gebhart/patrepeval huggingface dataset:
Surface-Enhanced Raman Spectroscopy in Single Living Cells Using Gold Nanoparticles (2002)

Ultrasensitive Raman measurements in single living cells are possible through exploiting the effect of surface-enhanced Raman scattering (SERS). Colloidal gold particles (60 nm in size) that are deposited inside cells as “SERS-active nanostructures” result in strongly enhanced Raman signals of the native chemical constituents of the cells. Particularly strong field enhancement can be observed when gold colloidal particles form colloidal clusters. The strongly enhanced Raman signals allow Raman measurements of a single cell in the 400–1800 cm −1 range with 1-μm lateral resolution in relatively short collection times (1 second for one mapping point) using 3–5 mW near-infrared excitation. SERS mapping over a cell monolayer with 1-μm lateral resolution shows different Raman spectra at almost all places, reflecting the very inhomogeneous chemical constitution of the cells. Colloidal gold supported Raman spectroscopy in living cells provides a tool for sensitive and structurally selective detection of native chemicals inside a cell, such as DNA and phenylalanine, and for monitoring their intracellular distributions. This might open up exciting opportunities for cell biology and biomedical studies.
Optimization of Chromone-2-carboxamide Melanin Concentrating Hormone Receptor 1 Antagonists:  Assessment of Potency, Efficacy, and Cardiovascular Safety (2006)

Evaluation of multiple structurally distinct series of melanin concentrating hormone receptor 1 antagonists in an anesthetized rat cardiovascualar assay led to the identification of a chromone-2-carboxamide series as having excellent safety against the chosen cardiovascular endpoints at high drug concentrations in the plasma and brain. Optimization of this series led to considerable improvements in affinity, functional potency, and pharmacokinetic profile. This led to the identification of a 7-fluorochromone-2-carboxamide (22) that was orally efficacious in a diet-induced obese mouse model, retained a favorable cardiovascular profile in rat, and demonstrated dramatic improvement in effects on mean arterial pressure in our dog cardiovascular model compared to other series reported by our group. However, this analogue also led to prolongation of the QT interval in the dog that was linked to affinity for hERG channel and unexpectedly potent functional blockade of this ion channel.
Low dose plastic optical fibre radiation dosimeter for clinical dosimetry applications (2009)

PMMA optical fibres offer the opportunity to monitor ionising radiation doses online and in real-time. The work presented here investigates the use of these fibres in clinical dosimetry applications. Tests to determine the sensitivity of the PMMA optical fibres at low radiation doses were carried out at the MD Anderson Cancer Center Orlando, Florida. The results demonstrate that PMMA optical fibres exhibit a quantifiable response to low doses (up to 12Gy) of radiation, similar to that received during radiation treatment.
Correction: High expression of HMGA2 independently predicts poor clinical outcomes in acute myeloid leukemia (2019)

Since the publication of the original article the authors noticed the the affiliation details for Paresh Vyas are incorrect. The correct affiliation details for this author are given below.
Spectroscopic Studies of the Super Relaxed State of Skeletal Muscle (2016)

In the super-relaxed state of myosin, ATPase activity is strongly inhibited by binding of the myosin heads to the core of the thick filament in a structure known as the interacting-heads motif. In the disordered relaxed state myosin heads are not bound to the core of the thick filament and have an ATPase rate that is 10 fold greater. In the interacting-heads motif the two regulatory light chains appear to bind to each other. We have made single cysteine mutants of the regulatory light chain, placed both paramagnetic and fluorescent probes on them, and exchanged them into skinned skeletal muscle fibers. Many of the labeled light chains tended to disrupt the stability of the super-relaxed state, and showed spectral changes in the transition from the disordered relaxed state to the super-relaxed state. These data support the putative interface between the two regulatory light chains identified by cryo electron microscopy and show that both the divalent cation bound to the regulatory light chain and the N-terminus of the regulatory light chain play a role in the stability of the super-relaxed state. One probe showed a shift to shorter wavelengths in the super-relaxed state such that a ratio of intensities at 440nm to that at 520nm provided a measure of the population of the super-relaxed state amenable for high throughput screens for finding potential pharmaceuticals. The results provide a proof of concept that small molecules that bind to this region can destabilize the super-relaxed state and provide a method to search for small molecules that do so leading to a potentially effective treatment for Type 2 diabetes and obesity.
MOESM1 of Host immune response to anti-cancer camptothecin conjugated cyclodextrin-based polymers (2019)

