gebhart/patrepeval huggingface dataset:
A Structural Model to Explain the Partial Catalytic Activity of Human Prorenin (1989)

Human prorenin, secreted from a Chinese hamster ovary cell line transfected with the cDNA for preprorenin, has been purified in mg quantities by a novel single-step procedure. The method takes advantage of reversible acid activation as a means of generating active prorenin that may be bound and eluted from an affinity column for renin. Analysis of the prorenin so purified revealed that it contained about 80% intact zymogen; the remaining 20% comprised a mixture of various prorenin derivatives truncated in the prosegment, and a small amount of renin. After exposure to 37 degrees C and pH 7.5, the refolded, partially active preparation was passed once more over the affinity column to remove renin and any truncated prorenin forms that were still active and that were, therefore, again retained by the column. Over a period of several hours, refolded and inactive prorenin not bound to the column slowly regains 5% to 10% renin activity, even when maintained under conditions that are optimal for zymogen inactivation. This activity is observed toward both model peptide substrates and natural human angiotensinogen. On the basis of these findings, we propose a model in which, under physiological conditions, a small amount of open, active prorenin is in equilibrium with a predominant, closed, and inactive form of the zymogen. Support for the model is provided by binding studies with a strong renin inhibitor that displaces the equilibrium entirely to a 1:1 zymogen:inhibitor complex. Limited cleavage of prorenin by several different proteinases has provided a number of fully active renin derivatives with varying N-terminal sequences. Results thus obtained, together with analysis of prorenin and its truncated forms bound, or not bound, to the affinity column under a variety of conditions, suggest that the propeptide region, -Arg-Ile-Phe-Leu-Lys- (positions 10P-14P), is essential for the reversible refolding of the prosegment that leads to zymogen inactivation.
Adjuvant dendritic cell vaccination induces tumor-specific immune responses in the majority of stage III melanoma patients (2016)

DC vaccination induces a functional TAA-specific T cell response in the majority of stage III melanoma patients, indicating it is more effective in stage III than in stage IV melanoma patients. Furthermore, performing multiple cycles of vaccinations enhances the chance of a broader immune response.
Modulation of oculomotor control & adaptation with cerebellar TMS: effects on slow-tonic vergence adaptation. (2017)

The adaptation of heterophoria to horizontal base-out prism reflects a slow change in the underlying tonic vergence neural innervation. Recent fMRI evidence suggests the posterior cerebellum may play a role in this unique adaptive process. We applied continuous theta-bust stimulation (cTBS) to the oculomotor vermis (OMV) of the posterior cerebellum to investigate a causal relationship between this neural structure and slow-tonic vergence (STV) adaptation. 14 subjects fused a 0.18 LogMAR chart at 40cm through a 15 prism diopter (PD) base-out prism for 4 minutes after receiving active or sham cTBS stimulation (3-50Hz pulses at 200ms intervals for 40 seconds) to the OMV over the posterior cerebellum. Change in heterophoria, measured with Modified Thornington Technique every 15 seconds, defined the amplitude and rate of STV adaptation. cTBS was applied at 80% of the individual's active motor threshold via a 2x75mm butterfly coil. Stimulation sites were localized using the BrainSight® neuro-navigation system and anatomical landmarks. The amplitude of STV adaptation was not different between active (6.31 ± 0.40 PD) and sham (6.97 ± 0.41 PD) conditions, p = 0.18. There was also no difference between the maximum rate of tonic vergence adaptation in the active (0.41 ± 0.07 PD/s) or sham (0.33 ± 0.05 PD/s) conditions, p = 0.18. Baseline levels of tonic vergence innervation, measured before and after stimulation at each visit, were not different between conditions (p > 0.15). cTBS applied to the OMV of the posterior cerebellum did not affect tonic vergence innervation or STV adaptation to base-out prism in healthy controls. This is in contrast to other types of oculomotor adaptation, where cTBS has been shown to affect both reflexive pro-saccade generation and adaptation to double step stimuli. These results suggest the OMV of the posterior cerebellum plays a limited role in the management and adaptation of tonic vergence neural innervation. Meeting abstract presented at VSS 2017
Compact atomic magnetometer for global navigation (NAV-CAM) (2018)

