gebhart/patrepeval huggingface dataset:
Supplementary Table 3 from BAD Phosphorylation Determines Ovarian Cancer Chemosensitivity and Patient Survival (2023)

&lt;p&gt;PDF file - 65KB, BAD pathway signature genes: probe sets representing 47 unique genes comprising a BAD-pathway signature.&lt;/p&gt;
Interactive Tools for Collaborative Architectural Design (2002)

Today's rapidly changing society is continuously developing towards an increased demand for multistakeholder knowledge and influence in the architectural planning and design process. Accordingly, we are working with developing and setting up a partner engaged collaborative design process. It includes active collaboration between users, external partners and designers, and visualizations in conceptual design and scenario building. My research is focusing on integrating visualization technology in theseprocesses by application of digital tools. We have developed a working prototype for an interactive design tool. The prototype is an extremely “easy to use” digital modelling tool called “ForeSite Designer.” With this tool one builds oneis own spatial environment with elements on a 2D surface.With one command the 2D layout is exported to a lit-up 3D/Virtual Reality world in the computer game “Half-Life”. ForeSite Designer has lately been used in a series of workshops together with external users. In these processes ForeSite Designer has played a crucial role as an arena of building spatially arranged concepts of future environments. The results show that it works, and, importantly, promotes a collaborative engagement among the users.
Data-driven modeling and control of an X-ray bimorph adaptive mirror (2022)

Adaptive X-ray mirrors are being adopted on high-coherent-flux synchrotron and X-ray free-electron laser beamlines where dynamic phase control and aberration compensation are necessary to preserve wavefront quality from source to sample, yet challenging to achieve. Additional difficulties arise from the inability to continuously probe the wavefront in this context, which demands methods of control that require little to no feedback. In this work, a data-driven approach to the control of adaptive X-ray optics with piezo-bimorph actuators is demonstrated. This approach approximates the non-linear system dynamics with a discrete-time model using random mirror shapes and interferometric measurements as training data. For mirrors of this type, prior states and voltage inputs affect the shape-change trajectory, and therefore must be included in the model. Without the need for assumed physical models of the mirror's behavior, the generality of the neural network structure accommodates drift, creep and hysteresis, and enables a control algorithm that achieves shape control and stability below 2 nm RMS. Using a prototype mirror and ex situ metrology, it is shown that the accuracy of our trained model enables open-loop shape control across a diverse set of states and that the control algorithm achieves shape error magnitudes that fall within diffraction-limited performance.
Huntington disease in Finland: linkage disequilibrium of chromosome 4 RFLP haplotypes and exclusion of a tight linkage between the disease and D4S43 locus. (1990)

The question about heterogeneity of Huntington disease (HD) at the DNA level can be approached by analyzing the RFLP haplotypes formed by several RFLP loci of the diseased chromosome in different populations. In genetically isolated populations such as Finland, it is further possible to use this approach to test the hypothesis of a single mutation enriched in this population demonstrating an exceptionally low prevalence of HD. In this study covering 70% of all diagnosed HD cases in Finland, linkage disequilibrium of RFLP haplotypes of D4S10 and D4S43 loci polymorphisms was found. This phenomenon, not so far reported in any other population, could support the hypothesis of one ancestor HD mutation in the Finnish population. Despite the lower heterozygosity obtained with some RFLP markers, the proportion of individuals receiving informative DNA test results did not significantly differ from that reported in more mixed populations. In one HD family we established a recombination event between HD and the D4S43 locus, an event which can be highly useful in the more precise mapping of the HD gene.
On-Body Bluetooth Link Budget: Effects of Surrounding Objects and Role of Surface Waves (2007)

Bluetooth is very popular to be used in mobile handsets for short range data transfers. Evolution of Bluetooth headsets has added to its popularity and made it an essential part of wireless body area networks (WBAN) and wireless personal area networks (WPAN) notably the cellular phones. Human body is the integral part of such applications and affects their performance due to its lossy nature. This paper investigates the effects of human body and the surrounding objects on the Bluetooth link budget of a mobile handset antenna and Bluetooth headset antenna. A thorough analysis is carried out to demonstrate the importance of surface waves in the on-body Bluetooth link.
Levels Of Expression And Immunogenicity Of Attenuated Salmonella Enterica Serovar Typhimurium Strains Expressing Escherichia Coli Mutant Heat- Labile Enterotoxin (1998)

