gebhart/patrepeval huggingface dataset:
Inhibition of sterol biosynthesis in Saccharomyces cerevisiae and Candida albicans by 22,23-epoxy-2-aza-2,3-dihydrosqualene and the corresponding N-oxide (1994)

The abilities of 22,23-epoxy-2-aza-2,3-dihydrosqualene and the corresponding N-oxide, 22,23-epoxy-2-aza-2,3-dihydrosqualene-N-oxide, to inhibit sterol biosynthesis were studied in microsomes and cells of Saccharomyces cerevisiae and Candida albicans. 22,23-Epoxy-2-aza-2,3-dihydrosqualene, which differs from the other inhibitor only in lacking oxygen at position 2, exhibited higher inhibitory properties in all preparations tested. The different levels of effectiveness of the two azasqualene derivatives were evident mostly in microsomes from S. cerevisiae (the 50 inhibitory concentrations of the 2-aza derivative and the corresponding N-oxide on oxidosqualene cyclase were 30 and 120 microM respectively) and in cell cultures of the same strain (1 order of magnitude separated the inhibitory activities of the two compounds on sterol biosynthesis). A possible explanation for the differences between 22,23-epoxy-2-aza-2,3-dihydrosqualene and the corresponding N-oxide arose from the study of their metabolic fates in vivo and in vitro. While the 2-aza derivative did not undergo any transformation, the N-oxide compound was actively reduced to the corresponding amine in microsomes and in cells of both yeast strains. 22,23-Epoxy-2-aza-2,3-dihydrosqualene-N-oxide seems to behave as a proinhibitor of sterol biosynthesis, becoming active only after transformation into the active form 22,23-epoxy-2-aza-2,3-dihydrosqualene.
Strain Distribution on the Sagittal Plane of an Intervertebral Disc. (1991)

A Clarification of the mechanical causes for low-back pain requires a knowledge of the states of stress and/or strain throughout the thoraco-lumbar spine. However, the deformation behavior of an intervertebral disc in vivo has not been investigated sufficiently. This paper presents a new method to evaluate the state of strain occurring on the sagittal plane of an intervertebral disc in vivo under flexion and extension. That is, the displacement on the plane of a disc was measured by FCR (Fuji computer radiography) at the medical hospital of Hokkaido University. The internal strain distribution of a disc was estimated by use of an isoparametric shape function introduced to express the deformation of a disc. Consequently, compressive strain at the anterior part of lumbar discs, and tensile strain at the posterior part were confirmed to occur in vivo under flexion. On the other hand, the strain distribution under extension was opposite to that under flexion.
Towards a Spread Spectrum VNA (2021)

Spectral (STDR) and spread spectrum time domain reflectometry (SSTDR) are proposed as a new method of measuring electrical impedance. We describe this new method, its potential applications, and an introduction to the system parameters necessary for success in these measurements.
Construction of angstrom-scale ion channels with versatile pore configurations and sizes by metal-organic frameworks (2023)

Controllable fabrication of angstrom-size channels has been long desired to mimic biological ion channels for the fundamental study of ion transport. Here we report a strategy for fabricating angstrom-scale ion channels with one-dimensional (1D) to three-dimensional (3D) pore structures by the growth of metal-organic frameworks (MOFs) into nanochannels. The 1D MIL-53 channels of flexible pore sizes around 5.2 × 8.9 Å can transport cations rapidly, with one to two orders of magnitude higher conductivities and mobilities than MOF channels of hybrid pore configurations and sizes, including Al-TCPP with 1D ~8 Å channels connected by 2D ~6 Å interlayers, and 3D UiO-66 channels of ~6 Å windows and 9 - 12 Å cavities. Furthermore, the 3D MOF channels exhibit better ion sieving properties than those of 1D and 2D MOF channels. Theoretical simulations reveal that ion transport through 2D and 3D MOF channels should undergo multiple dehydration-rehydration processes, resulting in higher energy barriers than pure 1D channels. These findings offer a platform for studying ion transport properties at angstrom-scale confinement and provide guidelines for improving the efficiency of ionic separations and nanofluidics.
Magnetic Nanoparticles: Hierarchically Structured Magnetic Nanoconstructs with Enhanced Relaxivity and Cooperative Tumor Accumulation (Adv. Funct. Mater. 29/2014) (2014)