Northrop Grumman is developing an atom-based magnetometer technology that has the potential for providing a global position reference independent of GPS. The NAV-CAM sensor is a direct outgrowth of the Nuclear Magnetic Resonance Gyro under development by the same technical team. It is capable of providing simultaneous measurements of all 3 orthogonal axes of magnetic vector field components using a single compact vapor cell. The vector sum determination of the whole-field scalar measurement achieves similar precision to the individual vector components. By using a single sensitive element (vapor cell) this approach eliminates many of the problems encountered when using physically separate sensors or sensing elements.
Patient-specific iPSC-derived photoreceptor precursor cells as a means to investigate retinitis pigmentosa (2013)

Next-generation and Sanger sequencing were combined to identify disease-causing USH2A mutations in an adult patient with autosomal recessive RP. Induced pluripotent stem cells (iPSCs), generated from the patient's keratinocytes, were differentiated into multi-layer eyecup-like structures with features of human retinal precursor cells. The inner layer of the eyecups contained photoreceptor precursor cells that expressed photoreceptor markers and exhibited axonemes and basal bodies characteristic of outer segments. Analysis of the USH2A transcripts of these cells revealed that one of the patient's mutations causes exonification of intron 40, a translation frameshift and a premature stop codon. Western blotting revealed upregulation of GRP78 and GRP94, suggesting that the patient's other USH2A variant (Arg4192His) causes disease through protein misfolding and ER stress. Transplantation into 4-day-old immunodeficient Crb1 (-/-) mice resulted in the formation of morphologically and immunohistochemically recognizable photoreceptor cells, suggesting that the mutations in this patient act via post-developmental photoreceptor degeneration. DOI:http://dx.doi.org/10.7554/eLife.00824.001.
A Stabilizing, High-Performance Controller for Input Series-Output Parallel Converters (2008)

A form of sensorless current mode (SCM) control stabilizes sharing in multiphase input-series-output-parallel (ISOP) dc-dc converter topologies. Previously, ISOP converters have been proposed to reduce the voltage and current ratings of switching devices. Since the inputs are all connected in series, each phase need only be rated for a fraction of the total input voltage. Voltage and current sharing are key - if there is any phase-to-phase imbalance, the system benefits are substantially reduced. In the present work, a simple SCM controller is shown to guarantee stable sharing. Each phase acts independently on the same output reference and desired input voltage. The algorithm and the physics of the circuit lead to balanced input voltages and output currents, even during transients. The ISOP topology is a special case of an interleaved multiphase system. A reduced-order small-signal model is presented. The model is composed of two factors, a single-phase equivalent and a multidelay comb filter. The model fits a measured transfer function well and can be used in feedback design. Experimental results for a five-phase converter demonstrate fast response to a load step, line disturbance rejection, accurate static and dynamic sharing, and high efficiency.
Analysis of short-term and long-term characteristics of PV power production (2014)

Solar photovoltaic (PV) energy has one of the fastest growth among renewable energies, reaching an installed capacity of 100 GW in year 2012, mainly due by the cost reduction of PV panels. However, one of the main disadvantages of this kind of energy source is their highly variability. The main source of variability is, of course, the day/night cycle. Nevertheless, short-term effects such as cloud shadowing and supply interruptions and long-term effects such as dust accumulation, seasonal variation and ageing of panels will also appear as sources of variability. The combined effect of all these variability sources makes the analysis of the power production data very complex. The reliability and accuracy of this data analysis could becomes significant because it is required to expand the PV plant size, to design a new one, to incorporate energy storage for power smoothing or to economically evaluate the PV system. This work presents a methodology to obtain statistically consistent data from a PV plant, in order to evaluate all the mentioned effects separately. The method is based on the correlation of PV power production data with an ideal value of solar power obtained from geographical and astronomical data. The proposed methodology is applied to data obtained from a PV plant located in northern Chile.
Selective, Orally Active γ-Aminobutyric Acid A α5 Receptor Inverse Agonists as Cognition Enhancers (2004)