The effects of heterologous gene dosage as well as Salmonella typhimurium strain variability on immune response toward both the heterologous antigen, the nontoxic mutant of the Escherichia coli heat-labile enterotoxin LTK63, and the carrier Salmonella strain have been analyzed. Effects of a single integration into the host DNA and different-copy-number episomal vectors were compared in S. typhimurium Îcya Îcrp Îasd strains of two different serotypes, UK-1 and SR-11. Expression of the enterotoxin in the different Salmonella isolates in vitro was found to vary considerably and, for the episomal vectors, to correlate with the plasmid copy number. LTK63-specific serum immunoglobulin G (IgG) and mucosal immunoglobulin A (IgA) antibodies were highest in mice immunized with the high-level-expression strain. High anti-LTK63 IgG and IgA titers were found to correspond to higher anti-Salmonella immunity, suggesting that LTK63 exerts an adjuvant effect on response to the carrier. Statistically significant differences in anti-LTK63 immune response were observed between groups of mice immunized with the attenuated Îcya Îcrp UK-1 and SR-11 derivatives producing the antigen at the same rate. These data indicate that the same attenuation in S. typhimurium strains of different genetic backgrounds can influence significantly the immune response toward the heterologous antigen. Moreover, delivery of the LTK63 enterotoxin to the immune system by attenuated S. typhimurium strains is effective only when synthesis of the antigen is very high during the initial phase of invasion, while persistence of the S. typhimurium strain in deep tissues has only marginal influence.
A Potent, Orally Bioavailable Benzazepinone Growth Hormone Secretagogue (1998)

The identification of L-739,943 (8b), a potent, orally bioavailable benzolactam growth hormone secretagogue, is obtained from zwitterionic L-692,429 through modification of its amino acid side chain and replacement of the acidic 2'-tetrazole with the neutral and potency enhancing 2'-(N-methylaminocarbonylamino)methyl substituent. L-739,943 is orally active for the release of growth hormone in beagle dogs at doses as low as 0.5 mg/kg. Oral bioavailability in dogs of 8b is 24% at a dose of 2 mg/kg with a mean drug Cmax of 145 +/- 46 ng/mL. L-739,943 represents a significant breakthrough in terms of both potency and oral bioavailability as compared to the prototype benzolactam L-692,429.
Numerical Study of a Solar Thermophotovoltaic Energy Converter With High Performance 2D Photonic Crystals (2012)

Solar thermophotovoltaic (STPV) systems convert solar energy into electricity via thermally radiated photons at tailored wavelength to increase energy conversion efficiency. In this work we report the design and analysis of a STPV using a high- fidelity 2D axisymmetric thermal-electrical hybrid model that includes thermal coupling between the absorber/emitter/PV cell and accounts for non-idealities such as temperature gradients and parasitic thermal losses. The radiative spectra of the absorber and emitter are engineered by using two-dimensional periodic square array of cylindrical holes on a tantalum (Ta) substrate. The optimal solar concentration and resulting temperature are determined by considering the energy losses associated with re-emission at the absorber, low energy (below band gap) emission at the emitter, and carrier thermalization /recombination in the PV cell. The modeling results suggest that the overall efficiency of a realistic planar STPV consisting of Ta PhCs and existing InGaAsSb PV cells with a filter can be as high as ~8%. The use of high performance PhCs allows us to simplify the system layout and operate STPVs at a significantly lower optical concentration level and operating temperature compared with STPVs using metallic cavity receivers. This work shows the importance of photon engineering for the development of high efficiency STPVs and offers design guidelines for both the PhC absorber/emitter and the overall system.
Récupération d'Energie Biomécanique et Systèmes Autonomes (2014)

National audience
Fhit–Fdxr interaction in the mitochondria: modulation of reactive oxygen species generation and apoptosis in cancer cells (2019)

