gebhart/patrepeval huggingface dataset:
Prionet Canada: A Network of Centres of Excellence for Research into Prions and Prion Diseases (2009)

PrioNet Canada's strength in basic, applied, and social research is helping to solve the food, health safety, and socioeconomic problems associated with prion diseases. Prion diseases are transmissible, fatal neurodegenerative diseases of humans and animals. Examples of prion diseases include bovine spongiform encephalopathy (BSE, commonly known as "mad cow" disease), Creutzfeldt-Jakob disease in humans, and chronic wasting disease (CWD) in deer and elk. As of March 31, 2008, PrioNet's interdisciplinary network included 62 scientific members, 5 international collaborators, and more than 150 students and young professionals working in partnership with 25 different government, nongovernment, and industry partners. PrioNet's activities are developing strategies based on a sustained, rational approach that will mitigate, and ultimately control, prion diseases in Canada.
Spatio-Temporal Localization of Intense Pulses in Gas-Filled Capillaries (2016)

We investigate pulse propagation from the ultraviolet to the mid-infrared in gas-filled capillaries. For shorter wavelength pulses and smaller capillary diameters, ionization-induced refraction excites higher-order modes, and their constructive interference leads to spatio-temporal localization.
Bounding Errors Caused by Nominal GNSS Signal Deformations (2011)

Nominal signal deformations are present in GNSS-GPS and WAAS-GEO satellite signals. They result in pseudorange errors, which in turn cause navigation errors for GNSS users. These navigation errors depend on the user- and reference-receiver configuration parameters as well as satellite geometry and user location. Previous papers by the authors focused on obtaining a better understanding of the pseudorange errors caused by nominal signal deformations. For this paper, we examine the user navigation error effects of nominal signal deformations from many perspectives: based on the pseudorange tracking errors from real GPS data, what would be the resultant worst case position errors? When do they become a significant integrity concern? Which user receiver configurations appear least (or most) sensitive to them? What are the effects in the dual-frequency and/ or depleted constellation configurations? The user errors are also a function of best-case and worst-case satellite geometries at the user receiver, which are in turn dependent on user/ reference receiver locations. Nominal and degraded satellite geometries for different user locations were generated using the MATLAB Algorithm Availability Simulation Tool (MAAST) Matlab toolbox, developed at Stanford, and the best and worst case position errors were determined for these cases.The results presented are for typical WAAS aviation users of a single-frequency, GPS-only constellation, but they can be easily extended to multiple-frequency, multi-constellation systems. These results may be especially important with the upcoming increasing availability of dual-frequency systems – the use of linear combinations of signals from the same satellite to remove ionospheric errors in turn scales the signal-deformation-induced errors.
A Highly Reliable Cu Interconnect Technology for Memory Device (2007)

This paper describes the development of Cu interconnect technology for memory devices. A highly reliable sub 50 nm Cu interconnect lines were successfully fabricated by using optimized iPVD barrier/seed and electroplating process. The resistivity of Cu lines was reviewed with that of Al for extendibility of Cu. The Cu TDDB lifetime in user conditions was investigated to confirm the reliability of Cu process integration. It can be predicted that Cu metallization can satisfy the requirements of sub 50 nm trench pattern, which are lower resistance than Al and good reliabilities.
Safety and pharmacokinetics of an anti-PcrV PEGylated monoclonal antibody fragment in mechanically ventilated patients colonized with Pseudomonas aeruginosa (2012)

