gebhart/patrepeval huggingface dataset:
Photophysical and Structural Properties of Saddle-Shaped Free Base Porphyrins:  Evidence for an “Orthogonal” Dipole Moment (2001)

Ground- and excited-state absorption and fluorescence properties of three free base porphyrins with graded degrees of a macrocycle distortion have been studied. The different degrees of nonplanarity were introduced by successive addition of ethyl groups at the β-pyrrole positions of free base 5,10,15,20-tetraphenylporphyrin (H2TPP): from four ethyl groups in cis-tetraethyl-TPP (H2cTETPP) to six ethyl groups in hexaethyl-TPP (H2HETPP) and eight ethyl groups in octaethyl-TPP (H2OETPP). The static and dynamic optical properties of the compounds change systematically with an increase of the porphyrin macrocycle nonplanarity. These perturbations include significant broadening of the absorption and fluorescence bands, an increased spacing between the long-wavelength absorption and short-wavelength emission maxima, and reduced excited-state lifetimes. In nonpolar solvents, these perturbations directly reflect the steric/electronic consequences of the distortion of the porphyrin π-system. In polar media, all the photophysical consequences of nonplanar distortion are markedly enhanced as a function of solvent polarity. These effects derive from electronic interactions between the polar solvent molecules and the polar S1(π,π*) excited state of the nonplanar free base porphyrin. The origin of the polar nature of these nonplanar chromophores is indicated by semiempirical calculations, which show that free-base porphyrins with saddle-type macrocycle distortions have a permanent dipole moment (1−2 D) with a significant projection orthogonal to the nitrogen mean plane. Among the contributions to this macroscopic dipole moment are structural/electronic asymmetries derived from the pyrrole rings, N−H bonds and nitrogen lone pairs. The specific factors and the macroscopic dipole moment provide foci for solvent interactions that are amplified in nonplanar porphyrins relative to their planar counterparts. The studies demonstrate the strong interrelated effects of the conformation(s) involving the porphyrin macrocycle and its peripheral substituents, electronic structure, and solvent interactions (including macrocycle-nonplanarity-induced dipole moments) in dictating the photophysical properties of distorted porphyrins. The findings have implications for the function of tetrapyrrole cofactors in the biological proteins and for the use of nonplanar porphyrins in molecular optoelectronics.
Family of single-inductor multi-output DC-DC converters (2009)

This paper presents the family of the single-inductor multi-output DC-DC converters. Conventional transformer-based multi-output DC-DC converters are proposed to provide multiple output voltages, which, however, have the drawbacks of high cost and large volume. Therefore, the single-inductor multi-output three-terminal configuration is developed in order to reduce the component count and cost for multi-output DC-DC converters, including the boost, buck, buck-boost, and flyback DC-DC converters. In this paper, the boost-type single-inductor dual-output DC-DC converter is introduced and analyzed. Furthermore, the family of the single-inductor multi-output DC-DC converters is presented.
Identification of Phosphorylation Sites within the Signaling Adaptor APPL1 by Mass Spectrometry (2010)

APPL1 is a membrane-associated adaptor protein implicated in various cellular processes, including apoptosis, proliferation, and survival. Although there is increasing interest in the biological roles as well as the protein and membrane interactions of APPL1, a comprehensive phosphorylation profile has not been generated. In this study, we use mass spectrometry (MS) to identify 13 phosphorylated residues within APPL1. By using multiple proteases (trypsin, chymotrypsin, and Glu C) and replicate experiments of linear ion trap (LTQ) MS and LTQ-Orbitrap-MS, a combined sequence coverage of 99.6% is achieved. Four of the identified sites are located in important functional domains, suggesting a potential role in regulating APPL1. One of these sites is within the BAR domain, two cluster near the edge of the PH domain, and one is located within the PTB domain. These phosphorylation sites may control APPL1 function by regulating the ability of APPL1 domains to interact with other proteins and membranes.
Tumor Detection by Nuclear Magnetic Resonance (1971)

