gebhart/patrepeval huggingface dataset:
Localization of the Plasmodium falciparumPfNT1 Nucleoside Transporter to the Parasite Plasma Membrane (2001)

Nutrient transporters play critical roles in parasite metabolism, but the membranes in which they reside have not been clearly defined. The transport of purine nutrients is crucial to the survival of the malaria parasite Plasmodium falciparum, and nucleoside transport activity has been associated with a number of different membrane components within the parasitized erythrocyte. To determine the location of the PfNT1 nucleoside transporter, the first component of the nucleoside permeation pathway to be studied at the molecular level in P. falciparum (Carter, N. S., Ben Mamoun, C., Liu, W., Silva, E. O., Landfear, S. M., Goldberg, D. E., and Ullman, B. (2000) J. Biol. Chem. 275, 10683-10691), polyclonal antisera against the NH2-terminal 36 amino acids of PfNT1 were raised in rabbits. Western blot analysis of parasite lysates revealed that the antibodies were specific for PfNT1 and that the level of PfNT1 protein in the infected erythrocyte is regulated in a stage-specific fashion. The amount of PfNT1 polypeptide increases dramatically during the early trophozoite stage and reaches its maximal level in the late trophozoite and schizont stages. Deconvolution and immunoelectron microscopy using these monospecific antibodies revealed that PfNT1 localizes predominantly, if not exclusively, to the plasma membrane of the parasite and not to the parasitophorous vacuolar or erythrocyte membranes.
Cloning and characterization of the rat homologues of the Inhibitor of Apoptosis protein 1, 2, and 3 genes. (2002)

We have identified three rat homologues of the IAP genes. The elevated expression of rat iap-1 and iap2 in testes suggests that these two genes play an important antiapoptotic role in spermatogenesis.
Reduced Expression of the IL-7 Receptor (CD127) on CD8AA+ T-cells and IL-7 Signalling Defects in Patients With Breast Cancer (2005)

s: Abstracts for the 20th Annual Scientific Meeting of the International Society for Biological Therapy of Cancer (Primary Authors are Italicized): CYTOKINES: BIOLOGY AND THERAPEUTICS
Development of a New Reservoir-Friendly Drilling Fluid for Higher Gas Production (2018)

Abstract Drilling gas reservoir requires high mud density to balance the reservoir pressure. To formulate such fluids, calcium carbonate (CaCO3) was used because of its high acid solubility. However, due to the high concentration of CaCO3 required for high density drilling fluid, sticking might occur which might result in fishing and/or sidetracks operations. To minimize sticking problems, barite (BaSO4) is added with CaCO3 to reduce the amount of solids needed to formulate the drilling fluid. However, barite can cause potential damage because it does not dissolve in commonly used acids. Drilling fluids were developed at a wide range of densities using CaCl2 salt with Manganese Tetroxide (Mn3O4). No similar formulations were developed before to the best of the authors’ knowledge. The properties of small particle size (D50=1 microns), spherical shape and high specific gravity (4.9 g/cm3) of Mn3O4 make it good weighting material to reduce solids loading and settling compared to CaCO3 (2.78 g/cm3 and D50=10 microns) and BaSO4 (4.20 g/cm3 and D50=20 microns). The objective of this study is to show the lab work involved in designing water-based drilling fluids using CaCl2 / Mn3O4. The experimental work in this paper involved rheological properties, thermal stability, API and HT/HP filtration. The data generated from this study showed that Lignite and Vinyl amide/vinyl sulfonate copolymer are recommended to provide good rheological stability and filtration control for CaCl2/Mn3O4 drilling fluid. Polyanionic cellulose polymer and starch can used to formulate KCl/Mn3O4 drilling fluid with good properties at 300 °F.
Consistent Modelling of I-V and C-V Behaviour of GaN HEMTs in Presence of Trapping (2019)

Charge trapping in Gallium Nitride (GaN) based high electron mobility transistors (HEMTs) is known to change the I-V behaviour of these devices. Trapping also changes the C-V behaviour of the device. In this paper, for the first time, we present a physics-based compact model which captures the I-V and the C-V characteristics of the device in presence of trapping effects consistently with I-V and C-V modelled using the same set of model formulations and physical model parameters. The developed model shows excellent agreement to the measured data. The importance of a consistent I-V and C-V model is also shown.
Application of nonsense-mediated primer exclusion (NOPE) for preparation of unique molecular barcoded libraries (2017)