Objective: The type III secretion system is an important Pseudomonas aeruginosa-virulence determinant in animal models of infection and in humans. Antibody-mediated inhibition of the PcrV protein, an essential component of this system, might abrogate the Pseudomonas aeruginosa ability to damage epithelial cells, neutrophils, and macrophages, thereby limiting its pathogenicity. The objective of the trial was to determine the safety, pharmacokinetics, and ability to prevent Pseudomonas aeruginosa ventilator–associated pneumonia of KB001, a recombinant, PEGylated, engineered, human Fab′ fragment that specifically binds to a Pseudomonas aeruginosa PcrV epitope and blocks its function. Design: Multicenter, randomized, placebo-controlled, double-blind, phase-2a trial. Setting: Ten intensive care units across France. Patients: Thirty-nine Pseudomonas aeruginosa-colonized, but not infected, mechanically ventilated patients. Interventions: Patients were randomized 1:1:1 to receive a single intravenous infusion of KB001, 3 mg/kg (n = 13) or 10 mg/kg (n = 14), or placebo (n = 12). Measurements and Main Results: The primary end points were KB001 safety and tolerability, assessed as treatment-related adverse-event frequency and severity. Secondary end points included serum and lung KB001 pharmacokinetics, and Pseudomonas aeruginosa pneumonia rate within 28 days of its infusion. KB001 was well tolerated and not immunogenic. The 3- and 10-mg/kg groups had respective maximum serum concentrations of 52,811–88,660 and 121,857–285,454 ng/mL, with mean elimination half-lives of 8.1 and 9.3 days. KB001 was detected in endotracheal aspirates from all patients receiving it, as early as day 1 and up to 28 days. Respective mean endotracheal aspirate/serum concentration ratios were 0.092 and 0.085 for the 3- and 10-mg/kg groups, who developed Pseudomonas aeruginosa pneumonia less frequently (33% and 31%, respectively) than placebo recipients (60%). Conclusions: KB001 was safe and well tolerated in this study, with a favorable pharmacokinetic profile and promising potential for reducing Pseudomonas aeruginosa pneumonia incidence in intensive care unit mechanically ventilated patients colonized with this bacterium.
Prime-boost vaccination regimens with INO-4800 and INO-4802 augment and broaden immune responses against SARS-CoV-2 in nonhuman primates (2021)

SUMMARY The enhanced transmissibility and immune evasion associated with emerging SARS-CoV-2 variants demands the development of next-generation vaccines capable of inducing superior protection amid a shifting pandemic landscape. Since a portion of the global population harbors some level of immunity from vaccines based on the original Wuhan-Hu-1 SARS-CoV-2 sequence or natural infection, an important question going forward is whether this immunity can be boosted by next-generation vaccines that target emerging variants while simultaneously maintaining long-term protection against existing strains. Here, we evaluated the immunogenicity of INO-4800, our synthetic DNA vaccine candidate for COVID-19 currently in clinical evaluation, and INO-4802, a next-generation DNA vaccine designed to broadly target emerging SARS-CoV-2 variants, as booster vaccines in nonhuman primates. Rhesus macaques primed over one year prior with the first-generation INO-4800 vaccine were boosted with either INO-4800 or INO-4802 in homologous or heterologous prime-boost regimens. Both boosting schedules led to an expansion of antibody responses which were characterized by improved neutralizing and ACE2 blocking activity across wild-type SARS-CoV-2 as well as multiple variants of concern. These data illustrate the durability of immunity following vaccination with INO-4800 and additionally support the use of either INO-4800 or INO-4802 in prime-boost regimens.
Multiple-Breath Washout Outcomes Are Sensitive to Inflammation and Infection in Children with Cystic Fibrosis (2017)

Rationale: The lung clearance index is a measure of ventilation distribution derived from the multiple-breath washout technique. The lung clearance index is increased in the presence of lower respiratory tract inflammation and infection in infants with cystic fibrosis; however, the associations during the preschool years are unknown.Objectives: We assessed the ability of the lung clearance index to detect the presence and extent of lower respiratory tract inflammation and infection in preschool children with cystic fibrosis.Methods: Ventilation distribution outcomes were assessed at 82 visits with 58 children with cystic fibrosis and at 38 visits with 31 healthy children aged 3–6 years. Children with cystic fibrosis also underwent bronchoalveolar lavage fluid collection for detection of lower respiratory tract inflammation and infection. Associations between multiple-breath washout indices and the presence and extent of airway inflammation and infection were assessed using linear mixed effects models.Resu...
MSK1 is required for the beneficial synaptic and cognitive effects of enriched experience across the lifespan (2023)

Positive experiences, such as social interaction, cognitive training and physical exercise, have been shown to ameliorate some of the harms to cognition associated with ageing. Animal models of positive interventions, commonly known as environmental enrichment, strongly influence neuronal morphology and synaptic function and enhance cognitive performance. While the profound structural and functional benefits of enrichment have been appreciated for decades, little is known as to how the environment influences neurons to respond and adapt to these positive sensory experiences. We show that adult and aged male wild-type mice that underwent a 10-week environmental enrichment protocol demonstrated improved performance in a variety of behavioural tasks, including those testing spatial working and spatial reference memory, and an enhancement in hippocampal LTP. Aged animals in particular benefitted from enrichment, performing spatial memory tasks at levels similar to healthy adult mice. Many of these benefits, including in gene expression, were absent in mice with a mutation in an enzyme, MSK1, which is activated by BDNF, a growth factor implicated in rodent and human cognition. We conclude that enrichment is beneficial across the lifespan and that MSK1 is required for the full extent of these experience-induced improvements of cognitive abilities, synaptic plasticity and gene expression.
Systematically controlling the error rates in variation-prone networks-on-chip for energy efficiency (2015)

