regulates Pax7 through interaction with RBP-Jκ, which binds to two consensus sites upstream of the Pax7 gene. Importantly, satellite cell-specific NICD(OE) results in impaired regeneration of skeletal muscles along with increased Pax7(+) mononuclear cells. Our results establish a role of Notch signaling in actively promoting the self-renewal of muscle stem cells through direct regulation of Pax7.
On the mechanism of succinyl transfer from aryl enolsuccinates to enolates of arylketones: addition–elimination vs. alkoxide-assisted retro-ene reaction (1996)

The mechanism of succinyl transfer from aryl enolsuccinates to the enolates of aryl ketones has been studied by deuterium exchange experiments and semi-empirical calculations. The calculations indicate that direct elimination is favoured over the ene mechanism. The results of a deuterium labelling study were also inconsistent with the ene mechanism.
A fully collusion resistant broadcast, trace, and revoke system (2006)

We introduce a simple primitive called Augmented Broadcast Encryption (ABE) that is sufficient for constructing broadcast encryption, traitor-tracing, and trace-and-revoke systems. These ABE-based constructions are resistant to an arbitrary number of colluders and are secure against adaptive adversaries. Furthermore, traitor tracing requires no secrets and can be done by anyone. These broadcast systems are designed for broadcasting to arbitrary sets of users. We then construct a secure ABE system for which the resulting concrete trace-and-revoke system has ciphertexts and private keys of size √N where N is the total number of users in the system. In particular, this is the first example of a fully collusion resistant broadcast system with sub-linear size ciphertexts and private keys that is secure against adaptive adversaries. The system is publicly traceable.
An Ultra-Low Power Microbridge Gas Sensor (2010)

A miniature, ultra-low power, sensitive, microbridge-based thermal conductivity gas sensor has been developed. The batch fabrication of the sensors was realized by CMOS compatible processes and surface micromachining techniques. Doped polysilicon was used as the structural material of the bridge with critical dimension of 1µm. The sensor has been tested with nitrogen, carbon dioxide, and helium. Heat loss from constant voltage application was observed to be a function of the thermal conductivity of the gas ambient, resulting in different magnitude of resistance change. The response time to a voltage pulse was found to be less than 0.5µs and stability of the sensor excellent. We demonstrated that the sensitivity for helium in nitrogen was 2.05mΩ/ppm when operated at 3.6V dc supplies (a power level in the order of 4 milliwatts). With a Wheatstone bridge with ac excitation and a Lock-in amplifier the sensor limit of detection was ~100ppm helium in nitrogen.
Protein– Protein Interactions (2008)

Abstract Although proteins have numerous capabilities, one of their most important functions is to bind other proteins. These protein–protein interactions are critical for nearly every cellular process, and when they become corrupted, they often result in a diseased state. Because of the importance of protein–protein interactions in nearly all aspects of biology, efforts to decipher the rules that govern these associations have been underway for many decades. This review provides an overview of the evolution of the study of protein–protein interactions with an emphasis on recent developments in the field that concern the modular architecture of protein–protein interfaces and the networked communications within these binding sites that serve as a driving force for protein complex specificity and affinity. Relationships between biophysical studies performed to quantify the myriad factors that contribute to protein molecular recognition and computational analysis and interaction prediction algorithm development, as well as drug discovery and development, are also highlighted.
Removing Penetrating Fishhooks-Reply (1993)

<h3>In Reply.</h3> —We thank Dr Coyle for detailing another method for extracting a fishhook from the eye. Indeed, there are at least four other techniques described in the medical literature to date<sup>1,2</sup>and each has its own particular advantages and drawbacks. The method described in our article has yielded excellent long-term visual outcomes,<sup>3</sup>although its benefits have not been rigorously compared with other procedures. We have found that the small hooks often associated with ocular injuries are usually transected easily and with minimal trauma. Instead of the large cutting instrument depicted in Fig 3 of our Photo Essay,<sup>4</sup>we currently use thoracotomy wire-cutting scissors, which are easily manipulated and readily available. It should be noted that the method advocated by Dr Coyle has several potential disadvantages. Unlike the technique we described, bending the barb against the hook shaft does not entirely remove the barb. As fishermen who
Demonstration of 90&#x00B0; optical hybrid at 2 &#x03BC;m wavelength range based on 4&#x00D7;4 MMI using diluted waveguide (2014)

A 4×4 MMI 90° optical hybrid for 2 μm is designed, fabricated and characterized using a monolithically integrated MZI. A phase deviation around ±10°, Common Mode Rejection Ratio > 15.6 dB and an excess loss of 2.2 dB are obtained.
Utilising the ubiquity of the cell phone to record physiological activities (2009)

Lifelogging is a term used to describe recording different aspects of your daily life, in digital form, for your own exclusive personal use. It is a form of reverse surveillance, sometimes termed sousveillance, referring to us - the subjects - doing the watching, of ourselves. In today's healthcare world where we react to conditions that have already developed, lifelogging technologies may offer a glimpse into a future world of proactive healthcare where symptoms of conditions are detected at much earlier stages. &#13;\n&#13;\nAt the end of last year it was estimated that there were 4 billion cell phones in the world, in comparison to just over 1 billon PCs. In this presentation I will discuss a framework, which leverages the ubiquity of the cell phone, to aggregate multiple wearable biological sensors. This physiological lifelogged data can then be easily queried via an interface which utilises contextual memory retrieval cues to assist people remember what type of activity they were doing at a particular time. This may be helpful for the diagnosis of potential medical conditions e.g. to explain that my heart rate was very high because I was at the gym, or that I had a disturbed night's sleep because I was in an unfamiliar hotel room.
Chemically Tunable Electrochemical Dissolution of Noncontinuous Polyelectrolyte Assemblies: An In Situ Study Using ecAFM (2010)