We describe a simple, robust and cheap modification of UMI-labeled HTS libraries preparation procedure, that allows to bypass purification step and thus to preserve starting material which may be limited, e.g. circulating tumor DNA, circulating fetal DNA, or small amounts of isolated cells of interest. Furthermore, demonstrated simplicity and robustness of NOPE method should make it popular in various PCR protocols.
Saccharin Intake Predicts Ethanol Intake in Genetically Heterogeneous Rats as Well as Different Rat Strains (1993)

Saccharin and ethanol intakes were measured in seven strains of rats known to differ in their preferences for ethanol: The Fawn-Hooded (FH), alcohol-preferring (P) and Maudsley Reactive rats have been reported to drink ethanol voluntarily, whereas the alcohol-nonpreferring, Maudsley Nonreactive and Flinders Line (FSL and FRL) rats do not. Saccharin and ethanol intakes were highly correlated (r = +0.61) over all strains, with the FH rats drinking the most of both solutions. Correlation coefficients between pairs of drinking versus nondrinking rat strains were even higher. In a second experiment, genetically heterogeneous F2 progeny from cross-breeding the ethanol-preferring FH rats with the ethanol-nonpreferring Flinders Resistant Line (FRL) rats were studied. The results indicated a high positive correlation between saccharin and ethanol intakes (+0.65). These findings suggest that the association between saccharin and ethanol intakes previously reported in rat strains with different preferences for ethanol may have a similar genetic basis.
Second-order nonlinear optical properties of thiopheno-quinoid dipolar structures (1998)

The second order nonlinear optical response of two dipolar thiopheno-quinoid chromophores are calculated using extensive single and double-excitation configuration interaction. The (beta) values are found to be comparable in magnitude to those for the pheno-quinoid systems. The sign of the nonlinear response is, however, found to be positive in these systems, in contrast to the second-order nonlinear optical response of pheno-quinoid structures which are known to be negative.
Risk factors for surgical site infections and other complications in elective surgery in patients with rheumatoid arthritis with special attention for anti-tumor necrosis factor: a large retrospective study. (2007)

The most important risk factor for SSI is history of SSI or skin infection. Although our study was not powered to detect small differences in infection rates, perioperative continuation of anti-TNF does not seem to be an important risk factor for SSI.
Myeloperoxidase-dependent Inactivation of Surfactant Protein D in Vitro and in Vivo (2010)

Surfactant protein D (SP-D) plays diverse and important roles in innate immunity and pulmonary homeostasis. Neutrophils and myeloperoxidase (MPO) colocalized with SP-D in a murine bacterial pneumonia model of acute inflammation, suggesting that MPO-derived reactive species might alter the function of SP-D. Exposure of SP-D to the complete MPO-H(2)O(2)-halide system caused loss of SP-D-dependent aggregating activity. Hypochlorous acid (HOCl), the major oxidant generated by MPO, caused a similar loss of aggregating activity, which was accompanied by the generation of abnormal disulfide-cross-linked oligomers. A full-length SP-D mutant lacking N-terminal cysteine residues and truncation mutants lacking the N-terminal domains were resistant to the oxidant-induced alterations in disulfide bonding. Mass spectroscopy of HOCl-treated human SP-D demonstrated several modifications, but none involved key ligand binding residues. There was detectable oxidation of cysteine 15, but no HOCl-induced cysteine modifications were observed in the C-terminal lectin domain. Together, the findings localize abnormal disulfide cross-links to the N-terminal domain. MPO-deficient mice showed decreased cross-linking of SP-D and increased SP-D-dependent aggregating activity in the pneumonia model. Thus, MPO-derived oxidants can lead to modifications of SP-D structure with associated alterations in its characteristic aggregating activity.
Computational modeling of a carbon nanotube-based DNA nanosensor (2010)

