gebhart/patrepeval huggingface dataset:
P1‐038: Pyroglutamate formation at the N‐termini of ABri molecules in familial British dementia occurs at the sites of deposition and is not restricted to the central nervous system (2010)

Amyloid molecules harboring pyroGlu residue at the N-termini are considered to be important for the development of cerebral amyloidosis such as Alzheimer's disease (AD) and thought to be either spontaneously generated or being catalyzed by glutaminyl cyclase (QC). In mammals, QC exists abundantly in the central nervous system (CNS) but in lower amounts in peripheral tissue. In neurons, QC is found in secretory granules, being QC-activity detected in cerebrospinal fluid (CSF). Familial British dementia (FBD) is an autosomal dominant form of cognitive impairment characterized by parenchymal amyloid and pre-amyloid deposits, cerebral amyloid angiopathy and neurofibrillary tangles, closely mimicking neuropathological features of AD. FBD is caused by a stop to Arg mutation in BRI2 gene, de novo generating the amyloid molecule ABri which is released from mutant BRI2 protein by pro-hormone convertase(s). ABri molecules extracted from FBD brains are 34 amino acids long species bearing abundant pyroGlu residue at the N-termini (ABri1-34pE). To further clarify the mechanism(s) of ABri deposition we investigated whether pyroGlu formation indeed occurs outside the CNS taking advantage that FBD is also a systemic amyloidosis. ABri molecules extracted from systemic organs were biochemically analyzed using a combination of immunoprecipitation, mass spectrometry and Western blot analysis, being compared with ABri molecules isolated from plasma and CSF. Soluble ABri molecules present in the circulation and CSF are monomeric, exclusively harboring Glu residue at the N-termini (ABri1-34E). In contrast, both soluble and fibrillar ABri molecules were shown to be oligomeric in size containing a variable proportion of ABri1-34pE in systemic deposits, suggesting that pyroGlu formation occurs at the site of deposition. Pyroglutamate formation at the N-termini of ABri molecules is an early step in the process of ABri deposition, being not restricted to the CNS. Pyroglutamate formation is likely to occur by enzymatic activity like QC, although the exact mechanism is still unclear. Peripheral ABri deposits are good initial target to evaluate novel therapeutic strategies for FBD -e.g. for the inhibition of pyroGlu formation- which may have further applicability in other neurodegenerative disorders containing the same post-translational modification, including AD.
Supplementary Figure 1 from Intrinsic Breast Tumor Subtypes, Race, and Long-Term Survival in the Carolina Breast Cancer Study (2023)

&lt;p&gt;PDF file - 24K&lt;/p&gt;
SiO2-P2O5-B2O3Wood-Inorganic Composites Prepared by Metal Alkoxide Oligomers and their Fire-Resisting Properties (1998)

Article SiO2-P2O5-B2O3 Wood-Inorganic Composites Prepared by Metal Alkoxide Oligomers and their Fire-Resisting Properties was published on January 1, 1998 in the journal Holzforschung (volume 52, issue 4).
A 435MHz, 2.5Mbps/W Side-Channel-Attack Resistant Crypto-Processor for Secure RSA-4K Public-Key Encryption in 14nm CMOS (2020)

A 0.072mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> SCA-Resistant RSA-4K crypto-processor fabricated in 14nm CMOS achieves peak encryption throughput of 0.08Mbps at 750mV, 25°C. Exponent magnitude/timing randomization with dynamic RF addressing provide 711× lower means-separation in current/EM trace magnitudes, reducing attacker's accuracy to an ineffective random guess classification while limiting area/performance overhead to 3%.
Computing the Centerline of a Colon: A Robust and Efficient Method Based on 3D Skeletons (1999)

We present a robust and efficient algorithm for calculating the centerline of a computer-generated colon model created from helical CT image data. The centerline is an essential aid for navigating through complex anatomy such as the colon. Our algorithm involves three steps. In the first step, we generate a 3D skeleton of the binary colon volume using a fast topological thinning algorithm. In the second step, we employ a graph search algorithm to remove extra loops and branches. These loops and branches are caused by holes in the object that are artifacts produced during image segmentation. In the final step, we compute a smooth representation of the centerline by approximating the skeleton with cubic B-splines. This final step is necessary because the skeleton contains many abrupt changes in direction due to the discrete nature of image data. The user supplies two endpoints for the centerline; otherwise, the algorithm is fully automated. Experimental results demonstrate that the algorithm is not only robust but also efficient.
Balto-Slavic connective negation and negative concord (2021)

peer reviewed
Approaches to the creation of an active electrically small superconductive antenna (2013)