Additional file 1: Fig. S1. Working schemes for immunological analysis of nanoparticle IT-101 in mice. Fig. S2. Significant changes after 16â h IT-101 treatment were presented by dot plots. Fig. S3. Cytokine assay. Fig. S4. Changes of cytokine expression after CPT treatment. Fig. S5. Significant changes after 216â h treatment were presented by dot plots. Fig. S6. Early stage of tumorigenesis in F1B transgenic mice.
Achieving the Scaling Law of SNR-Monitoring in Dynamic Wireless Networks (2010)

The characteristics of wireless communication channels may vary with time due to fading, environmental changes and movement of mobile wireless devices. Tracking and estimating channel gains of wireless channels is therefore a fundamentally important element of many wireless communication systems. In particular, the receivers in many wireless networks need to estimate the channel gains by means of a training sequence. This paper studies the scaling law (on the network size) of the overhead for channel gain monitoring in wireless network. We first investigate the scenario in which a receiver needs to track the channel gains with respect to multiple transmitters. To be concrete, suppose that there are n transmitters, and that in the current round of channel-gain estimation, no more than k channels suffer significant variations since the last round. We proves that "Θ(k\log((n+1)/k)) time slots" is the minimum number of time slots needed to catch up with the k varied channels. At the same time, we propose a novel channel-gain monitoring scheme named ADMOT to achieve the overhead lower-bound. ADMOT leverages recent advances in compressive sensing in signal processing and interference processing in wireless communication, to enable the receiver to estimate all n channels in a reliable and computationally efficient manner within O(k\log((n+1)/k)) time slots. To our best knowledge, all previous channel-tracking schemes require Θ(n) time slots regardless of k. Note that based on above results for single receiver scenario, the scaling law of general setting is achieved in which there are multiple transmitters, relay nodes and receivers.
<i>In Silico</i> Approaches Accelerate Reverse Translational Research from Bedside to Bench (2017)

Corresponding with accelerated computing power, such as that found in supercomputers, simulation and big data are becoming increasingly important to modern science, second only to experimental and theoretical sciences research. The field of medicine is said to have entered the era of big data, with significant progress in recent years in the development of increasingly sophisticated equipment for measurement, observation, and information and communication technology (ICT). In particular, greater precision in personalized medicine will require the analysis of a large quantity of individual genome sequences. Research and development of techniques to analyze big data with respect to individual genome sequences are an urgent need. In clinical medicine and epidemiology, the analysis of clinical big data or real-world data has attracted attention as a new approach, which can be applied to examining occurrences at an actual clinical site. In this review, we have discussed the challenges and potential of an in silico approach for reverse translational research.
Fatty Acid (FFA) Transport in Cardiomyocytes Revealed by Imaging Unbound FFA Is Mediated by an FFA Pump Modulated by the CD36 Protein (2010)

Free fatty acid (FFA) transport across the cardiomyocyte plasma membrane is essential to proper cardiac function, but the role of membrane proteins and FFA metabolism in FFA transport remains unclear. Metabolism is thought to maintain intracellular FFA at low levels, providing the driving force for FFA transport, but intracellular FFA levels have not been measured directly. We report the first measurements of the intracellular unbound FFA concentrations (FFA(i)) in cardiomyocytes. The fluorescent indicator of FFA, ADIFAB (acrylodan-labeled rat intestinal fatty acid-binding protein), was microinjected into isolated cardiomyocytes from wild type (WT) and FAT/CD36 null C57B1/6 mice. Quantitative imaging of ADIFAB fluorescence revealed the time courses of FFA influx and efflux. For WT mice, rate constants for efflux (∼0.02 s(-1)) were twice influx, and steady state FFA(i) were more than 3-fold larger than extracellular unbound FFA (FFA(o)). The concentration gradient and the initial rate of FFA influx saturated with increasing FFA(o). Similar characteristics were observed for oleate, palmitate, and arachidonate. FAT/CD36 null cells revealed similar characteristics, except that efflux was 2-3-fold slower than WT cells. Rate constants determined with intracellular ADIFAB were confirmed by measurements of intracellular pH. FFA uptake by suspensions of cardiomyocytes determined by monitoring FFA(o) using extracellular ADIFAB confirmed the influx rate constants determined from FFA(i) measurements and demonstrated that rates of FFA transport and etomoxir-sensitive metabolism are regulated independently. We conclude that FFA influx in cardiac myocytes is mediated by a membrane pump whose transport rate constants may be modulated by FAT/CD36.
Hexsil Bimorphs For Vertical Actuation (2005)