Nanoconstructs are realized by P. Decuzzi and co-workers by confining ultra-small (5 nm) superparamagnetic iron oxide nanoparticles (USPIOs) within two different mesoporous structures (silicon and polymers). On page 4584, they exhibit transversal relaxivities up to around 10 times higher than conventional USPIOs and, under external magnetic fields, collectively cooperate to amplify tumor accumulation in mice to provide an MRI contrast enhancement at much smaller doses of iron as compared to current practice.
Phase Noise Resilient Three-Level Continuous-Phase Modulation for DFT-Spread OFDM (2022)

In this paper, a novel waveform with low peak-to-average power ratio (PAPR) and high robustness against phase noise (PN) is presented. It follows the discrete Fourier transform spread orthogonal frequency division multiplexing (DFT-s-OFDM) signal model. This scheme, called 3MSK, is inspired by continuous-phase frequency shift keying (CPFSK), but it uses three frequencies in the baseband model – specifically, 0 and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\pm f_{symbol}/4$ </tex-math></inline-formula> , where <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$f_{symbol}$ </tex-math></inline-formula> is the symbol rate – which effectively constrains the phase transitions between consecutive symbols to 0 and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\pm \pi /2$ </tex-math></inline-formula> rad. Motivated by the phase controlled model of modulation, different degrees of phase continuity can be achieved, allowing to reduce the out-of-band (OOB) emissions of the transmitted signal, while supporting receiver processing with low complexity. Furthermore, the signal characteristics are improved by generating an initial time-domain constant envelope signal at higher than the symbol rate. This helps to reach smooth phase transitions between 3MSK symbols, while the information is encoded in the phase transitions. Also the possibility of using excess bandwidth is investigated by transmitting additional non-zero frequency bins outside the active frequency bins of the basic DFT-s-OFDM model, which provides the capability to greatly reduce the PAPR. The most critical tradeoffs of the oversampled schemes are that improved PAPR is achieved with the cost of somewhat reduced link performance and, in case of excess band, also the spectrum efficiency is reduced. Due to the fact that the information is encoded in the phase transitions, a receiver model that tracks the phase variations without needing reference signals is developed. To this end, it is shown that this new modulation is well-suited for non-coherent receivers, even under strong phase noise (PN) conditions, thus allowing to reduce the overhead of reference signals. Evaluations of this physical-layer modulation and waveform scheme are performed in terms of transmitter metrics such as PAPR, OOB emissions and achievable output power after the power amplifier (PA), using a practical PA model. Finally, coded radio link evaluations are also provided, demonstrating that 3MSK has a similar bit error rate (BER) performance as that of traditional quadrature phase-shift keying (QPSK), but with significantly lower PAPR, higher achievable output power, and the possibility of using non-coherent receivers.
Quantitative hepatitis B virus DNA assessment by the limiting‐dilution polymerase chain reaction in chronic hepatitis B patients: evidence of continuing viral suppression with longer duration and higher dose of lamivudine therapy (1998)

Lamivudine, a novel cytosine analogue, exhibits potent antiviral activity against hepatitis B virus (HBV) in vitro and in vivo. The standard HBV DNA hybridization assay used in phase II clinical studies has a low sensitivity, the detection limit of HBV DNA levels being approximately 10(7) genome equivalents per ml (geq ml-1). In this work we used a semiquantitative polymerase chain reaction (PCR) assay (detection limit approximately 10(3) geq ml-1) to determine HBV DNA levels during a 24-week study of lamivudine in 51 stable chronic hepatitis B patients who were positive for hepatitis B surface antigen (HBsAg) and hepatitis B e antigen (HBeAg). Patients were randomly allocated to receive oral doses of 25, 100 or 300 mg lamivudine once daily. At week 24 the median serum concentration of HBV DNA had fallen from 10(8) to 10(4) geq ml-1, a 4-log median reduction. A trend towards more profound suppression of viral replication with an increased dose of lamivudine was observed. After 12 weeks of therapy, 12% of patients had an HBV DNA level that was undetectable in the PCR assay; this increased to 26% after 24 weeks, while in an additional 20% of patients, HBV DNA decreased to the level of detection of the PCR assay. We conclude that a 24-week course of lamivudine decreases serum HBV DNA to the level of PCR detection in 46% of patients. Such additional viral suppressive activity with higher doses and more protracted lamivudine may be of clinical utility prior to liver transplantation. Further studies are needed to define the degree of virus suppression required in clinical practice, and methods are required to increase the efficacy of virus suppression.
The Effects of Ligand Exchange and Mobility on the Peroxidase Activity of a Bacterial Cytochrome c upon Unfolding (2005)