Fhit protein is lost in cancers of most, perhaps all, cancer types; when restored, it can induce apoptosis and suppress tumorigenicity, as shown in vitro and in mouse tumor models in vivo. Following protein cross-linking and proteomics analyses, we characterized a Fhit protein complex involved in triggering Fhit-mediated apoptosis. The complex includes the heat-shock chaperonin pair, HSP60/10, which is likely involved in importing Fhit into the mitochondria, where it interacts with ferredoxin reductase, responsible for transferring electrons from NADPH to cytochrome P450 via ferredoxin, in electron transport chain complex III. Overexpression of Fhit protein in Fhit-deficient cancer cells modulates the production of intracellular reactive oxygen species, causing increased ROS, following peroxide treatment, with subsequent increased apoptosis of lung cancer cells under oxidative stress conditions; conversely, Fhit-negative cells escape ROS overproduction and ROS-induced apoptosis, likely carrying oxidative damage. Thus, characterization of Fhit-interacting proteins has identified direct effectors of a Fhit-mediated apoptotic signal pathway that is lost in many cancers. This is of translational interest considering the very recent emphasis in a number of high-profile publications, concerning the role of oxidative phosphorylation in the treatment of human cancers, and especially cancer stem cells that rely upon oxidative phosphorylation for survival. Additionally, we have shown that cells from a Fhit-deficient lung cancer cell line, are sensitive to killing by exposure to atovaquone, thought to act as a selective oxidative phosphorylation inhibitor by targeting the CoQ10 dependence of the mitochondrial complex III, while the Fhit-expressing sister clone is resistant to this treatment.
Antagonism of Fipronil Toxicity by Piperonyl Butoxide and S, S, S-Tributyl Phosphorotrithioate in the German Cockroach (Dictyoptera: Blattellidae) (1997)

Toxicity of the phenylpyrazole insecticide fipronil was determined in laboratory and field-collected strains of the German cockroach, Blattella gennanica (L.). Fipronil effectively killed German cockroaches when applied in nanogram quantities. Orlando (insecticide susceptible), HRDC (carbamate- and organophosphorus-resistant), and Village Green (pyrethroid-resistant) strains were equally susceptible to fiproni with LD50 values between 4.6 and 5.4 nanograms per insect. The Marietta strain (pyrethroid-, organophosphorus-, and carbamateresistant) was 1.6 times more tolerant of fipronil compared with the Orlando susceptible strain. Five German cockroach strains collected from the field were considerably more tolerant of fipronil than Marietta cockroaches. Piperonyl butoxide and S, S, S-tributyl phosphorotrithioate antagonized the toxicity of fipronil in all strains evaluated. Fipronil was 2.2-3 times less toxic when cockroaches were pretreated with piperonyl butoxide or S, S, S-tributyl phosphorotrithioate compared with fipronil alone. These data suggest that fipronil is metabolically activated in German cockroaches, possibly via sulfone formation catalyzed by microsomal oxidases.
Brutus (2009)

We describe a semantic role labeling system that makes primary use of CCG-based features. Most previously developed systems are CFG-based and make extensive use of a treepath feature, which suffers from data sparsity due to its use of explicit tree configurations. CCG affords ways to augment treepathbased features to overcome these data sparsity issues. By adding features over CCG wordword dependencies and lexicalized verbal subcategorization frames ("supertags"), we can obtain an F-score that is substantially better than a previous CCG-based SRL system and competitive with the current state of the art. A manual error analysis reveals that parser errors account for many of the errors of our system. This analysis also suggests that simultaneous incremental parsing and semantic role labeling may lead to performance gains in both tasks.
Induction of Interleukin‐6 Production by Rituximab in Human B Cells (2014)

RTX-mediated trogocytosis of B cells in vitro results in acute production and release of IL-6. The nature of this effect and how it is related to the acute infusion reactions seen with RTX administration remain to be determined.
Supplementary Figure S17 from Evolution of Castration-Resistant Prostate Cancer in ctDNA during Sequential Androgen Receptor Pathway Inhibition (2023)

&lt;p&gt;Supplementary Figure S17 provides whole exome somatic mutation profiles in patients that did not show temporal changes in 72-gene panel mutation profiles&lt;/p&gt;
Abstract 5161:β 1 (Arg389Gly, Ser49Gly)- and β2 (Arg16Gly) -adrenoceptor Polymorphisms are Related to Left Ventricular Hypertrophy in Middle-aged, Nonobese, Normotensive Men, but Through Different Mechanisms (2008)