Networks-on-Chip (NoCs) are prone to within-die process variation as they\nspan the whole chip. To tolerate variation, their voltages (Vdd) carry overprovisioned\nguardbands. As a result, prior work has proposed to save energy\nby dynamically managing Vdd, operating at reduced Vdd while occasionally\nsu ering and xing errors. Unfortunately, these proposals use ad-hoc controller\ndesigns that may not work under other scenarios and do not provide\nerror bounds.\nThis thesis develops a scheme that dynamically minimizes the Vdd of groups\nof routers in a variation-prone NoC using formal control-theory methods.\nThe scheme, called Contra, saves substantial energy while guaranteeing the\nstability and convergence of error rates. Moreover, the scheme is enhanced\nwith a low-cost secondary network that retransmits erroneous packets for\nhigher energy e ciency. The enhanced scheme is called Contra+. Both\nContra and Contra+ are evaluated using simulations of NoCs with 64{100\nrouters. In an NoC with 8 routers per Vdd domain, the proposed schemes\nreduce the average energy consumption of the NoC by 27%; in a futuristic\nNoC with one router per Vdd domain, Contra+ and Contra reduce the average\nenergy consumption by 37% and 32%, respectively. The performance impact\nis negligible. These savings are signi cant over the state-of-the-art. The\nresults categorically state that formal control is essential to attain a stable,\nscalable, and energy-efficient design. Additionally, it is found that while the\nsecondary network helps Contra+ attain higher energy savings, it has a nonnegligible\nhardware cost. Hence, Contra is the most cost-effective design.
Lithium Perchlorate (2001)

[7791-03-9] ClLiO4 (MW 106.39) (mild Lewis acid1 for cycloaddition reactions,2 conjugate additions,3 ring opening of epoxides,4 and ring expansion of cyclopropanes5) Physical Data: mp 236 °C; bp 430 °C (dec); d 2.428 g cm−3. Solubility: 60 g/100 mL H2O (25 °C); 150 g/100 mL H2O (89 °C); 152 g/100 mL EtOH (25 °C); 137 g/100 mL acetone (25 °C); 182 g/100 mL MeOH (25 °C); 114 g/100 mL ether. Form Supplied in: white solid; widely available in anhydrous form or as the trihydrate; it is usually used in solution in ether or MeOH. Purification: anhydrous lithium perchlorate is prepared by heating the commercially available anhydrous material or its trihydrate at 160 °C for 48 h under high vacuum (P2O5 trap). Handling, Storage, and Precautions: the anhydrous material should be used as prepared for best results. The decomposition of lithium perchlorate starts at about 400 °C and becomes rapid at 430 °C, yielding lithium chloride and oxygen. Perchlorates are potentially explosive and should be handled with caution.
No Genetic Linkage Detected for Schizophrenia to Xq27–q28 (1991)

The hypothesis that at least a subgroup of familial cases of schizophrenia could be due to a genetic defect on the X chromosome is supported by the observation of an excess of X-chromosome aneuploidies (XXX and XXY) among populations of patients with psychosis. The distal long arm, Xq27-q28, is a candidate region where linkage has been claimed to manic-depressive disorder and a fragile site has been associated with schizophrenia spectrum disorders. The present study excluded linkage to a large part of this region using four polymorphic probes and multipoint lod-score analysis in 10 families with multiple members with schizophrenia.
Nickel oxide decorated MoS2nanosheet-based non-enzymatic sensor for the selective detection of glucose (2020)