Three designs are demonstrated for molded structures that move vertically upon HF etch release. Deflection is due to differences in residual stress in two or more deposited films. Displacements of 700 /spl mu/m to 1.1 mm occurred in 9 mm long, 30 /spl mu/m high molded polysilicon cantilevers. A 4 level tower 8 x 8 mm square rose 840 /spl mu/m. Lifters patterned 400 /spl mu/m wide in surface films rose 35 to 45 /spl mu/m. Hexsil test structures were also made to measure a lower bound for the ultimate strength in compression (> 206 MPa) and in tension (> 128 MPa).
Improving the Round Complexity of VSS in Point-to-Point Networks. (2007)

We revisit the following question: what is the optimal round complexity of verifiable secret sharing (VSS)? We focus here on the case of perfectly-secure VSS where the number of corrupted parties t satisfies t < n/3, with n being the total number of parties. Work of Gennaro et al. (STOC 2001) and Fitzi et al. (TCC 2006) shows that, assuming a broadcast channel, 3 rounds are necessary and sufficient for efficient VSS. The efficient 3-round protocol of Fitzi et al., however, treats the broadcast channel as being available “for free” and does not attempt to minimize its usage. This approach leads to relatively poor round complexity when protocols are compiled for a point-to-point network. We show here a VSS protocol that is simultaneously optimal in terms of both the number of rounds and the number of invocations of broadcast. Our protocol also has a certain “2-level sharing” property that makes it useful for constructing protocols for general secure computation.
CLINICAL CHARACTERISTICS OF 208 CASES OF CORONARY ANGIOGRAPHY IN ELDERLY PATIENTS WITH CORONARY ARTERY DISEASE (2012)

Objectives To explore clinical features of coronary angiography (CAG) in elderly patients with coronary artery disease. Methods Selective CAG was performed by Judkins method. Coronary heart disease was defined as at least a subepicardial vascular diameter stenosis greater than or equal to 50% (visual method). Coronary arteries were divided into three main branches, namely left anterior descending artery, left circumflex artery and right coronary and the left main coronary artery lesion was treated as two lesions. Lesion sub-type was divided into A, B and C. Type A lesions were less than or equal to 10 mm in length, with localised lesions and no calcification; type B lesions were 10–20 mm in length and moderate calcification; type C lesions were greater than or equal to 20 mm in lesion, diffuse stenosis or severe calcification. Results Multi-vessel lesions of the older group (149/208) were significantly higher than in the young group (74/176), while single vessel lesions (59/208) were significantly lower than in the young group (102/176) (p&lt;0.01). Type B and C lesions in older group (180/208) were significantly higher than in the young group (82/176) (p&lt;0.01), while type A lesions (28/208) were significantly lower than in the young group (94 /176) (p&lt;0.01). Multivessel lesions and diffuse calcified lesions in elderly patients with coronary artery disease were significantly higher than in young patients. Conclusions Multivessel lesions and diffuse calcified lesions in elderly patients with coronary artery disease are significantly higher than in young patients, suggesting that elderly patients with coronary artery disease are usually in severe condition and poor prognosis.
Effectiveness of low power dual-Vt designs in nano-scale technologies under process parameter variations (2005)