Spin echo nuclear magnetic resonance measurements may be used as a method for discriminating between malignant tumors and normal tissue. Measurements of spin-lattice (T(1)) and spin-spin (T(2)) magnetic relaxation times were made in six normal tissues in the rat (muscle, kidney, stomach, intestine, brain, and liver) and in two malignant solid tumors, Walker sarcoma and Novikoff hepatoma. Relaxation times for the two malignant tumors were distinctly outside the range of values for the normal tissues studied, an indication that the malignant tissues were characterized by an increase in the motional freedom of tissue water molecules. The possibility of using magnetic relaxation methods for rapid discrimination between benign and malignant surgical specimens has also been considered. Spin-lattice relaxation times for two benign fibroadenomas were distinct from those for both malignant tissues and were the same as those of muscle.
Coulomb blockade at 77 K in nanoscale metallic islands in a lateral nanostructure (1995)

Clear Coulomb blockade effects have been observed in lateral metal nanostructures fabricated by combined electron beam lithography and ionized beam deposition. Islands between 2 and 3 nm in diameter were formed in a 25 nm gap for which the effective tunneling capacitance is calculated to be 0.2 aF. Clear Coulomb gaps and staircases were observed at 77 K in current–voltage characteristics. The staircases can still be seen at room temperature but the gaps tend to a nonlinearity in I–V characteristics around zero bias voltage. The total device area is about 0.01 μm2.
Investigating the speech characteristics of suicidal adolescents (2013)

Suicide is a very serious problem. In the United states it ranks as the second most frequent cause of death among teenagers between the ages of 12 and 17. In this work, we investigate speech characteristics of prosody as well as voice quality in a dyadic interview corpus with suicidal and non-suicidal adolescents. In these interviews the adolescents answer specifically designed questions. Based on this limited dataset, we reveal statistically significant differences in the speech patterns of suicidal adolescents within the investigated interview corpus. Further, we investigate the classification capabilities of machine learning approaches both on an utterance as well as an interview level. The work shows promising results in a speaker-independent classification experiment based on only a dozen speech features. We believe that once the algorithms are refined and integrated with other methods, they may be of value to the clinician.
Phosphors help switch on xenon (1999)

A phosphor material that emits almost twice as many photons as it absorbs has been discovered by researchers at Utrecht University in the Netherlands (R Wegh et al. 1999 Science 283 663). The discovery may lead to a new generation of highly efficient fluorescent lights and plasma displays that are also environmentally safe.
Immunologic differences between the 19 S and 7 S components of normal human gamma-globulin. (1957)

Summary 1.The presence in normal human γ-globulin of molecules with an S 20,w = 19 S in addition to those with an S 20,w = 7 S is again demonstrated. 2.Antigenic differences between these molecules are shown by agar diffusion studies. 3.Quantitative precipitin studies confirm these differences and demonstrate that the “7” and “19” components partially cross react and are antigenically related. 4.The possibility is raised that the larger molecules are polymers of a smaller unit similar to 7 S γ-globulin but richer in carbohydrate and that antigenic differences may be due to the higher carbohydrate content as well as differences in size and shape.
Two Mechanisms for Mannose-binding Protein Modulation of the Activity of Its Associated Serine Proteases (2004)

Serum mannose-binding protein (MBP) neutralizes invading microorganisms by binding to cell surface carbohydrates and activating MBP-associated serine proteases-1, -2, and -3 (MASPs). MASP-2 subsequently cleaves complement components C2 and C4 to activate the complement cascade. To analyze the mechanisms of activation and substrate recognition by MASP-2, zymogen and activated forms have been produced, and MBP.MASP-2 complexes have been created. These preparations have been used to show that MBP modulates MASP-2 activity in two ways. First, MBP stimulates MASP-2 autoactivation by increasing the rate of autocatalysis when MBP.MASP-2 complexes bind to a glycan-coated surface. Second, MBP occludes accessory C4-binding sites on MASP-2 until activation occurs. Once these sites become exposed, MASP-2 binds to C4 while separate structural changes create a functional catalytic site able to cleave C4. Only activated MASP-2 binds to C2, suggesting that this substrate interacts only near the catalytic site and not at accessory sites. MASP-1 cleaves C2 almost as efficiently as MASP-2 does, but it does not cleave C4. Thus MASP-1 probably enhances complement activation triggered by MBP.MASP-2 complexes, but it cannot initiate activation itself.
The Concrete Distribution: A Continuous Relaxation of Discrete Random Variables (2016)