Understanding blood glucose levels in our body can be a key part in identifying and diagnosing prediabetes. Herein, nickel oxide (NiO) decorated molybdenum disulfide (MoS<sub>2</sub>) nanosheets have been synthesized <i>via</i> a hydrothermal process to develop a non-enzymatic sensor for the detection of glucose. The surface morphology of the NiO/MoS<sub>2</sub> nanocomposite was comprehensively investigated by field-emission scanning electron microscopy (FE-SEM), high-resolution transmission electron microscopy (HR-TEM), powder X-ray diffraction (PXRD), X-ray photoelectron spectroscopy (XPS) and Brunauer-Emmett-Teller (BET) analysis. The electro-catalytic activity of the as-prepared NiO/MoS<sub>2</sub> nanocomposite towards glucose oxidation was investigated by cyclic voltammetry, electrochemical impedance spectroscopy (EIS) and amperometry in 0.1 M NaOH. The NiO/MoS<sub>2</sub> nanocomposite-based sensor showed outstanding electrocatalytic activity for the direct electro-oxidation of glucose due to it having more catalytic active sites, good conductivity, excellent electron transport and high specific surface area. Meanwhile, the NiO/MoS<sub>2</sub> modified glassy carbon electrode (GCE) showed a linear range of glucose detection from 0.01 to 10 mM by amperometry at 0.55 V. The effect of other common interferent molecules on the electrode response was also tested using alanine, l-cysteine, fructose, hydrogen peroxide, lactose, uric acid, dopamine and ascorbic acid. These molecules did not interfere in the detection of glucose. Moreover, this NiO/MoS<sub>2</sub>/GCE sensor offered rapid response (2 s) and a wide linear range with a detection limit of 1.62 μM for glucose. The reproducibility, repeatability and stability of the sensor were also evaluated. The real application of the sensor was tested in a blood serum sample in the absence and presence of spiked glucose and its recovery values (96.1 to 99.8%) indicated that this method can be successfully applied to detect glucose in real samples.
Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 7 (2007)

Crystals of baculovirus-expressed adeno-associated virus serotype 7 capsids diffract X-rays to approximately 3.0 A resolution. The crystals belong to the rhombohedral space group R3, with unit-cell parameters a = 252.4, c = 591.2 A in the hexagonal setting. The diffraction data were processed and reduced to an overall completeness of 79.0% and an R(merge) of 12.0%. There are three viral capsids in the unit cell. The icosahedral threefold axis is coincident with the crystallographic threefold axis, resulting in one third of a capsid (20 monomers) per crystallographic asymmetric unit. The orientation of the viral capsid has been determined by rotation-function searches and is positioned at (0, 0, 0) by packing considerations.
Drift-based methodology for seismic proportioning of coupled shear walls (1996)

This paper presents a design tool for size proportioning of reinforced concrete coupled shear walls built in seismic regions. It is based on the maximum allowable drift that can be selected by the designer. Free vibration and modal analyses are performed on a variety of coupled shear walls of different heights and geometries. From these analyses, fundamental periods are first related to geometric properties of coupled shear walls and then to maximum interstorey drifts. These maximum drifts are obtained from both spectrum analysis and pseudo-static approach. Closed-form formulas for estimating the required fundamental periods of coupled wall systems as a function of maximum allowable drift are derived. The design of the wall system can be based on geometric dimensions to yield the stiffness to achieve the required period. These formulas not only are thought to be useful for preliminary size proportioning, but also can constitute an advantageous starting point for more sophisticated analyses. To demonstrate the applicability of these formulas and to clarify design issues, a design example is treated and results are compared with static and dynamic analyses. Key words: coupled shear wall, reinforced concrete, ductility, force modification factor, interstorey drift, fundamental period, seismic.
Transplantation tolerance and its outcome during infections and inflammation (2014)

Much progress has been made toward understanding the mechanistic basis of transplantation tolerance in experimental models, which implicates clonal deletion of alloreactive T and B cells, induction of cell-intrinsic hyporesponsiveness, and dominant regulatory cells mediating infectious tolerance and linked suppression. Despite encouraging success in the laboratory, achieving tolerance in the clinic remains challenging, although the basis for these challenges is beginning to be understood. Heterologous memory alloreactive T cells generated by infections prior to transplantation have been shown to be a critical barrier to tolerance induction. Furthermore, infections at the time of transplantation and tolerance induction provide a pro-inflammatory milieu that alters the stability and function of regulatory T cells as well as the activation requirements and differentiation of effector T cells. Thus, infections can result in enhanced alloreactivity, resistance to tolerance induction, and destabilization of the established tolerance state. We speculate that these experimental findings have relevance to the clinic, where infections have been associated with allograft rejection and may be a causal event precipitating the loss of grafts after long periods of stable operational tolerance. Understanding the mechanisms by which infections prevent and destabilize tolerance can lead to therapies that promote stable life-long tolerance in transplant recipients.
IGKV3 proteins as candidate “off-the-shelf” vaccines for kappa-light chain-restricted B cell non-Hodgkin’s lymphomas (156.15) (2011)