This paper explores the effectiveness of dual-V/sub t/ design under aggressive scaling of technology, which results in significant increase in all components of leakage (subthreshold, gate and junction tunneling) while having large variations in process parameters. The present way of realizing high-V/sub t/ devices results in high junction tunneling leakage compared to low-V/sub t/, devices, which in turn may result in negligible leakage savings for dual-V/sub t/, designs in scaled technologies. Moreover, increase in process variation severely affects the yield of such designs. This paper suggests important measures that need to be incorporated in conventional dual-V/sub t/, design to achieve total leakage power improvement while ensuring yield. It also shows that different process options, such as metal gate work function engineering, are required to realize high-performance and low-leakage dual- V/sub t/ designs in sub-50nm technologies.
Electrically switchable large, thin, and fast optics (2018)

Diffractive waveplates enable stackable ultrathin light-weight large area optics fast-switchable with low-voltage/low power fields. State-of-the-art systems and low-cost manufacturing opportunities will be presented aimed at next generation augmented, virtual reality, flexible, polarizer-free displays, LiDARs, etc.
Supplementary Data from Discovery, Validation, and Application of Novel Methylated DNA Markers for Detection of Esophageal Cancer in Plasma (2023)

&lt;p&gt;Supplemental Tables 1 and 2&lt;/p&gt;
Mid-infrared electroluminescence from InAs self-assembled quantum dots (2006)

Electroluminescence from self-assembled InAs quantum dots in cascade-like unipolar heterostructures is demonstrated. Initial results show weak luminescence signals in the mid-infrared from such structures, though more recent designs exhibit significantly stronger luminescence with improved designs of the active region of these devices. Further studies of mid-infrared emitting quantum dot structures have shown anisotropically polarized emission at multiple wavelengths. A qualitative explanation of such luminescence is developed and used to understand the growth morphology of buried quantum dots grown on AlAs layers. Finally, a novel design for future mid-infrared quantum dot emitters, intended to increase excited state scattering times and, at the same time, more efficiently extract carriers from the lowest states of our quantum dots, is presented.
Fast and accurate facial pose estimation by aligning a 3D appearance model (2004)

This paper proposed a method to estimate pose including large rotation in depth by aligning the 3D appearance model with the target image captured under various illumination conditions. Pose estimation is formulated by the minimization of the error between the target image and an image reproduced by the model. In the experiments, the performances of our proposed method for static and realtime pose estimation has been evaluated with test images including pose variations up to 60 degrees even from frontal and drastic illumination variations. It has shown that the proposed method is fast enough.
Modified elastic model for viscosity in glass-forming systems (2017)

For most glass-forming liquids, the temperature dependence of viscosity is non-Arrhenius. Despite the technological and geological importance, the origin of this non-Arrhenius temperature dependence of viscosity remains elusive to date and constitutes an important but unsolved problem in condensed-matter physics. It has become increasingly clear in recent years that high-temperature elasticity and viscosity of glass-forming liquids are strongly correlated. This work proposes a modified elastic model to predict equilibrium viscosity of glass-forming liquids. The modified elastic model considers the configurational entropy as a factor controlling the activation energy for viscous flow in addition to the high-frequency shear modulus as in the Dyre shoving model. It works much better than the shoving model in fitting equilibrium viscosity for both strong and fragile systems. The modified model also has the capability to estimate the nonequilibrium isostructural viscosity of glass from the equilibrium viscosity and the temperature-dependent elasticity of the glassy state.
Finite-state rate-distortion for individual sequences (2004)

We introduce a class of lossy finite-state machines for lossy compression of an individual sequence drawn from a finite alphabet at a fixed distortion, and define a fundamental quantity finite-state rate-distortion that is an asymptotically attainable lower bound on the compression rate of any lossy finite-state machine. For Hamming distortion, we obtain a universal lower bound on the finite-state rate-distortion of any individual sequence.
Second order statistics of NLOS indoor MIMO channels based on 5.2 GHz measurements (2002)