The effect on the heme environment upon unfolding Paracoccus versutus ferricytochrome c-550 and two site-directed variants, K99E and H118Q, has been assessed through a combination of peroxidase activity increase and one-dimensional NMR spectroscopy. At pH 4.5, the data are consistent with a low- to high-spin heme transition, with the K99E mutation resulting in a protein with increased peroxidase activity in the absence of or at low concentrations of denaturant. Furthermore, the mobility of the polypeptide chain at pH 4.5 for the wild-type protein has been monitored in the absence and presence of denaturant through heteronuclear NMR experiments. The results are discussed in terms of local stability differences between bacterial and mitochondrial cytochromes c that are inferred from peroxidase activity assays. At pH 7.0, a mixture of misligated heme states arising from protein-based ligands assigned to lysine and histidine is detected. At low denaturant concentrations, these partially unfolded misligated heme forms inhibit the peroxidase activity. Data from the K99E mutation at pH 7.0 indicate that K99 is not involved in heme misligation, whereas histidine coordination is proven by the data from the H118Q variant.
Direct Fluorination of Poly(3-hydroxybutyrate-co)-hydroxyhexanoate (2013)

Polyhydroxyalkanoates (PHAs) are a class of polymers synthesized by bacteria as intracellular carbon and energy storage granules. PHAs are biodegradable with tailorable physical properties; however, often their properties are not ideal for many applications. The incorporation of fluorine containing substituents within these polymers or direct surface modification to enhance the fluorine content of these polymers, and thus their surface properties, should greatly enhance their utility and speed their adoption for a range of applications. Direct fluorination of poly(3-hydroxybutyrate-co)-hydroxyhexanoate (hereafter P3HB-co-HH) was carried out at elevated pressure with elemental F2/N2 gas mixture. Fluorination of P3HB-co-HH showed marked changes in both thermal and chemical characteristics. Fluorination was demonstrated by X-Ray Photoelectron Spectroscopy (XPS), Attenuated Total Reflectance – Fourier Transform Infrared Spectroscopy (ATR-FTIR), and Nuclear Magnetic Resonance Spectroscopy (19F NMR). The effect of fluorination on the physical properties of F-P3HB-co-HH was probed by Gel Permeation Chromatography (GPC), Thermo Gravimetric Analysis (TGA) and Differential Scanning Calorimetry (DSC).
Translation of psbA mRNA is regulated by light via the 5′‐untranslated region in tobacco plastids (1994)

The plastid psbA gene encodes the 32 kDa D1 polypeptide of photosystem II. It has previously been shown that the initiation of psbA mRNA translation in tobacco is regulated by sequences outside of the coding region. To identify the cis-acting regulatory sequences involved in the translational control, a series of chimeric uidA genes, encoding the beta-glucuronidase (GUS) reporter enzyme, were introduced into the plastid genome. GUS accumulation in response to the light (135- to 200-fold), and the arrest of uidA mRNA translation in light-grown seedlings following transfer for 2 h to the dark, was observed only if the transgenes contained the psbA 5'-untranslated leader region (UTR). Changes in GUS accumulation were accompanied by little or no changes in the uidA mRNA levels. The data indicate that the initiation of D1 translation in tobacco plastids is controlled via the psbA 5'-UTR.
Quasi-solid state uniaxial and biaxial deformation of PET/MWCNT composites: structural evolution, electrical and mechanical properties (2013)