The reparameterization trick enables optimizing large scale stochastic computation graphs via gradient descent. The essence of the trick is to refactor each stochastic node into a differentiable function of its parameters and a random variable with fixed distribution. After refactoring, the gradients of the loss propagated by the chain rule through the graph are low variance unbiased estimators of the gradients of the expected loss. While many continuous random variables have such reparameterizations, discrete random variables lack useful reparameterizations due to the discontinuous nature of discrete states. In this work we introduce Concrete random variables---continuous relaxations of discrete random variables. The Concrete distribution is a new family of distributions with closed form densities and a simple reparameterization. Whenever a discrete stochastic node of a computation graph can be refactored into a one-hot bit representation that is treated continuously, Concrete stochastic nodes can be used with automatic differentiation to produce low-variance biased gradients of objectives (including objectives that depend on the log-probability of latent stochastic nodes) on the corresponding discrete graph. We demonstrate the effectiveness of Concrete relaxations on density estimation and structured prediction tasks using neural networks.
A probabilistic approach to coordinated multi-robot indoor surveillance (2005)

In this paper we discuss the problem of monitoring and searching an indoor environment for an intruder with a group of mobile robots. We present a graph-based algorithm to coordinate a group of robots which takes the limitations and uncertainties of sensors into account and is able to find good coordination plans efficiently even for large environments. We analyze and compare the approach against other coordination strategies based on a new probabilistic framework that allows to evaluate the performance of any coordination strategy based on a probabilistic sensor model and a worst case behavior model for intruders. Using this framework we demonstrate the capabilities of the planning algorithm in several simulation experiments.
Machine Learning in Genomic Medicine: A Review of Computational Problems and Data Sets (2015)

In this paper, we provide an introduction to machine learning tasks that address important problems in genomic medicine. One of the goals of genomic medicine is to determine how variations in the DNA of individuals can affect the risk of different diseases, and to find causal explanations so that targeted therapies can be designed. Here we focus on how machine learning can help to model the relationship between DNA and the quantities of key molecules in the cell, with the premise that these quantities, which we refer to as cell variables, may be associated with disease risks. Modern biology allows high-throughput measurement of many such cell variables, including gene expression, splicing, and proteins binding to nucleic acids, which can all be treated as training targets for predictive models. With the growing availability of large-scale data sets and advanced computational techniques such as deep learning, researchers can help to usher in a new era of effective genomic medicine.
Integrin α5β1 Ligands: Biological Evaluation and Conformational Analysis (2005)

Breaking up is easy. Integrin α5β1 is a cell-surface receptor involved in many physiological and pathological processes. Small cyclic peptides can influence the interaction between this receptor and its natural ligand, fibronectin. The peptide shown, c-(-Arg-Gly-Asp-D-Phe-Val-β-Ala-), can bind α5β1 with submicromolar affinity. A conformational analysis of the peptide provided information on the structural properties responsible for binding to α5β1. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2268/2005/z400279_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
The Metabolic Enzyme ManA Reveals a Link between Cell Wall Integrity and Chromosome Morphology (2010)