Herein, results from measurements conducted by the University of Bristol are presented. The channel characteristics of multiple input multiple output (MIMO) indoor systems at 5.2 GHz are studied. Our investigation shows that the envelope of the channel for non-line-of-sight (NLOS) indoor situations are approximately Rayleigh distributed and consequently we focus on a statistical description of the first and second order moments of the narrowband MIMO channel. Furthermore, it is shown that for NLOS indoor scenarios, the MIMO channel covariance matrix can be well approximated by a Kronecker product of the covariance matrices describing the correlation at the transmitter and receiver side respectively. A statistical narrowband model for the NLOS indoor MIMO channel based on this covariance structure is presented.
De Novo Design (1995)

The availability of a therapeutic target of known three-dimensional structure challenges the computational chemist to design and predict the affinity of novel ligands. A set of computational tools (CAVITY, FOUNDATION, SPLICE, DBMAKER, FLOOD) have been developed to discover sets of molecular fragments which optimize binding in subdomains of the active site. These are then spliced together combinatorially and optimized in size to fit within the active site cavity. A crucial aspect is the method of predicting the affinity so that compounds can be prioritized for retrosynthetic analysis and synthesis. We have used CoMFA, a 3D QSAR paradigm, to develop a predictive model for HIV protease. The robustness of this model was confirmed by a different 3D-QSAR method (HASL), and has good predictive and explanatory power. Novel ligands for HIV protease have been designed subject to chemical constraints which minimize their synthetic difficulty. Their relative affinities have been predicted using the CoMFA model and the series is undergoing synthesis and binding assays.
Circulating Mitochondrial Biomarkers for Drug-Induced Liver Injury (2015)

Liver mitochondria affected by drugs can be released into circulation and serve as biomarkers for drug-induced liver injury (DILI). The tissue specificity of ALT was improved by differentiating cytosolic ALT1 and mitochondrial ALT2 isoforms released in circulation. Prior to ALT elevation, mitochondrial cytochrome c, OCT, GLDH, CPS1 and DNA were increased in circulation following DILI. The baseline expression of mt-Nd6 was predictive of individual DILI susceptibility in animals. As mitochondrial DILI biomarkers appeared to be drug or species dependent, they might have value in clinical scenarios when culprit drugs are established, but may not be ideal tools to assess DILI potentials of new drugs.
Fast atom bombardment tandem mass spectrometry of the anti‐parasitic agent pentamidine and its oxygenated metabolites (1995)

Abstract Although pentamidine (1,5‐bis(4′‐amidinophenoxy)pentane) is currently in use for the treatment of a variety of parasitic infections, including acquired immune deficiency syndrome‐related Pneumocystis carinii pneumonia, its metabolism is still under investigation. Positive‐ion fast atom bombardment mass spectrometry was used with high‐energy collision‐activated dissociation (CAD) and linked scanning at constant B / E to obtain tandem mass spectra of protonated molecules of pentamindine and seven synthetic oxygenated derivatives, which are known metabolites of pentamidine. Charge‐initiated fragmentation produced abundant fragment ions of m / z 120 and 137 and loss of neutral ammonia from the protonated analyte that characterized the amidinophenoxy group. The structures of isomeric 2‐hydroxypentamidine, 3‐hydroxypentamidine and N ‐hydroxypentamidine could be distinguished based on charge‐remote fragmentation that produced a series of fragment ions of the pentyl chain and permitted the exact location of the hydroxyl group in each molecule to be determined. Next, tandem mass spectra were obtained and the charge‐initiated and charge‐remote fragmentation discussed for four other metabolites of pentamidine, including N , N ′‐dihydroxypentamidine, 5‐(4′‐amidinophenoxy)pentanoic acid, 5‐(4′‐amidinophenoxy) pentan‐1‐ol, and p ‐hydroxybenzamidine. Finally, tandem mass spectrometry was used to identify pentamidine and three pentamidine metabolites contained in high‐performance liquid chromatographic (HPLC) fractions from rat liver perfusate and rat urine following treatment with pentamidine. Pentamidine metabolites identified in rat urine and liver perfusate using mass spectrometry and HPLC retention times included 2‐hydroxypentamidine, 3‐hydroxypentamidine and 5‐(4′‐amidinophenoxy)pentanoic acid.