Nonselective inverse agonists at the gamma-aminobutyric acid(A) (GABA-A) benzodiazepine binding site have cognition-enhancing effects in animals but are anxiogenic and can precipitate convulsions. Herein, we describe novel GABA-A alpha5 subtype inverse agonists leading to the identification of 16 as an orally active, functionally selective compound that enhances cognition in animals without anxiogenic or convulsant effects. Compounds of this type may be useful in the symptomatic treatment of memory impairment associated with Alzheimer's disease and related dementias.
Control of the Orbital Delocalization and Implications for Molecular Rectification in the Radical Anions of Porphyrins with Coplanar 90° and 180° β,β‘-Fused Extensions (2008)

Through-porphyrin electronic communication is investigated using "linear-type" and "corner-type" bis(quinoxalino)porphyrins in free-base form and their ZnII, CuII, NiII, and PdII derivatives. These compounds are porphyrins with quinoxalines fused on opposite or adjacent beta,beta'-pyrrolic positions; they were synthesized from 5,10,15,20-tetrakis(3,5-di-tert-butylphenyl)-porphyrin-2,3,12,13- and -2,3,7,8-tetraone, respectively, by reaction with 1,2-phenylenediamine. The degree of electron spin delocalization into the fused rings in the pi-radical anions of the free-base and metal(II) bisquinoxalinoporphyrins was elucidated by electrochemistry, UV-vis absorption, and electron spin resonance (ESR) spectra of the singly reduced species and density functional theory calculations. Hyperfine splitting patterns in the ESR spectra of the pi-radical anions show that symmetric molecules have delocalized electron spin, indicating that significant inter-quinoxaline interactions are mediated through the central porphyrin unit, these interactions being sufficient to guarantee through-molecule conduction. However, when molecular symmetry is broken by tautomeric exchange of the inner nitrogen hydrogens in the free-base porphyrin with a corner-type quinoxaline substitution pattern, the pi-radical anion becomes confined so that one quinoxaline group is omitted from spin delocalization. This indicates the appearance of a unidirectional barrier to through-molecule conduction, suggesting a new motif for chemically controlled rectification.
Cathodoluminescence study of the properties of stacking faults in 4H-SiC homoepitaxial layers (2009)

In-grown stacking faults in n-type 4H-SiC epitaxial layers have been investigated by real-color cathodoluminescence imaging and spectroscopy carried out at room and liquid helium temperatures. Stacking faults with 8H stacking order were observed, as well as double layer and multilayer 3C-SiC structures and a defect with an excitonic band gap at 2.635 eV. It was found that 8H stacking faults and triangular surface defects can be generated from similar nucleation sources. Time-resolved measurements reveal that compared to defect-free regions, the carrier lifetimes are severely reduced by the presence of stacking faults corresponding to triangular surface defects and three-dimensional 3C-SiC inclusions.
Characterization of a Multi-User Indoor Positioning System Based on Low\n Cost Depth Vision (Kinect) for Monitoring Human Activity in a Smart Home (2016)

An increasing number of systems use indoor positioning for many scenarios\nsuch as asset tracking, health care, games, manufacturing, logistics, shopping,\nand security. Many technologies are available and the use of depth cameras is\nbecoming more and more attractive as this kind of device becomes affordable and\neasy to handle. This paper contributes to the effort of creating an indoor\npositioning system based on low cost depth cameras (Kinect). A method is\nproposed to optimize the calibration of the depth cameras, to describe the\nmulti-camera data fusion and to specify a global positioning projection to\nmaintain the compatibility with outdoor positioning systems.\n The monitoring of the people trajectories at home is intended for the early\ndetection of a shift in daily activities which highlights disabilities and loss\nof autonomy. This system is meant to improve homecare health management at home\nfor a better end of life at a sustainable cost for the community.\n
Integration of MIRAS breadboard and future activities (2002)