The physical principles of designing active electrically small superconductive antennas are investigated. These antennas are based on an array of superconducting quantum interference cells characterized by a high linearity of magnetic-signal conversion into voltage. The results of experimental investigation into an active antenna prototype containing 80 cells connected in series and occupying an area of 3.3 × 3.3 m are presented. The proposed integrated circuit is fabricated via the standard niobium technique of the formation of Josephson-junction elements with a critical current density of 4.5 kA/cm2.
Design Variability: Challenges and Solutions at Microarchitecture-Architecture Level (2008)

Provides an abstract of the tutorial presentation and a brief professional biography of the presenter. The complete presentation was not made available for publication as part of the conference proceedings.
Electrically tunable Dicke effect in a double-ring resonator (2010)

We study the finite-element method analysis of the Dicke effect using numerical simulations in an all-optical system of an optical waveguide side-coupled to two interacting ring resonators in a liquid crystal environment. The system is shown to exhibit all the signatures of the Dicke effect under active and reversible control by an applied voltage.
Protective role of V-set and immunoglobulin domain-containing 4 expressed on kupffer cells during immune-mediated liver injury by inducing tolerance of liver T- and natural killer T-cells (2012)

Collectively, our results suggest that VSIG4(+) KCs play a critical role in the induction and maintenance of liver T- and NKT-cell tolerance, and that modulation of the VSIG4 pathway using a VSIG4.Ig fusion protein may provide useful immunological therapies against immune-mediated liver injury including autoimmune hepatitis.
New Optional IVC Filter for Percutaneous Retrieval - In Vitro Evaluation of Embolus Capturing Efficiency (2005)

The new Celect filter showed similar in-vitro capture properties as the Gunther Tulip filter and deserves further in-vivo testing.
Activation of Polymorphonuclear Leukocytes by Candidate Biomaterials for an Implantable Glucose Sensor (2011)

Three of the 15 candidate materials triggered PMN activation in a complement-dependent manner and should therefore be avoided for implementation in implantable microsensors.
A highly thermostable crude endoglucanase produced by a newly isolated Thermobifida fusca strain UPMC 901 (2019)

A thermophilic Thermobifida fusca strain UPMC 901, harboring highly thermostable cellulolytic activity, was successfully isolated from oil palm empty fruit bunch compost. Its endoglucanase had the highest activity at 24 hours of incubation in carboxymethyl-cellulose (CMC) and filter paper. A maximum endoglucanase activity of 0.9 U/mL was achieved at pH 5 and 60 °C using CMC as a carbon source. The endoglucanase properties were further characterized using crude enzyme preparations from the culture supernatant. Thermal stability indicated that the endoglucanase activity was highly stable at 70 °C for 24 hours. Furthermore, the activity was found to be completely maintained without any loss at 50 °C and 60 °C for 144 hours, making it the most stable than other endoglucanases reported in the literature. The high stability of the endoglucanase at an elevated temperature for a prolonged period of time makes it a suitable candidate for the biorefinery application.
Non-Orthogonal Multicast and Unicast Robust Beamforming in Integrated Terrestrial-Satellite Networks (2022)

This paper studies the non-orthogonal multicast and unicast coordinated beamforming design for integrated terrestrial and satellite networks (ITSN), when the channel state information at the transmitter (CSIT) is imperfect. In order to mitigate the interference induced by simultaneous multicast and unicast links along with the spectrum coexisting mechanism for integrated terrestrial and satellite transmissions, we consider a two-layer layered division multiplexing (LDM) structure where the mul-ticast and unicast services are provided in different layers. We formulate a coordinated beamforming problem with the objective to minimize the transmit power under individual quality of service (QoS) constraints. With regard to the unknown convexity of the transmit power minimization problem, we transform the original infeasible optimization into a deterministic optimization form with linear matrix inequality (LMI) by utilizing S-procedure and semi-definite relaxation (SDR) methods. Then, we introduce a penalty function and propose an iterative algorithm with guaranteed convergence to obtain optimal solutions. Simulation results demonstrate the superiority of the proposed coordinated beamforming scheme, especially for the case of imperfect CSIT, while our LDM based coordinated beamforming scheme signifi-cantly outperforms the conventional ones in terms of sum rate.
CLONETS-DS – Clock Network Services-Design Study Strategy and innovation for clock services over optical-fibre networks in Europe (2021)

