gebhart/patrepeval huggingface dataset:
Iron-Tolerant Cyanobacteria for Human Habitation beyond Earth (2006)

In light of the President's Moon/Mars initiative, lunar exploration has once again become a priority for NASA. In order to establish permanent bases on the Moon and proceed with human exploration of Mars, two key problems will be addressed: first, the production of O2 and second, the production of methane (CH4). While O2 is required for life support systems (LSS), both liquid O2 and CH4 are needed as an oxidizer and a propellant, respectively for the Lunar Surface Access Module (LSAM) and the Crew Exploration Vehicle (CEV). Unlike previous propulsion systems, the new CEV will use liquid oxygen (LO2) as an oxidizer and liquid methane (LCH4) as a propellant. Existing technology (e.g. hydrogen reduction) for the production of liquid oxygen from lunar regolith is very energy intensive and requires high temperature reactors. We propose an alternative approach using iron-tolerant cyanobacteria. We have found that iron-tolerant cyanobacteria (IT CB) are capable of etching iron-bearing minerals, which may lead to bonds breaking between Fe and O of common lunar mare basalt Feoxides including ilmenite, pseudobrookite, ferropseudobrookite, and armalcolite with the subsequent release of both Fe, Ti and oxygen as by-products. We also propose to use CB biomass for CH4 production as carbon stock and a propellant. Both processes can be accomplished in an energy and cost effective manner because sunlight will be used as an energy source and allows the reactions at ambient temperatures between 10-60 C. Current evaluations include assessing the thermodynamics of such biogenic reactions using a variety of nutrients and atmospheric parameters, as well as assessing the rates and species variation effects of the driving reactions.
Classical Electrodynamics Coupled to Quantum Mechanics for Calculation of Molecular Optical Properties: a RT-TDDFT/FDTD Approach (2010)

A new multiscale computational methodology was developed to effectively incorporate the scattered electric field of a plasmonic nanoparticle into a quantum mechanical (QM) optical property calculation for a nearby dye molecule. For a given location of the dye molecule with respect to the nanoparticle, a frequency-dependent scattering response function was first determined by the classical electrodynamics (ED) finite-difference time-domain (FDTD) approach. Subsequently, the time-dependent scattered electric field at the dye molecule was calculated using the FDTD scattering response function through a multidimensional Fourier transform to reflect the effect of polarization of the nanoparticle on the local field at the molecule. Finally, a real-time time-dependent density function theory (RT-TDDFT) approach was employed to obtain a desired optical property (such as absorption cross section) of the dye molecule in the presence of the nanoparticle’s scattered electric field. Our hybrid QM/ED methodology was demonstrated by investigating the absorption spectrum of the N3 dye molecule and the Raman spectrum of pyridine, both of which were shown to be significantly enhanced by a 20 nm diameter silver sphere. In contrast to traditional quantum mechanical optical calculations in which the field at the molecule is entirely determined by intensity and polarization direction of the incident light, in this work we show that the light propagation direction as well as polarization and intensity are important to nanoparticle-bound dye molecule response. At no additional computation cost compared to conventional ED and QM calculations, this method provides a reliable way to couple the response of the dye molecule’s individual electrons to the collective dielectric response of the nanoparticle.
Ordered systems of site-controlled pyramidal quantum dots incorporated in photonic crystal cavities (2011)

The coupling of a prescribed number of site-controlled pyramidal quantum dots (QDs) with photonic crystal (PhC) cavities was studied by polarization and power-dependent photoluminescence measurements. The energy of the cavity mode could be readily tuned, making use of the high spectral uniformity of the QDs and designing PhC cavities with different hole radii. Efficient coupling of the PhC cavity modes both to the ground state and to the excited state transitions of the QDs was observed, whereas no evidence for far off-resonant coupling was found.
Effects of cerium addition on non-basal slip in magnesium single crystals (2019)