Synchronizing cell growth, division and DNA replication is an essential property of all living cells. Accurate coordination of these cellular events is especially crucial for bacteria, which can grow rapidly and undergo multifork replication. Here we show that the metabolic protein ManA, which is a component of mannose phosphotransferase system, participates in cell wall construction of the rod shaped bacterium Bacillus subtilis. When growing rapidly, cells lacking ManA exhibit aberrant cell wall architecture, polyploidy and abnormal chromosome morphologies. We demonstrate that these cellular defects are derived from the role played by ManA in cell wall formation. Furthermore, we show that ManA is required for maintaining the proper carbohydrate composition of the cell wall, particularly of teichoic acid constituents. This perturbed cell wall synthesis causes asynchrony between cell wall elongation, division and nucleoid segregation.
A directly fed Ku- to W-Band 2-Arm Archimedean spiral antenna (2011)

An 18 to 110 GHz two-arm Archimedean spiral antenna is directly fed using a monolithically integrated micro-coaxial Dyson balun. The feed line includes a multi-stage impedance transformer realized to match the nominal impedance of the antenna to 50 Ω. The antenna is designed for and fabricated with a surface micromachining process PolyStrata™ using a predetermined strata configuration. Impedance measurements of the antenna are performed up to 110GHz, with a VSWR < 2.5:1 achieved throughout the entire measured frequency band. The performance of a similar antenna with a custom tailored strata configuration was also discussed.
Biodegradable Long-Circulating Polymeric Nanospheres (1994)

Injectable nanoparticulate carriers have important potential applications such as site-specific drug delivery or medical imaging. Conventional carriers, however, cannot generally be used because they are eliminated by the reticulo-endothelial system within seconds or minutes after intravenous injection. To address these limitations, monodisperse biodegradable nanospheres were developed from amphiphilic copolymers composed of two biocompatible blocks. The nanospheres exhibited dramatically increased blood circulation times and reduced liver accumulation in mice. Furthermore, they entrapped up to 45 percent by weight of the drug in the dense core in a one-step procedure and could be freeze-dried and easily redispersed without additives in aqueous solutions.
HPLC Separation and Characterization of Flavonols in the Skins of Vitis vinifera var. Cinsault (1986)

A high performance liquid chromatography (HPLC) method to investigate the flavonol composition of grape skins was developed using Cinsault grapes. In addition to the expected main grape flavonols, several unknown compounds were separated. They were isolated by semi-preparative HPLC and identified by means of ultraviolet spectrophotometry, mass spectrometry, proton nuclear magnetic resonance (NMR), and thin layer chromatography (TLC) analysis of the sugars released from the glycosides by acidic and enzymic hydrolysis. The main flavonols were quercetin-3-glucoside, quercetin-3-glucuronide, and myricetin-3-glucoside. Minor compounds included kaempferol-3-glucoside, kaempferol-3-galactoside, and isorhamnetin-3-glucoside. The kaempferol- and myricetin-3-glucuronides and three diglycosides were also tentatively identified. Evidence was obtained that six additional pigments consisted of the chalcone forms of anthocyanins.
Automated Acquisition of Aptamer Sequences (2002)

While the in vitro selection of nucleic acid binding species (aptamers) requires numerous liquid-handling steps, these steps are relatively straightforward and the overall process is therefore amenable to automation. Here we demonstrate that automated selection techniques are capable of generating aptamers against a number of diverse protein targets. Automated selection techniques can be integrated with automated analytical methods, including sequencing, determination of binding constants, and structural analysis. The methods that have so far been developed can be further multiplexed, and it should soon be possible to attempt the selection of aptamers against organismal proteomes or metabolomes.
Single nucleotide polymorphisms as tools in human genetics (2000)

The development of detailed single nucleotide polymorphism (SNP) maps of the human genome coupled with high-throughput genotyping technologies may allow us to unravel complex genetic traits, such as multifactorial disease or drug response, over the next few years. Here we describe the current efforts to identify and characterize the large numbers of SNPs required and discuss the practicalities of association studies for the identification of genes involved in complex traits.
RNA Template-dependent 5′ Nuclease Activity ofThermus aquaticus and Thermus thermophilus DNA Polymerases (2000)