Long-distance time and frequency transfer methods based on optical fibre links have evolved rapidly in recent years, demonstrating excellent performance for frequency transfer and considerable promise for accurate time transfer. CLONETS-DS is a European Union-funded research and innovation action intended to facilitate the vision of a sustainable, pan-European optical fibre network for precise time and frequency reference dissemination.
<title>Ultrasonic Imaging Using Two-Dimensional Transducer Arrays</title> (1976)

Instrumentation for echocardiography has progressed through the first generation with single-transducer TM-mode scanning, into the second generation with real-time B-mode imaging using linear arrays of transducers. A third generation with great future potential is represented by two-dimensional piezoelectric transducer arrays which are inherently capable of imaging in a three-dimensional volume as illustrated schematically in Fig. 1. The volume is shown divided into basic depth elements that project through the region with width equal to the lateral resolution. Depth information is obtained by insonifying one or more depth elements with acoustic pulses and receiving echoes from reflecting and scattering objects. Practical methods of displaying real-time three-dimensional information are unavailable, and consequently the most significant capability is the electronic selectability of image data in three dimensions. A scanned system, where electronically selected depth elements are processed sequentially using the same transducers for both insonification and echo reception, is particularly well suited to this use.
Effect of transverse guiding on the velocity distribution of an atomic beam (1989)

We have observed that the transverse guiding that results when an intense light field with a Gaussian intensity distribution is superimposed upon an atomic beam can increase the total number of atoms in the beam and select atoms according to transverse velocity. This guiding preferentially retains atoms with small longitudinal velocities; consequently the expected value of the longitudinal velocity will decrease, even though no particular atom is slowed. The density of cold atoms in an atomic beam that has been slowed and cooled by a strong standing-wave field can be enhanced by such a process since the standing wave provides its own transverse guide.
Revision Wrist Arthroscopy after Failed Primary Arthroscopic Treatment (2014)

Level IV Therapeutic.
The Hsp60 protein of Helicobacter pylori: structure and immune response in patients with gastroduodenal diseases (1993)

Helicobacter pylori is a human pathogen that has been associated with gastritis, peptic ulcer and gastric carcinoma. The role of the direct action of H. pylori virulence factors and of the induction of autoreactive immunity in the development of chronic gastritis has not been clarified yet. Here we report the cloning and molecular characterization of a gene of H. pylori coding for a protein of 58 kDa, recognized by sera of patients affected by H. pylori-induced gastroduodenal diseases. This antigen is present in all the H. pylori strains tested and it belongs to the Hsp60 family of heat-shock proteins, with high homology with other bacterial and eukaryotic proteins of the same family. This class of homologous proteins has been implicated in the induction of autoimmune disorders in different systems. The presence in infected patients of anti-H. pylori Hsp60 antibodies, potentially cross-reactivity between human Hsp60 and a rabbit antiserum against H. pylori Hsp60 suggest that a role of this protein in gastroduodenal diseases is possible.
Decision making for multi-objective multi-agent search and rescue missions (2017)

In this paper we introduce a novel rewarding scheme for the classical POMDP formulation. The proposed scheme aims to reinforce preference of objectives. It ensures that a high-priority preferences get high accumulative rewards, solve ambiguities and it can be conducted before the low-priority-preference. In order to show conflicting of objectives, context of search and rescue has been selected for this paper. It involves heterogeneous team with potential conflicting multiobjective situations. Our rewarding scheme has been tested in simulated scenarios using multiple POMDP solvers. Results obtained from the simulated experiments show that the system is able to represent an impact on the human (first responder) through enforcing priority of objectives and iteratively optimize policies to better suit the first responder and the search and rescue mission goals.
Exonuclease VII of Escherichia coli (1974)