Mg–Ce alloy single crystals with different quantities of cerium were subjected to [1̄100] and [112̄0] tensile tests so as to clarify effects of cerium addition on activation of non-basal slips at room temperature. Mg–0.016 mol%Ce alloys yielded due to {101̄1} twins in [1̄100] tension tests. Mg–0.052 mol%Ce single crystals yielded due to {112̄2}〈1̄1̄23〉 second order pyramidal 〈c+a〉 slip (SPCS), similar to pure magnesium single crystals, in [112̄0] tensile tests. Cerium addition decreased critical resolved shear stresses (CRSS) for {101̄1} twinning and SPCS. The decrease in CRSS for SPCS likely results from that the frequency of sessile (c+a) dislocations decreased with decreasing stacking fault energy of second order pyramidal planes.
RARE-09. CYSTIC GLIOBLASTOMA PRESENTATION AS A BENEFICIAL PROGNOSTIC INDICATOR FOR OVERALL SURVIVAL (2019)

Abstract Glioblastoma (GBM) is the most aggressive primary brain tumor with a median overall survival of 15 months with standard-of-care treatment. GBM patients sometimes present with a cystic component, which can be identified through magnetic resonance imaging (MRI). Previous studies suggest that cysts occur in 7–22% of GBM patients and have reported mixed results regarding whether cystic GBM have a survival benefit compared to noncystic GBM. Using our large retrospective cohort of 493 first-diagnosis GBM patients, we aim to elucidate this link between cystic GBM and survival. Within this cohort, 88 patients had a significant cystic component at presentation as identified on MRI. Compared to noncystic GBM (n=405), cystic GBM patients had significantly better overall survival (15 vs 22 months median, log-rank, p=0.001) and were significantly younger at the time of presentation (t-test, p=0.002). However, within patients that received current standard-of-care treatment (n=184), cystic GBM (n=40) was not as beneficial for outcome (22 vs 25 months, log-rank, p=0.3). We also did not observe a significant survival benefit when comparing this standard-of-care cystic cohort to cystic GBM patients diagnosed before the standard was established (n=19, 25 vs 23 months, log-rank, p=0.3), but the analogous result for noncystic GBM patients gives a sizeable benefit, as expected (n=144, n=111, respectively, 22 vs 12 months, log-rank p &lt; 0.0001). Together, these results on current standard-of-care may explain later studies that note no significant survival benefit for cystic GBM patients receiving current standard-of-care. We also report differences in the absolute and relative sizes of imaging abnormalities on MRI and in prognostic impact of cysts based on sex. We discuss current hypotheses for these observed differences, including the possibility that the presence of a cyst could be indicative of a less aggressive tumor.
Antibody-Drug Conjugates Targeted to CD79 for the Treatment of Non-Hodgkin’s Lymphoma. (2006)

Abstract Non-Hodgkin’s lymphoma (NHL) is an attractive indication for the use of antibody-drug conjugate (ADC) therapeutics since NHL is responsive to conventional chemotherapeutic and antibody treatments. Additionally, experience with rituximab indicates that depletion of normal B-cells can be tolerated without untoward side effects, suggesting that B-cell specific surface proteins that are also prevalent in NHL are potential ADC targets. ADCs with stable linkers have lower toxicity than ADCs containing the same drugs with less stable linkers, however, for these ADCs to be effective the antibody must be degraded to release the active drug. This limits potential targets to surface antigens that upon antibody binding are highly internalized and subsequently degraded. We hypothesized that components of the B-cell receptor (BCR) would be excellent targets for stable-linker ADCs since, when cross-linked, the BCR is targeted to the lysosomal-like compartment MIIC as part of B-cell antigen presentation. In particular, CD79, the signaling component of the B-cell receptor, comprised of two peptide chains CD79a (Igα, mb-1) and CD79b (Igβ, B29), seemed a promising target for ADC treatment of NHL. CD79’s expression is restricted to the B-cell lineage and is on the surface of almost all NHLs. Unlike surface-Ig targeted therapies, which require a new drug for each cancer clone, CD79 sequences are invariant and a single drug is appropriate for the entire population. We found that ADCs targeted to CD79b were more effective than those targeted to CD79a. Furthermore, excellent efficacy is demonstrated with ADCs containing stable linkers and our data indicate in particular, that both anti-CD79b-MCC-DM1 and anti-CD79b-MC-MMAF are effective at low doses in subcutaneous cell-line xenograft models of follicular lymphoma, mantle cell lymphoma, Burkitt’s lymphoma and disseminated Burkitt’s lymphoma. Mechanism-of-action experiments show that anti-CD79b antibodies down regulate surface BCR expression and internalized antibody accumulates in the lysosomal-like MIIC compartment as hypothesized. We evaluated a number of ADCs targeted to other B-cell antigens and found that they were not effective if the ADC had a stable linker, indicating that CD79 has special properties as a target for ADCs. Our results suggest that anti-CD79b-MCC-DM1 and anti-CD79b-MC-MMAF are particularly promising therapeutics for the treatment of NHL.
Graph-aware Weighted Hybrid ADMM for Fast Decentralized Optimization (2018)