The European Space Agency (ESA) is conducting a feasibility study on MIRAS, a Microwave Imaging Radiometer using two dimensional aperture synthesis, for the mapping of soil moisture and ocean salinity from space. An aircraft breadboard of this instrument is discussed. This paper concentrates on the results achieved following the integration of the prototype. The breadboard consists of an 11 element Y-shaped bi-dimensional L-band interferometer which can be switched to measure the two polarizations. In addition the future activities related to MIRAS are presented. A technology demonstrator of MIRAS is proposed as a first major step towards a future spaceborne sensor.
Polymeric electro-optic modulator based on 1×2 Y-fed directional coupler (2000)

We have demonstrated a polymeric electro-optic modulator based on a 1×2 Y-fed directional waveguide coupler. The symmetric geometry of the 1×2 Y-fed directional coupler provided the modulator unique characteristics of intrinsic 3 dB operating point and two complementary output ends. A low switching voltage of 3.6 V and a high extinction ratio of 26 dB were obtained with the modulator operating at a wavelength of 1.34 μm. The modulator was fabricated with a novel electro-optic polymer that was synthesized from polyurethane cross-linking with a chromophore.
Variation with temperature of octanol/water partition coefficient for the homologous series from benzene to propylbenzene (2019)

Abstract Variation of octanol/water partition coefficient, log K ow , with temperature is seldom reported in the literature. A precise method for the evaluation of log K ow has been developed and the values of this parameter were measured for benzene, toluene, ethylbenzene, and n‐propylbenzene at six temperatures between 15 and 60°C. The procedure is based on a direct “shake flask” method, but utilizes a gas chromatography with mass spectrometry method for the measurement of the concentration of analytes in the water and octanol extracts. The results indicate that log K ow values for these analytes have only small variations with the temperature, and that this variation does not depend linearly on 1/ T . The results for log K ow in the evaluated temperature interval are close to the values reported in the literature for log K ow at 25°C. The variations of log K ow were found to be small and are non‐linear in 1/ T . Based on these variations the enthalpy ΔH 0 and entropy ΔS ° for the partition process were calculated. The obtained values for ΔH 0 and ΔS 0 indicated that for temperatures below about 40°C the process is entropy‐driven and does not involve large Gibbs free energies.
High Charge Storage Characteristics of CeO<inf>2</inf> Nanocrystals for Novolatile Memory Applications (2008)

This paper presents the formation of CeO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> nanocrystals on SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> tunneling layer and its annealing effect to the nonvolatile memory device. The characteristics including the program/erase behaviors, data retention, and endurance of Silicon-Oxide-Nitride-Oxide-Silicon type memories embedded with cerium oxide (CeO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ) nanocrystals were studied to demonstrate its advantages as a nonvolatile memory device.
Mannose-Specific Plant Lectins from the Amaryllidaceae Family Qualify as Efficient Microbicides for Prevention of Human Immunodeficiency Virus Infection (2004)

The plant lectins derived from Galanthus nivalis (Snowdrop) (GNA) and Hippeastrum hybrid (Amaryllis) (HHA) selectively inhibited a wide variety of human immunodeficiency virus type 1 (HIV-1) and HIV-2 strains and clinical (CXCR4- and CCR5-using) isolates in different cell types. They also efficiently inhibited infection of T lymphocytes by a variety of mutant virus strains. GNA and HHA markedly prevented syncytium formation between persistently infected HUT-78/HIV cells and uninfected T lymphocytes. The plant lectins did not measurably affect the antiviral activity of other clinically approved anti-HIV drugs used in the clinic when combined with these drugs. Short exposure of the lectins to cell-free virus particles or persistently HIV-infected HUT-78 cells markedly decreased HIV infectivity and increased the protective (microbicidal) activity of the plant lectins. Flow cytometric analysis and monoclonal antibody binding studies and a PCR-based assay revealed that GNA and HHA do not interfere with CD4, CXCR4, CCR5, and DC-SIGN and do not specifically bind with the membrane of uninfected cells. Instead, GNA and HHA likely interrupt the virus entry process by interfering with the virus envelope glycoprotein. HHA and GNA are odorless, colorless, and tasteless, and they are not cytotoxic, antimetabolically active, or mitogenic to human primary T lymphocytes at concentrations that exceed their antivirally active concentrations by 2 to 3 orders of magnitude. GNA and HHA proved stable at high temperature (50 degrees C) and low pH (5.0) for prolonged time periods and can be easily formulated in gel preparations for microbicidal use; they did not agglutinate human erythrocytes and were not toxic to mice when administered intravenously.
Immunopeptidomic Analyses of Colorectal Cancers With and Without Microsatellite Instability (2022)