Exonuclease VII from Escherichia coli is specific for single-stranded DNA, degrading denatured DNA, single-stranded regions extending from the ends of duplex DNA, or displaced single-stranded regions. Hydrolysis is initiated at both 3′ and 5′ termini. Exonuclease VII can also excise thymine dimers from duplex DNA following treatment of the DNA with the Micrococcus luteus endonuclease specific for thymine dimers. The enzyme has no detectable activity on RNA or DNA-RNA hybrid molecules. The limit products of exonuclease VII action are oligonucleotides bearing 5′-phosphoryl and 3′-hydroxyl termini predominantly in the range of tetramers to dodecamers; no mononucleotide products have been observed. The enzyme acts in a processive fashion, initially releasing large, acid-insoluble oligonucleotides which can be degraded further to produce a limit product of acid-soluble oligonucleotides. The possible role of exonuclease VII in recombination and in the repair of ultra-violet damage to DNA is discussed.
HmuY Haemophore and Gingipain Proteases Constitute a Unique Syntrophic System of Haem Acquisition by Porphyromonas gingivalis (2011)

Haem (iron protoporphyrin IX) is both an essential growth factor and virulence regulator for the periodontal pathogen Porphyromonas gingivalis, which acquires it mainly from haemoglobin via the sequential actions of the R- and K-specific gingipain proteases. The haem-binding lipoprotein haemophore HmuY and its cognate receptor HmuR of P. gingivalis, are responsible for capture and internalisation of haem. This study examined the role of the HmuY in acquisition of haem from haemoglobin and the cooperation between HmuY and gingipain proteases in this process. Using UV-visible spectroscopy and polyacrylamide gel electrophoresis, HmuY was demonstrated to wrest haem from immobilised methaemoglobin and deoxyhaemoglobin. Haem extraction from oxyhaemoglobin was facilitated after oxidation to methaemoglobin by pre-treatment with the P. gingivalis R-gingipain A (HRgpA). HmuY was also capable of scavenging haem from oxyhaemoglobin pre-treated with the K-gingipain (Kgp). This is the first demonstration of a haemophore working in conjunction with proteases to acquire haem from haemoglobin. In addition, HmuY was able to extract haem from methaemalbumin, and could bind haem, either free in solution or from methaemoglobin, even in the presence of serum albumin.
Palmitoylation of the recombinant human A1 adenosine receptor: enhanced proteolysis of palmitoylation-deficient mutant receptors (1999)

Palmitoylation of the recombinant human A1 adenosine receptor (A1AR) expressed in HEK-293 cells is demonstrated by showing that hexahistidine (His6)/Asp-Tyr-Lys-Asp-Asp-Asp-Asp-Lys (FLAG) (H/F) A1ARs, purified to homogeneity from cells metabolically labelled with [3H]palmitate, incorporate tritium into a 38-42 kDa receptor glycoprotein. The amount of palmitoylation is not affected by incubation of cells with the A1AR-selective agonist N6-cyclopentyladenosine (CPA). A1AR palmitoylation is abolished by treatment with neutral hydroxylamine or by mutation of Cys-309 to Ala (C309 → A). Based on Western blotting and pulse-chase experiments with [35S]methionine, at least 90% of wild-type receptors are palmitoylated and turn over with a t½ of 6.4 h. Of the C309 → A mutated receptors, 40% appear to turn over like wild-type receptors, with a t½ of 7.1 h, and 60% appear to be rapidly cleaved to form a 25 kDa receptor fragment that turns over with a t½ of 0.8 h. In HEK-293 cell lines expressing similar numbers of wild-type or C309 → A mutant A1Rs, there is little difference in the kinetics of CPA-induced receptor internalization (1 h), down-regulation (24 h), inhibition of forskolin-stimulated cAMP accumulation, or activation of co-transfected G-protein-activated inward rectifier K+/cardiac inward rectifying K+ (GIRK1/CIR K+) channels. Also unaffected by palmitoylation is guanosine 5′-[γ-thio]-triphosphate ([S]GTP)-sensitive binding to membranes by the agonist 125I-labelled aminobenzyladenosine. The results suggest that palmitoylation has little effect on receptor-effector coupling, agonist-induced internalization or down-regulation. We speculate that palmitoylation may divert newly synthesized A1ARs from a pathway leading to rapid degradation.
T Cell Recognition of Hypervariable Region-1 from Hepatitis C Virus Envelope Protein with Multiple Class II MHC Molecules in Mice and Humans: Preferential Help for Induction of Antibodies to the Hypervariable Region (1999)