During the last decade the design of biosensors, based on quantum transport in one-dimensional nanostructures, has developed as an active area of research. Here we investigate the sensing capabilities of a DNA nanosensor, designed as a semiconductor single walled carbon nanotube (SWCNT) connected to two gold electrodes and functionalized with a DNA strand acting as a bio-receptor probe. In particular, we have considered both covalent and non-covalent bonding between the DNA probe and the SWCNT. The optimized atomic structure of the sensor is computed both before and after the receptor attaches itself to the target, which consists of another DNA strand. The sensor's electrical conductance and transmission coefficients are calculated at the equilibrium geometries via the non-equilibrium Green's function scheme combined with the density functional theory in the linear response limit. We demonstrate a sensing efficiency of 70% for the covalently bonded bio-receptor probe, which drops to about 19% for the non-covalently bonded one. These results suggest that a SWCNT may be a promising candidate for a bio-molecular FET sensor.
MRI data confirm the selective involvement of thalamic and amygdalar nuclei in amyotrophic lateral sclerosis and primary lateral sclerosis (2020)

A standardised imaging protocol was implemented to evaluate disease burden in specific thalamic and amygdalar nuclei in 133 carefully phenotyped and genotyped motor neuron disease patients. "Switchboard malfunction in motor neuron diseases: selective pathology of thalamic nuclei in amyotrophic lateral sclerosis and primary lateral sclerosis" [1] "Amygdala pathology in amyotrophic lateral sclerosis and primary lateral sclerosis" [2] Raw volumetric data, group comparisons, effect sizes and percentage change are presented. Both ALS and PLS patients exhibited focal thalamus atrophy in ventral lateral and ventral anterior regions revealing extrapyramidal motor degeneration. Reduced accessory basal nucleus and cortical nucleus volumes were noted in the amygdala of <i>C9orf72</i> negative ALS patients compared to healthy controls. ALS patients carrying the GGGGCC hexanucleotide repeats in <i>C9orf72</i> exhibited preferential pathology in the mediodorsal-paratenial-reuniens thalamic nuclei and in the lateral nucleus and cortico-amygdaloid transition area of the amygdala. Considerable thalamic atrophy was observed in the sensory nuclei and lateral geniculate region of PLS patients. Our data demonstrate genotype-specific patterns of thalamus and amygdala involvement in ALS and a distinct disease-burden pattern in PLS. The dataset may be utilised for validation purposes, meta-analyses and the interpretation of thalamic and amygdalar profiles from other ALS genotypes.
Quantification of MET expression using mass spectrometry (MS): Assay precision and stability in FFPE tumor tissue. (2014)

16 Background: Overexpression of MET in gastroesophageal cancer (GEC) is associated with poor prognosis and potentially predictive of anti-MET therapeutic benefit. IHC has been the method chosen to quantify MET expression to date. However, IHC is semi-quantitative, suffers from cross-reactivity, and is low throughput. Moreover, MET IHC is hampered by antigenic instability in FFPE sections, limiting its utility to recently cut FFPE sections. Increasing recognition of the importance of other biomarkers in GEC suggests that ‘economic’ testing of scarce samples will be required. We sought to develop a MET quantitative assay within our ‘GEC-plex’ Liquid-Tissue-selected reaction monitoring (LT-SRM) MS test. Methods: We used trypsin digestion mapping of rMET to identify unique peptides for MS assay development. The assay was pre-clinically validated in 5 cell lines, where electrochemiluminescence (ECL) immunoassay measurement of MET was also performed. To assess the MET MS assay stability from archival FFPE sections, freshly cut FFPE tissue sections were immediately microdissected, processed and analyzed, while adjacent sections were processed and analyzed one year after cutting, to compare temporal quantification from the same FFPE samples (n=33). MET expression was assessed in GEC cases (n=121), and compared to IHC and FISH in select cases. Results: Tryptic digestion mapping of rMET showed that peptide TEFTTALQR was optimal for MET quantification. The LLOD for this peptide was 150 amol with CV&lt;20%. Validation of the MET MS assay on 5 cell lines revealed concordance when compared to ECL (R 2 =0.99). The MET MS assay demonstrated temporal stability of serial sections cut from 33 samples analyzed one year apart: CVs&lt;20%, R 2 =0.75. Analysis of 121 GEC FFPE tissues showed a broad range of MET expression levels (&lt;150-4600 amol/ug), with 36/121 (29.7%) having detectable levels, similar to that observed using IHC. MS expression thresholds were determined that reliably identified MET gene amplification; sensitivity and specificity of these thresholds will be presented. Conclusions: ‘GEC-plex’ has a quantitative, sensitive, and specific MET MS assay that can be multiplexed along with other GEC biomarkers.
Supplemental Fig 8 from Fibroblast Growth Factor Receptor Signaling Dramatically Accelerates Tumorigenesis and Enhances Oncoprotein Translation in the Mouse Mammary Tumor Virus–Wnt-1 Mouse Model of Breast Cancer (2023)