Colorectal cancer is the second leading cause of cancer death worldwide, and the incidence of this disease is expected to increase as global socioeconomic changes occur. Immune checkpoint inhibition therapy is effective in treating a minority of colorectal cancer tumors; however, microsatellite stable tumors do not respond well to this treatment. Emerging cancer immunotherapeutic strategies aim to activate a cytotoxic T cell response against tumor-specific antigens, presented exclusively at the cell surface of cancer cells. These antigens are rare and are most effectively identified with a mass spectrometry-based approach, which allows the direct sampling and sequencing of these peptides. Although the few tumor-specific antigens identified to date are derived from coding regions of the genome, recent findings indicate that a large proportion of tumor-specific antigens originate from allegedly noncoding regions. Here, we employed a novel proteogenomic approach to identify tumor antigens in a collection of colorectal cancer-derived cell lines and biopsy samples consisting of matched tumor and normal adjacent tissue. The generation of personalized cancer databases paired with mass spectrometry analyses permitted the identification of more than 30,000 unique MHC I-associated peptides. We identified 19 tumor-specific antigens in both microsatellite stable and unstable tumors, over two-thirds of which were derived from noncoding regions. Many of these peptides were derived from source genes known to be involved in colorectal cancer progression, suggesting that antigens from these genes could have therapeutic potential in a wide range of tumors. These findings could benefit the development of T cell-based vaccines, in which T cells are primed against these antigens to target and eradicate tumors. Such a vaccine could be used in tandem with existing immune checkpoint inhibition therapies, to bridge the gap in treatment efficacy across subtypes of colorectal cancer with varying prognoses. Data are available via ProteomeXchange with identifier PXD028309.
Caledonian hot zone magmatism in the “Newer Granites”: insight from the Cluanie and Clunes plutons, Northern Scottish Highlands (2022)

Scottish “Newer” Granites record the evolution of the Caledonides resulting from Iapetus subduction and slab breakoff during the Silurian-Devonian Scandian Orogeny, but relationships between geodynamics, petrogenesis and emplacement are incomplete. Laser ablation U-Pb results from magmatic zircons at the Cluanie Pluton (Northern Highlands) identify clusters of concordant Silurian data points. A cluster with a weighted mean 206Pb/238U age of 431.6 ± 1.3 Ma (2sigma confidence interval, n = 6) records emplacement whilst older points (clustered at 441.8 ± 2.3 Ma, n = 9) record deep crustal hot zone magmatism prior to ascent. The Cluanie Pluton, and its neighbour the ~428 Ma Clunes tonalite, have adakite-like high Na, Sr/Y, La/Yb and low Mg, Ni and Cr characteristics, and lack mafic facies common in other “Newer Granites”. These geochemical signatures indicate the tapping of batches of homogenised, evolved magma from the deeper crust. The emplacement age of the Cluanie Pluton confirms volumetrically modest subduction-related magmatism occurred beneath the Northern Highlands before slab breakoff, probably as a result of crustal thickening during the ~450 Ma Grampian 2 event. Extensive new in-situ geochemical-geochronological studies for this terrane may further substantiate the deep crustal hot zone model and the association between Caledonian magmatism and potentially metallogenesis. The term “Newer Granites” is outdated as it ignores the demonstrated relationships between magmatism, Scandian orogenesis and slab breakoff. Hence, “Caledonian intrusions” would be a more appropriate generic term to cover those bodies related to either Iapetus subduction or to slab breakoff.