The electrochemically triggered dissolution of noncontinuous polyelectrolyte assemblies presenting distinct nanomorphologies and its tuning by chemical cross-linking were monitored locally, in situ, by electrochemical atomic force microscopy. Poly-l-lysine and hyaluronic acid deposited layer-by-layer on indium tin oxide electrodes at specific experimental conditions formed well-defined nanostructures whose morphologies could be easily and precisely followed along the dissolution process. In addition to shrinkage of polyelectrolyte nanodroplets, ecAFM images revealed the faster dissolution of coalesced structures compared to droplet-like complexes, and the readsorption of dissolved polyelectrolytes onto slower dissolving neighboring structures. Covalently cross-linked PLL/HA assemblies dissolved only partially, and exhibited slower dissolution rates compared to native multilayers, with a clear dependence on the cross-link density. Tuning the electrochemical dissolution of polyelectrolyte multilayers through chemical cross-linking opens new prospects for future biomedical applications, such as the development of advanced drug or gene delivery platforms allowing for tightly controlled releases of different compounds at specific rates.
Feature-Based Visual Exploration of Text Classification (2015)

There are many applications of text classification such as gender attribution in market research or the identification of forged product reviews on e-commerce sites. Although several automatic methods provide satisfying performance in most application cases, we see a gap in supporting the analyst to understand the results and derive knowledge for future application scenarios. In this paper, we present a visualization driven application that allows analysts to gain insight in text classification tasks such as sentiment detection or authorship attribution on feature level, built with a practitioner’s way of reasoning in mind, the Text Classification Analysis Process.
Ductile Pd‐Catalysed Hydrodearomatization of Phenol‐Containing Bio‐Oils Into Either Ketones or Alcohols using PMHS and H2O as Hydrogen Source (2018)

Abstract A series of phenolic bio‐oil components were selectively hydrodearomatized by palladium on carbon into the corresponding ketones or alcohols in excellent yields using polymethylhydrosiloxane and water as reducing agent. The selectivity of the reaction was governed by the water concentration where selectivity to alcohol was favoured at higher water concentrations. As phenolic bio‐oil examples cardanol and beech wood tar creosote were studied as substrate to the developed reaction conditions. Cardanol was hydrodearomatized into 3‐pentadecylcyclohexanone in excellent yield. From beech wood tar creosote, a mixture of cyclohexanols was produced. No hydrodeoxygenation occurred, suggesting the applicability of the reported method for the production of ketone‐alcohol oil from biomass. magnified image
Transient Temperature Analysis of Airplane Carbon Composite Disk Brakes (1998)

results obtained in Eqs. (8) and (9) are in exact agreement with Tables III and II of Carslaw and Jaeger. The convergence of the series’ expressions for temperature distribution and heat  ow is rather slow for small values of time (t % 0.01). Therefore, it is required to determine the 250th root in Eq. (9). In each case, the summing process is terminated when the value of the last term computed is less than 0.000001. Figures 1a– 1c show that the relative errors of the base heat  ow between oneand two-dimensional transient solutions are affected by H for different Bia at G = 10, 5, and 2. The relative errors increase with increasing Bia and t, and decrease with G at the  xed value of H. The steady-state condition is reached later as the values of G and Bia decrease. The relative error is insensitive to the variation in H for smaller times at the different Bia number. For  xed values of Bia % 0.2, the effect of H on the relative error becomes more signi cant as G decreases at large times, but the effect of H on the relative error is insigni cant when Bia = 1.0 and the different values of G. Inspection of Figs. 1a– 1c reveals that the relative error is a minimum value as H ® ` and is a maximum value at H = 0 for the cases of Bia = 0.01 with various G values when steady state is reached. Similarly, this phenomenon is seen for the cases of G = 2 with various Bia values.
Large Volume Coagulation Utilizing Multiple Cavitation Clouds Generated by Array Transducer Driven by 32 Channel Drive Circuits (2013)

High-intensity focused ultrasound (HIFU) treatment is a noninvasive treatment, in which focused ultrasound is generated outside the body and coagulates a diseased tissue. The advantage of this method is minimal physical and mental stress to the patient, and the disadvantage is the long treatment time caused by the smallness of the therapeutic volume by a single exposure. To improve the efficiency and shorten the treatment time, we are focusing attention on utilizing cavitation bubbles. The generated microbubbles can convert the acoustic energy into heat with a high efficiency. In this study, using the class D amplifiers, which we have developed, to drive the array transducer, we demonstrate a new method to coagulate a large volume by a single HIFU exposure through generating cavitation bubbles distributing in a large volume and vibrating all of them. As a result, the coagulated volume by the proposed method was 1.71 times as large as that of the conventional method.