Supplemental Fig 8 from Fibroblast Growth Factor Receptor Signaling Dramatically Accelerates Tumorigenesis and Enhances Oncoprotein Translation in the Mouse Mammary Tumor Virus–Wnt-1 Mouse Model of Breast Cancer
ACCESSING THE INACCESSIBLE; AN INNOVATIVE APPROACH TO THE RADIOLOGICAL SURVEYING OF METAL WASTE. (2005)

Decommissioning and Decontamination (D&D) operations often results in the production of large volumes of scrap metal waste with little or no radioactive contamination. Proving that the waste is clean can be costly and time consuming, as the shape and size of the metallic waste items often means that it is difficult or impossible to monitor all surfaces using conventional hand-held survey meters. This is a particular problem for alpha contamination measurement. A survey system, IonSens ® , has been developed by BIL (formerly BNFL Instruments Ltd) which allows rapid surveying of scrap metal for alpha contamination at very low levels. The system comprises a large chamber into which scrap metal is placed with a door sealing the chamber while a measurement is carried out. A challenge to traditional radiological surveying techniques was faced by the decommissioning team at the Springfields Oxide Fuel Complex in the UK, where a number of reject fuel pin tubes from the fabrication of Advance Gas cooled Reactor (AGR) fuel assemblies had accumulated over a period. These tubes were approximately 80cm long with an inner diameter of 14mm, making surveying by traditional methods impractical. However, the Long Range Alpha Detection (LRAD) technique remotely detects and measures secondary ionization created in air by alpha particle interactions, allowing extremely low levels of alpha contamination to be measured. The LRAD technique is an original invention from the Los Alamos National Laboratory, and through a successful collaboration, has been developed into the commercial waste monitoring family of systems known as IonSens ® . The LRAD technique has proved to be an effective survey method, as large numbers of tubes could be surveyed simultaneously. More importantly, pre-processing of the metal is not required to allow surfaces to be accessed by a hand held survey meter, for example by cutting the tubes open.
Redox‐Active Heteroatom‐Functionalized Polyacetylenes (2021)

Abstract The discovery of metallic conductivity in polyacetylene [‐HC=CH‐] n upon doping represents a landmark achievement. However, the insolubility of polyacetylene and a dearth of methods for its chemical modification have limited its widespread use. Here, we employ a ring‐opening metathesis polymerization (ROMP) protocol to prepare functionalized polyacetylenes ( f PAs) bearing: (1) electron‐deficient boryl (‐BR 2 ) and phosphoryl (‐P(O)R 2 ) side chains; (2) electron‐donating amino (‐NR 2 ) groups, and (3) ring‐fused 1,2,3‐triazolium units via strain‐promoted Click chemistry. These functional groups render most of the f PAs soluble and can lead to intense light absorption across the visible to near‐IR region. Also, the presence of redox‐active boryl and amino groups leads to opposing near‐IR optical responses upon (electro)chemical reduction or oxidation. Some of the resulting f PAs show greatly enhanced air stability when compared to known polyacetylenes. Lastly, these f PAs can be cross‐linked to yield network materials with the full retention of optical properties.
Mobility Modes for Pulse-Shaped OTFS with Linear Equalizer (2020)