DNA replication and repair require a specific mechanism to join the 3'- and 5'-ends of two strands to maintain DNA continuity. In order to understand the details of this process, we studied the activity of the 5' nucleases with substrates containing an RNA template strand. By comparing the eubacterial and archaeal 5' nucleases, we show that the polymerase domain of the eubacterial enzymes is critical for the activity of the 5' nuclease domain on RNA containing substrates. Analysis of the activity of chimeric enzymes between the DNA polymerases from Thermus aquaticus (TaqPol) and Thermus thermophilus (TthPol) reveals two regions, in the "thumb" and in the "palm" subdomains, critical for RNA-dependent 5' nuclease activity. There are two critical amino acids in those regions that are responsible for the high activity of TthPol on RNA containing substrates. Mutating glycine 418 and glutamic acid 507 of TaqPol to lysine and glutamine, respectively, increases its RNA-dependent 5' nuclease activity 4-10-fold. Furthermore, the RNA-dependent DNA polymerase activity is controlled by a completely different region of TaqPol and TthPol, and mutations in this region do not affect the 5' nuclease activity. The results presented here suggest a novel substrate binding mode of the eubacterial DNA polymerase enzymes, called a 5' nuclease mode, that is distinct from the polymerizing and editing modes described previously. The application of the enzymes with improved RNA-dependent 5' nuclease activity for RNA detection using the invasive signal amplification assay is discussed.
A Computational Method for Automated Characterization of Genetic Components (2014)

The ability to design and construct synthetic biological systems with predictable behavior could enable significant advances in medical treatment, agricultural sustainability, and bioenergy production. However, to reach a stage where such systems can be reliably designed from biological components, integrated experimental and computational techniques that enable robust component characterization are needed. In this paper we present a computational method for the automated characterization of genetic components. Our method exploits a recently developed multichannel experimental protocol and integrates bacterial growth modeling, Bayesian parameter estimation, and model selection, together with data processing steps that are amenable to automation. We implement the method within the Genetic Engineering of Cells modeling and design environment, which enables both characterization and design to be integrated within a common software framework. To demonstrate the application of the method, we quantitatively characterize a synthetic receiver device that responds to the 3-oxohexanoyl-homoserine lactone signal, across a range of experimental conditions.
Studies of two-photon pumped frequency-upconverted lasing properties of a new dye material (1997)

The two-photon absorption (TPA), TPA-induced frequency upconversion emission, and two-photon-pumped (TPP) lasing properties of a new dye, trans-4[p-(N-hydroxyethylN-methylamino)stryryl]-N-methylpyridinium iodide (abbreviated as ASPI) were experimentally investigated. This new dye has a moderate TPA cross section (σ2≈3.9×20−20 cm4/GW in benzyl alcohol), but exhibits a low lasing threshold and high lasing efficiency when pumped with a 1064 nm pulsed laser beam. Furthermore, the TPA-induced fluorescence yield is strongly dependent on the polarity of the solvent, making it a promising dye for sensing applications. The spectral, temporal, and spatial structures as well as the output/input characteristics of the TPP cavity lasing and the superradiant (cavityless) lasing are systematically measured using a 1 cm path quartz cuvette filled with the ASPI solution or a doped polymer rod. The net conversion efficiency from the absorbed 1064 nm pump pulse energy to the ∼615 nm upconverted cavity lasing energy was found to be as high as ∼17%.
PHOTOCHEMICAL PROPERTIES OF FLAVIN DERIVATIVES (1987)

Abstract— The triplet yields of 15 derivatives of riboflavin modified either in position 8 or in the ribityl side chain have been determined. The triplet yields measured range from 0.002 to 0.9. In addition, estimates for the rate constants of the photoreaction with EDTA and for the complex formation constants with EDTA at pH 7.0 are given. Evidence for an interaction in solution of at least the 2′ and 5′ hydroxyl groups of RF with the isoalloxazine ring is presented.