Distributed optimization has gained popularity in many areas because it can to cope with the increasing volume of data, and the corresponding demand for computational resources. A popular distributed solver is the alternating direction method of multipliers (ADMM). Fully decentralized (D) ADMM arises when node-to-node communications have to abide by the underlying network connectivity. DADMM's convergence however, slows down as the network diameter grows large. To deal with this challenge, the recently proposed hybrid (H) ADMM provides considerable performance boost over DADMM by exploiting local topology information. But HADMM only applies to unweighted graphs. The present contribution develops a weighted hybrid (WH) consensus-based ADMM approach that can deal with weighted graphs. The resultant scheme further improves the performance of HADMM through graph-aware weight tuning. Theoretical analysis offers convergence guarantees and establishes linear convergence rate, while numerical tests on various graphs demonstrate the WHADMM merits.
Enantioselective Synthesis of Kedarcidin Chromophore Aglycon in Differentially Protected Form (2002)

Four components, each prepared in multigram amounts, have been assembled in the convergent (25 steps in the longest linear sequence), enantioselective synthesis of the differentially protected kedarcidin chromophore aglycon (1). In addition to the enantioselective synthesis of each of the four components, the route features a transannular anionic cyclization to form the bicyclo[7.3.0]dodecadienediyne core in the presence of an ansa-bridged macrolactone. MOM=methoxymethyl, TIPS=triisopropylsilyl, TES=triethylsilyl.
The Herpes Simplex Virus LAT Gene is Associated with a Broader Repertoire of Virus-Specific Exhausted CD8+ T Cells Retained Within The Trigeminal Ganglia of Latently Infected HLA Transgenic Rabbits (2016)

Abstract Persistent pathogens, such as herpes simplex virus type 1 (HSV-1), have evolved a variety of immune evasion strategies to avoid being detected and destroyed by the host’s immune system. A dynamic cross talk appears to occur between the HSV-1 Latency-Associated Transcript (LAT), the only viral gene that is abundantly transcribed during latency, and the CD8+ T cells that reside in HSV-1 latently infected human and rabbit trigeminal ganglia (TG). The reactivation phenotype of TG that are latently infected with wild type HSV-1 (i.e. LAT(+) TG) is significantly higher than TG latently infected with LAT null mutant (i.e. LAT(−) TG). Whether LAT promotes virus reactivation by selectively shaping a unique repertoire of HSV-specific CD8+ T cells retained in LAT(+) TG is unknown. In the present study, we assessed the frequency, function, and exhaustion status of TG-resident CD8+ T cells specific to 40 different epitopes derived from HSV-1 gB, gD, VP11/12 and VP13/14 proteins, in Human Leukocyte Antigen (HLA-A*0201) transgenic rabbits infected ocularly with LAT(+) vs. LAT(−) virus. Compared to CD8+ T cells from LAT(−) TG, CD8+ T cells from LAT(+) TG: (i) recognized a broader selection of non-overlapping HSV-1 epitopes; (ii) expressed higher levels of PD-1, TIM-3 and CTLA-4 markers of exhaustion; and (iii) produced less TNF-a, IFN-g, and GzmB. These results suggest a novel immune evasion mechanism by which the HSV-1 LAT may contribute to the shaping of a broader repertoire of exhausted HSV-specific CD8+ T cells in latently infected TG, thus, allowing for increased viral reactivation.
Sensorless AC Current Control with Backstepping Desing for a PWM AC-DC Converter (2010)