Orthogonal time frequency and space (OTFS) modulation is a pulse-shaped Gabor signaling scheme with additional time-frequency (TF) spreading using the symplectic finite Fourier transform (SFFT). With a sufficient amount of accurate channel information and sophisticated equalizers, it promises performance gains in terms of robustness for high mobility users. To fully exploit diversity in OTFS, the 2D-deconvolution implemented by a linear equalizer should approximately invert the doubly dispersive channel operation, which however is a twisted convolution. In theory, this is achieved in a first step by matching the TF grid and the Gabor synthesis and analysis pulses to the delay and Doppler spread of the channel. However, in practice, one always has to balance between supporting high granularity in delay-Doppler (DD) spread, and multi-user and network aspects. In this paper, we propose mobility modes with distinct grid and pulse matching for different doubly dispersive channels. To account for remaining self-interference, we tune the minimum mean square error (MMSE) linear equalizer without the need of estimating channel cross-talk coefficients. We evaluate our approach with the QuaDRiGa channel simulator and with OTFS transceiver architecture based on a polyphase implementation for orthogonalized Gaussian pulses. In addition, we compare OTFS to a IEEE 802.11p compliant design of cyclic prefix (CP) based orthogonal frequency-division multiplexing (OFDM). Our results indicate that with an appropriate mobility mode, the potential OTFS gains can be indeed achieved with linear equalizers to significantly outperform OFDM.
Structuring unreliable radio networks (2011)

In this paper we study the problem of building a connected dominating set with constant degree (CCDS) in the dual graph radio network model [4,9,10]. This model includes two types of links: reliable, which always deliver messages, and unreliable, which sometimes fail to deliver messages. Real networks compensate for this differing quality by deploying low-layer detection protocols to filter unreliable from reliable links. With this in mind, we begin by presenting an algorithm that solves the CCDS problem in the dual graph model under the assumption that every process u is provided a local link detector set consisting of every neighbor connected to u by a reliable link. The algorithm solves the CCDS problem in O(Δ\log2 n/b + log3 n) rounds, with high probability, where Δ is the maximum degree in the reliable link graph, n is the network size, and b is an upper bound in bits on the message size. The algorithm works by first building a Maximal Independent Set (MIS) in log3 n time, and then leveraging the local topology knowledge to efficiently connect nearby MIS processes. A natural follow up question is whether the link detector must be perfectly reliable to solve the CCDS problem. With this in mind, we first describe an algorithm that builds a CCDS in O(Δpolylog(n)) time under the assumption of O(1) unreliable links included in each link detector set. We then prove this algorithm to be (almost) tight by showing that the possible inclusion of only a single unreliable link in each process's local link detector set is sufficient to require Ω(Δ) rounds to solve the CCDS problem, regardless of message size. We conclude by discussing how to apply our algorithm in the setting where the topology of reliable and unreliable links can change over time.
Effect of strain on the band structure of GaAs and In0.2Ga0.8As (1988)

The valence-band structures of 50-Å-thick layers of GaAs(001) in tension and In0.2Ga0.8As(001) in compression have been determined using angle-resolved photoemission spectroscopy. Our studies show that the Δ3+Δ4 bands and the Δ1 band respond differently to the strain perturbation. For strained GaAs(001), the Δ3+Δ4 bands (Px+Py-like) are shifted up in energy by a maximum amount of 0.3 eV, while in contrast, the Δ1 band (Pz-like) is shifted down by about 0.1 eV. For strained In0.2Ga0.8As(001), the band shifts are in the opposite direction, consistent with the opposite strain conditions. For both materials, the strain-induced changes cannot be characterized simply by rigid band shifts, but rather exhibit significant wave vector dependence. This results in a reduction of the effective mass of the Δ3+Δ4 bands for both GaAs and In0.2Ga0.8As.
Spectral Response of Ternary Logic Netlists (2013)

Past methods for computation of the spectrum of a multiple-valued logic network usually rely on first characterizing the network in terms of a switching function, secondly in mapping the function values to complex numbers, and thirdly in performing the computation resulting in the spectrum. More recent approaches use decision diagram (DD) representations but still require initial formation of a DD representing the logic network switching function before the spectrum is computed. A method is described that derives a spectral transfer function directly from a netlist representation. The spectral transfer function can then be used to compute either the logic network spectral response for a specified input, or for computation of the entire Chrestenson spectrum. This method avoids the need for representing the network as a DD before computing the spectrum and can be used to directly compute either a single spectral response, the entire netlist spectrum, or the spectrum of subcircuits contained within a netlist.