Abstract An increasing set of B-cell non-Hodgkin’s lymphomas (B-NHLs) show a biased usage of IGKV3-20 and IGKV3-15 immunoglobulin genes, but it is not known whether the corresponding proteins are immunogenic in the majority of patients. We herein demonstrate that IGK+ lymphoma patients show spontaneous T cell responses to these proteins and that IGKV3-specific cytotoxic T lymphocytes (CTLs) can be easily induced ex vivo. IGKV3-20-specific CTLs cross-react against different IGKV3 proteins, an effect mediated by the presence of 21 shared, sometimes promiscuous, T cell epitopes, presented by the most common HLA class I allele products, thus assuring a broad HLA coverage of IGKV3-based vaccines. Many natural variants of these epitopes are carried by IGK light chains expressed by a broad spectrum of B-NHLs and we show that IGKV3-20-specific CTLs cross-react also against several of these variant epitopes. Both humoral and CTL specific responses were induced by KLH-conjugated IGKV3-20 protein in HLA-A2-transgenic mice and co-injection of IGKV3-20-specific CTLs with IGKV3-20+ lymphoma cells into SCID mice totally prevented tumor growth, thus confirming the ability of these effectors to mediate efficient cytotoxic responses also in vivo. These results provide the rationale to exploit IGKV3 proteins as “off-the-shelf” vaccines for a large fraction of lymphoma patients.
Tables S1-S9 from Circulating Tumor DNA Genomics Correlate with Resistance to Abiraterone and Enzalutamide in Prostate Cancer (2023)

&lt;p&gt;Supplementary Tables S1 - S9&lt;/p&gt;
The Prc and RseP proteases control bacterial cell‐surface signalling activity (2013)

Summary Extracytoplasmic function ( ECF ) sigma factors play a key role in the regulation of vital functions in the bacterial response to the environment. In Gram‐negative bacteria, activity of these sigma factors is often controlled by cell‐surface signalling ( CSS ), a regulatory system that also involves an outer membrane receptor and a transmembrane anti‐sigma factor. To get more insight into the molecular mechanism behind CSS regulation, we have focused on the unique Iut system of Pseudomonas putida . This system contains a hybrid protein containing both a cytoplasmic ECF sigma domain and a periplasmic anti‐sigma domain, apparently leading to a permanent interaction between the sigma and anti‐sigma factor. We show that the Iut ECF sigma factor regulates the response to aerobactin under iron deficiency conditions and is activated by a proteolytic pathway that involves the sequential action of two proteases: Prc , which removes the periplasmic anti‐sigma domain, and RseP , which subsequently removes the transmembrane domain and thereby generates the ECF active transcriptional form. We furthermore demonstrate the role of these proteases in the regulation of classical CSS systems in which the sigma and anti‐sigma factors are two different proteins.
Monitoring of Incoming Silicon PV Wafers with Modified Surface Photovoltage (SPV) Minority Carrier Diffusion Length Method (2011)

The noncontact ac-surface photovoltage technique is modified to enable reliable measurement of the minority diffusion length in incoming silicon PV wafers. The modifications to overcome very low SPV signal in wafers with saw damage include three elements; 1- increased photon flux in a range that still maintains advantages of low injection level; 2- elevated frequency light modulation with increased averaging that enhances signal to noise ratio and 3- thermal preconditioning of surface to create depletion layer SPV. The technique is tested using comparative measurements on Cz wafers and MC wafers with saw damage and after a saw damage removal etch. Consistently similar results were obtained before and after etching for diffusion length L, and for iron and boronoxygen defect concentrations. The results demonstrate excellent repeatability that for a L of about 100μm is 0.1%. The repeatability data for Fe and boron-oxygen enable to evaluate defect detection limits in low e9 atoms/cm3 range. To our knowledge, no other techniques can match such sensitivity for as-cut saw damaged wafers.