In this paper, a novel sensorless AC current control scheme is proposed for the design of PWM AC-DC converter. This design strategy deals with nonlinear backstepping controllers and AC current observer to achieve the purpose of current following. In general, PWM AC-DC converter design requires AC current measurement to achieve control goals, the backstepping observer employed estimates the AC current, and then nonlinear controllers based on backstepping design algorithm are developed to realize the sensorless AC current for the PWM AC-DC converter system. The proposed control scheme is not only to stabilize the PWM AC-DC converter system, but also to drive the current tracking error to converge to zero asymptotically. Furthermore, some simulation results are shown to illustrate excellent performances of the nonlinear backstepping control design scheme applied to a PWM AC-DC converter.
Scalable error isolation for distributed systems: modeling, correctness proofs, and additional experiments (2015)

This technical report complements the paper entitled “Scalable error isolation for distributed systems” published at USENIX NSDI 15.
Control of an industrial robot subjected to base mobility (1994)

To remove the cell size limitation and to make cellular manufacturing systems more flexible, research has been conducted in which an industrial robot has been given base mobility via an air pallet base and use of existing joint actuators and strategically located, compliant posts. For investigating this new approach of robot mobility within a cell, an appropriate control system has been designed and implemented that interfaces with the standard industrial controller. This paper is a presentation of the resulting control system consisting of multiple-sensor integration into its hierarchical levels. Using the concept of logical sensors, experimental verification is presented for each of the logical sensor subsystems and its successful integration with the existing industrial controller. Experimental results obtained for the fully integrated robot controller illustrate the effectiveness of the multiple-sensor, hierarchical controller for self-propelled mobile robots operating within a manufacturing cell.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Spatial quantization via local texture masking (2005)

Wavelet-based transform coding is well known for its utility in perceptual image compression. Psychovisual modeling has lead to a variety of perceptual quantization schemes, for efficient at-threshold compression. Successfully extending these models to supra-threshold compression, however, is a more difficult task. This work attempts to bridge the gap between at threshold modeling and supra-threshold compression by combining a spatially-selective quantization scheme, designed for at-threshold compression with simple MSE-based rate-distortion optimization. A psychovisual experiment is performed to determine how textured image regions can be used to mask quantization induced distortions. Texture masking results from this experiment are used to derive a spatial quantization scheme, which hides distortion in high-contrast image regions. Unlike many spatial quantizers, this technique requires explicit side information to convey contrast thresholds to generate step-sizes. A simple coder is presented that is designed that applies spatially-selective quantization to meet any rate constraints near and above threshold. This coder leverages this side information to reduce the rate required to code the quantized data. Compression examples are compared with JPEG-2000 examples with visual frequency weighting. When matched for rate, the spatially quantized images are highly competitive with and in some cases superior to the JPEG-2000 results in terms of visual quality.
Mitochondrial DAMPs Increase Endothelial Permeability through Neutrophil Dependent and Independent Pathways (2013)

Trauma and sepsis can cause acute lung injury (ALI) and Acute Respiratory Distress Syndrome (ARDS) in part by triggering neutrophil (PMN)-mediated increases in endothelial cell (EC) permeability. We had shown that mitochondrial (mt) damage-associated molecular patterns (DAMPs) appear in the blood after injury or shock and activate human PMN. So we now hypothesized that mitochondrial DAMPs (MTD) like mitochondrial DNA (mtDNA) and peptides might play a role in increased EC permeability during systemic inflammation and proceeded to evaluate the underlying mechanisms. MtDNA induced changes in EC permeability occurred in two phases: a brief, PMN-independent 'spike' in permeability was followed by a prolonged PMN-dependent increase in permeability. Fragmented mitochondria (MTD) caused PMN-independent increase in EC permeability that were abolished with protease treatment. Exposure to mtDNA caused PMN-EC adherence by activating expression of adherence molecule expression in both cell types. Cellular activation was manifested as an increase in PMN calcium flux and EC MAPK phosphorylation. Permeability and PMN adherence were attenuated by endosomal TLR inhibitors. EC lacked formyl peptide receptors but were nonetheless activated by mt-proteins, showing that non-formylated mt-protein DAMPs can activate EC. Mitochondrial DAMPs can be released into the circulation by many processes that cause cell injury and lead to pathologic endothelial permeability. We show here that mitochondria contain multiple DAMP motifs that can act on EC and/or PMN via multiple pathways. This can enhance PMN adherence to EC, activate PMN-EC interactions and subsequently increase systemic endothelial permeability. Mitochondrial DAMPs may be important therapeutic targets in conditions where inflammation pathologically increases endothelial permeability.
Human biological variation in sesamoid bone prevalence: the curious case of the fabella (2019)