Composites of multi-walled carbon nanotubes (MWCNTs) and a poly(ethylene terephthalate)(PET), prepared by melt mixing, were uniaxially and biaxially deformed at 100 °C using a strain rate of 2 s−1 and at stretch ratios (SR) up to 2. A hierarchical organization of randomly well dispersed and distributed agglomerates, smaller bundles and individual MWCNTs was identified in the as extruded composite from extensive microscopic examination across the length scales using polarised optical microscopy (POM), field emission scanning electron microscopy (FESEM) and high resolution transmission electron microscopy (HRTEM). Evidence from X-ray diffraction (XRD) and differential scanning calorimetry (DSC) confirmed the MWCNTs induced crystallization via a heterogeneous mechanism and altered the crystallization behaviour of PET. Uniaxial deformation of the composite materials resulted in orientation of the MWCNTs in the direction parallel to the applied strain and for biaxial deformation at an angle approaching 45° to the vertical axis (extrusion direction), evidence for the latter obtained by HRTEM and from small angle X-ray scattering experiments (SAXS). In both instances, XRD and DSC confirmed the occurrence of significant strain induced crystallization resulting in large increases in tensile mechanical properties. Evidence from wide angle X-ray scattering experiments (WAXS), supported by XRD and DSC showed the overall crystalline content and degree of long-range ordering increased with MWCNT addition. The decrease in diffraction (SAXS) associated with lamella spacing implies the MWCNTs disrupt formation of lamella and reside in the inter-lamellar spacing. Annealing the composites, particularly at Tm −50 °C, results in an increase in PET crystalline content. Prior to deformation the MWCNTs formed an electrically conducting interconnected network throughout the PET matrix, however, this was partially destroyed when the composite was uniaxially or biaxially deformed, as the probability of conductor–conductor contacts decreased. It was possible to restore a MWCNT conducting network similar to that achieved prior to uniaxial deformation only by annealing the sample at Tm −50 °C.
Preferential Growth of α'-FeN Films under a High Magnetic Field (2002)

The effect of a magnetic field on the structure and magnetic properties of Fe–N films has been studied. It is found that application of a high magnetic field during sputter-deposition plays an important role in controlling the phase formation and orientation in Fe–N films. Highly oriented metastable α'-FeN (001) films can be easily obtained on MgO (001) single crystal substrates by nitrogen-reactive rf sputtering in a high magnetic field for a wide range of N2 ratios. The α'-FeN (001) films grown in the high magnetic field show high saturation magnetization of 2.2–2.3 T.
Semantic Role Labeling Without Treebanks (2011)

We describe a method for training a semantic role labeler for CCG in the absence of gold-standard syntax derivations. Traditionally, semantic role labeling is performed by placing human-annotated semantic roles on gold-standard syntactic parses, identifying patterns in the syntaxsemantics relationship, and then predicting roles on novel syntactic analyses. The gold standard syntactic training data can be eliminated from the process by extracting training instances from semantic roles projected onto a packed parse chart. This process can be used to rapidly develop NLP tools for resource-poor languages of interest. 1
Vehicle's energy estimation using low frequency speed signal (2012)

Everyday vehicles fleets positions and speeds are collected by private companies and public authorities, stored in servers and used for vehicles tracking and diagnostic. These data are usually sampled and transferred over the long-range wireless network with low sampling rates for cost savings in term of network bandwidth and storage. This policy limits the use of the data for fine-grained estimation of vehicle energy, and therefore of fuel consumption and CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> emissions. This paper analyzes the effect of a low-frequency sampling rate of inertial variables on vehicle's energy estimation. It statistically quantifies the error with respect to accurate signals. An experimental campaign carried out on different vehicles in different days supports the analysis. Experimental results show that the estimation error mean and variance depends on the sample rate and the time window size and that they do not significantly varies within vehicles of the same class.
A high performance all-organic flexural piezo-FET and nanogenerator via nanoscale soft-interface strain modulation (2014)

Flexural strain fields are encountered in a wide variety of situations and invite novel device designs for their effective use in sensing, actuating, as well as energy harvesting (nanogenerator) applications. In this work we demonstrate an interesting all-organic device design comprising an electrospun P(VDF-TrFE) fiber-mat built directly on a conducting PANI film, which is also grown on a flexible PET substrate, for flexural piezo-FET and nanogenerator applications. Orders of magnitude stronger modulation of electrical transport in PANI film is realized in this device as compared to the case of a similar device but with a uniform spin-coated P(VDF-TrFE) film. We find that in the flexural mode of operation, the interaction between the laterally modulated nanoscale strain field distributions created by the fibers and the applied coherent strain field strongly influences the carrier transport in PANI. The transport modulation is suggested to occur due to strain-induced conformational changes in P(VDF-TrFE) leading to changes in carrier localization-delocalization. We further show that the fiber-mat based device system also works as an efficient nanogenerator capable of delivering power for low power applications.
Supplementary Table 6 from Impact of Screening Test Performance and Cost on Mortality Reduction and Cost-effectiveness of Multimodal Ovarian Cancer Screening (2023)