Hypervariable region-1 (HVR1) from the hepatitis C virus (HCV) envelope protein is thought to be a target for neutralizing Abs. To explore HVR1 recognition by helper T cells, and their role in Ab responses, we attempted to generate helper T cells specific for HVR1 in mice of three MHC types, and with PBMC from HCV-infected HLA-diverse humans. In both species, HVR1 was presented by >1 class II MHC molecule to CD4+ helper T cells and showed surprising interisolate cross-reactivity. The epitope for two DR4+ patients was mapped to a more conserved C-terminal sequence containing a DR4 binding motif, possibly accounting for cross-reactivity. Strikingly, Abs to patients' own HVR1 sequences were found only in patients with T cell responses to HVR1, even though all had Abs to envelope protein, suggesting that induction of Abs to HVR1 depends on helper T cells specific for a sequence proximal to the Ab epitope. Thus, helper T cells specific for HVR1 may be functionally important in inducing neutralizing Abs to HCV. These results may be the first example of "T-B reciprocity," in which proximity of a helper T cell epitope determines Ab epitope specificity, in a human disease setting.
Acoustic analysis of sodium boiling stability tests using THORS bundle 6A (1977)

Acoustic data from boiling stability tests on the THORS (Thermal-Hydraulic Out-of-Reactor Safety) facility are presented and discussed. The THORS sodium loop is a high temperature test facility that contains the bundle 6A, a full length stimulated fuel subassembly with nineteen electrically heated pins. Boiling stability tests on the THORS facility were designed to determine if a stable boiling region exists during the thermal hydraulic test at normal and off-normal conditions. Boiling was observed and the stable boiling region was determined. The acoustic data observed by three ANL sodium-immersible microphones have provided the following information: (1) the boiling signal is clearly observed and shows a correlation with the inlet flow fluctuations; (2) the signal level and the repetition rate of the boiling signal are directly related to the applied heat flux; (3) a typical boiling pulse consists of a high frequency signal due mainly to the bubble collapse and a low frequency (approximately 75 Hz) void oscillation; (4) a boiling pulse yields a frequency spectrum with significant amplitudes up to 80 KHz as compared with 4 KHz for background pulses; and (5) the frequency content of a boiling pulse can be mostly explained in terms of various resonance frequencies of the loop. The characterization of these data is pertinent to the design of sodium boiling detection systems.
Differential interactions between statins and P‐glycoprotein: Implications for exploiting statins as anticancer agents (2010)

Statins, prescribed for decades to control cholesterol, have more recently been shown to have promising anticancer activity. Statins induce tumor-selective apoptosis by inhibiting the mevalonate (MVA) pathway. In addition, we have recently demonstrated that lovastatin modulates drug accumulation in a MVA-independent manner in multidrug-resistant (MDR) tumor cells overexpressing the P-glycoprotein (P-gp) multidrug transporter. P-gp-mediated drug efflux can contribute to chemotherapy failure. However, direct statin-mediated inhibition of P-gp in human MDR tumor cells at clinically achievable concentrations remains unexplored. An understanding of these interactions is crucial, both to appreciate differences in the anticancer potential of different statins and to safely and effectively integrate statins into traditional chemotherapy regimens that include P-gp substrates. Here we evaluate interactions between 4 statins (lovastatin, atorvastatin, fluvastatin and rosuvastatin) and P-gp, at both the molecular level using purified P-gp and at the cellular level using human MDR tumor cells. Lovastatin bound directly to purified P-gp with high affinity and increased doxorubicin accumulation in MDR tumor cells, potentiating DNA damage, growth arrest and apoptosis. By contrast, while atorvastatin inhibited substrate transport by purified P-gp in proteoliposomes, it had no effect on doxorubicin transport in MDR tumor cells. Finally, fluvastatin and rosuvastatin only interacted with P-gp in vitro at high concentrations and did not inhibit doxorubicin transport in MDR cells. These differential interactions should be considered when combining statins with traditional chemotherapeutic drugs.