The fabella is a sesamoid bone located in the gastrocnemius behind the lateral femoral condyle. In humans, fabellae are 3.5 times more common today than they were 100 years ago, with prevalence rates varying between and within populations. In particular, fabellae have been assumed to be more common in Asians than non-Asians, equally common in men and women, potentially more common in older individuals, and bilateral cases (one per knee) appear to be more common than unilateral ones. The roles of genetic and environmental factors in this phenotypic variation have been hypothesized, but not rigorously investigated. Given its clinical and evolutionary significance (i.e. being associated with several knee ailments, causing medical issues on its own, interfering with medical devices, and being less common in humans than in other mammals), it is important comprehensively to understand prevalence rate variation, and the roles of genetics and environmental factors in that variation. To address these questions, we performed a meta-analysis on data from studies published from 1875 to 2018 to investigate possible variation in sexual dimorphic (n = 22 studies, 7911 knees), ontogenetic (n = 10 studies, 4391 knees), and global (n = 65 studies, 21 626 knees) fabella prevalence rates. In addition, we investigated what proportion of cases are bilateral (n = 37 studies, 900 individuals), and among unilateral cases (n = 20 studies, 204 individuals), if fabellae are more common in the left or right knee. Our results show that, today, fabellae are 2.47-2.60% more common in men than women, and prevalence rates increase ontogenetically in old age (i.e. 70 years old), implying that fabellae can ossify early (i.e. 12 years old) or late in life. Approximately 72.94% of cases are bilateral, and among unilateral ones, fabellae are equally common in right and left knees. There is marked regional variation in fabella prevalence rates, with rates being highest in Asia, followed by Oceania, South America, Europe, Middle East, and North America, and lowest in Africa. Worldwide, an average of 36.80% of knees has ossified fabellae detectable by dissection. These results imply that, while the ability to form a fabella may be genetically controlled, the mechanisms that trigger fabella ossification may be environmentally controlled. What these environmental factors are, can only be speculated.
Thrombotic microangiopathy and graft arteriopathy in pig hearts following transplantation into baboons (2004)

Cardiac xenograft survival in the pig-to-baboon model can be significantly prolonged by vigorous immunosuppressive treatment of recipient animals. Additional efforts to block humoral activation of graft endothelial cells and/or to overcome species-specific molecular coagulation pathway incompatibilities may prevent the development of microvascular thrombosis and myocardial infarction. Cardiac xenograft vasculopathy (chronic rejection) can occur with prolonged graft survival.
The mosaic receptor sorLA/LR11 binds components of the plasminogen-activating system and platelet-derived growth factor-BB similarly to LRP1 (low-density lipoprotein receptor-related protein), but mediates slow internalization of bound ligand (2004)

The type-1 receptor sorLA/LR11, a member of the Vps10p-domain receptor family that also contains domains characterizing members of the LDL (low-density lipoprotein) receptor family, has been shown to induce increased uPAR (urokinase receptor) expression as well as enhanced migration and invasion activities in smooth muscle cells in the presence of PDGF-BB (platelet-derived growth factor-BB). Here we show that sorLA interacts with both components of the plasminogen activating system and PDGF-BB similarly to LRP1 (LDL receptor-related protein/alpha2-macroglobulin receptor), which is an important clearance receptor with established functions in controlling uPAR expression as well as PDGF-BB signalling. In contrast with LRP1, sorLA does not interact with alpha2-macroglobulin, which is a binding protein for several growth factors, including PDGF-BB. By using LRP1-deficient cells transfected with sorLA, we demonstrate that sorLA-bound ligand is internalized at a much lower rate than LRP1-bound ligand, and that sorLA is inefficient in regulating cell surface uPAR expression, which depends on rapid internalization of the ternary complex between urokinase-type plasminogen activator, its type-1 inhibitor, and uPAR. Thus, although overlapping with regard to binding profiles, sorLA is substantially less efficient as a clearance receptor than LRP1. We propose that sorLA can divert ligands away from LRP1 and thereby inhibit both their clearance and signalling events mediated by LRP1.