&lt;p&gt;XLS file - 46K, Mortality reduction using estimates of serous cancer disease duration from physician survery (panel A)&lt;/p&gt;
Virtual Power Plant Control for Large Residential Communities Using HVAC Systems for Energy Storage (2021)

Heating, ventilation, and air-conditioning (HVAC) systems use the most electricity of any household appliance in residential communities. HVAC system modeling facilitates the study of demand response (DR) at both the residential and power system levels. In this article, the equivalent thermal model of a reference house is proposed. Parameters for the reference house were determined based on the systematic study of experimental data obtained from fully instrumented field demonstrators. Energy storage capacity of HVAC systems is calculated and an equivalent state-of-charge is defined. The uniformity between HVAC systems and battery energy storage system is demonstrated by DR control. The aggregated HVAC load model is based on the reference house and considers a realistic distribution of HVAC parameters derived from one of the largest smart grid field demonstrators in rural America. A sequential DR scheme as part of a virtual power plant control is proposed to reduce both ramping rate and peak power at the aggregated level, while maintaining human comfort according to ASHRAE standards.
Groups 5 and 6 Terminal Hydrazido(2−) Complexes: Nβ Substituent Effects on Ligand-to-Metal Charge-Transfer Energies and Oxidation States (2012)

Brightly colored terminal hydrazido(2-) (dme)MCl(3)(NNR(2)) (dme = 1,2-dimethoxyethane; M = Nb, Ta; R = alkyl, aryl) or (MeCN)WCl(4)(NNR(2)) complexes have been synthesized and characterized. Perturbing the electronic environment of the β (NR(2)) nitrogen affects the energy of the lowest-energy charge-transfer (CT) transition in these complexes. For group 5 complexes, increasing the energy of the N(β) lone pair decreases the ligand-to-metal CT (LMCT) energy, except for electron-rich niobium dialkylhydrazides, which pyramidalize N(β) in order to reduce the overlap between the Nb═N(α) π bond and the N(β) lone pair. For W complexes, increasing the energy of N(β) eventually leads to reduction from formally [W(VI)≡N-NR(2)] with a hydrazido(2-) ligand to [W(IV)═N═NR(2)] with a neutral 1,1-diazene ligand. The photophysical properties of these complexes highlight the potential redox noninnocence of hydrazido ligands, which could lead to ligand- and/or metal-based redox chemistry in early transition metal derivatives.
Trypsin specificity as elucidated by LIE calculations, X‐ray structures, and association constant measurements (2004)

The variation in inhibitor specificity for five different amine inhibitors bound to CST, BT, and the cold-adapted AST has been studied by use of association constant measurements, structural analysis of high-resolution crystal structures, and the LIE method. Experimental data show that AST binds the 1BZA and 2BEA inhibitors 0.8 and 0.5 kcal/mole more strongly than BT. However, structural interactions and orientations of the inhibitors within the S1 site have been found to be virtually identical in the three enzymes studied. For example, the four water molecules in the inhibitor-free structures of AST and BT are channeled into similar positions in the S1 site, and the nitrogen atom(s) of the inhibitors are found in two cationic binding sites denoted Position1 and Position2. The hydrophobic binding contributions for all five inhibitors, estimated by the LIE calculations, are also in the same order (-2.1 +/- 0.2 kcal/mole) for all three enzymes. Our hypothesis is therefore that the observed variation in inhibitor binding arises from different electrostatic interactions originating from residues outside the S1 site. This is well illustrated by AST, in which Asp 150 and Glu 221B, despite some distance from the S1 binding site, lower the electrostatic potential of the S1 site and thus enhance substrate binding. Because the trends in the experimentally determined binding energies were reproduced by the LIE calculations after adding the contribution from long-range interactions, we find this method very suitable for rational studies of protein-substrate interactions.