Objective: β2-adrenoceptor (ADRB2) polymorphisms are closely linked to hypertension and obesity, and both of them are major cardiac risk. Left ventricular hypertrophy (LVH) is more common in people who have hypertension or obesity. We examined the relationships between ADRB1 and ADRB2 polymorphisms and LVH in nonobese, normotensive subjects. Methods: In 447 middle-aged, normotensive, nonobese men, ADRB1 (Arg389Gly, Ser49Gly) and ADRB2 (Arg16Gly, Gln27Glu) polymorphisms, BMI, BP, heart rates (HR), total body fat-mass, waist-to-hip ratio (W/H), plasma norepinephrine (NE) and ECG were measured after overnight fasting in the supine position. LVH was determined by ECG. Results: Thirty-nine subjects (8.7%) showed LVH on ECG. Subjects with LVH had higher plasma NE and HR compared to those without LVH (both P&lt;.05). Distributions of Gly389 and Gly49 alleles of ADRB1 polymorphisms were 23.5% (Arg/Arg:Arg/Gly:Gly/Gly=270:144:33) and 14.1% (Ser/Ser:Ser/ Gly:Gly/Gly=327:114:6). Thirty-seven subjects with LVH (94.9%) carried Gly389 and Gly49 alleles, especially homozygous for Gly389 or Gly49. Subjects with Gly389 or Gly49 alleles had higher frequencies of LVH (20.9% vs. 0.7%, 30.8% vs. 0.6%). Subjects carrying Gly389 or Gly49 alleles had higher plasma NE and HR (both P&lt;.05), whereas BMI, fat mass, W/H and BP were similar. The Gly16 and Glu27 alleles of ADRB2 polymorphisms were noted in 42.8% (Arg/Arg :Arg/Gly:Gly/Gly=69:245:133) and 36.6% of the subjects (Gln/Gln:Gln/Glu:Glu/ Glu=176:215:56). Twenty-nine subjects with LVH (74.4%) carried Gly16 allele, especially Gly16 homozygous. Subjects with Gly16 allele had higher frequencies of LVH (P&lt;.05), and they had greater BMI, fat mass, W/H, BP, HR and NE compared to those without Gly16 allele (all P&lt;.05). Conclusions: Subjects carrying Gly389 and Gly49 alleles of ADRB1 polymorphisms and Gly16 allele of ADRB2 polymorphism had higher frequency of LVH accompanying high plasma NE. ADRB1 and ADRB2 polymorphisms play important roles in LVH even in nonobese, normotensive subjects. ADRB1 polymorphisms might relate to LVH through heightened sympathetic nerve activity, but ADRB2 polymorphisms might relate to LVH through obesity, hypertension and heightened sympathetic nerve activity.
A Switched-Capacitor Integer Compute Unit with Decoupled Storage and Arithmetic for Cloud AI Inference in 5nm CMOS (2023)

This paper presents a switched-capacitor-based integer compute unit in 5nm CMOS that is designed as a drop-in replacement for an equivalent digital unit to improve power efficiency by 2. 5X. Integer multiply-accumulate (MAC) operations are recast as a scaled sum of l-b MACs, where each l-b MAC is performed using a population counter (PPCTR) circuit. Each PPCTR is an enhanced SAR ADC that performs l-b multiplication, D-A conversion, accumulation, and A-D conversion with no loss of precision. The compute unit has 4864 PPCTRs arranged as 64 processing engines, with a total throughput of 104.9 TOPS and 650 TOPS/W power efficiency for l-b MACs.
Cherenkov radiation fluence estimates in tissue for molecular imaging and therapy applications (2015)

Cherenkov radiation has recently emerged as an interesting phenomenon for a number of applications in the biomedical sciences. Its unique properties, including broadband emission spectrum, spectral weight in the ultraviolet and blue wavebands, and local generation of light within a given tissue, have made it an attractive new source of light within tissue for molecular imaging and phototherapy applications. While several studies have investigated the total Cherenkov light yield from radionuclides in units of [photons/decay], further consideration of the light propagation in tissue is necessary to fully consider the utility of this signal in vivo. Therefore, to help further guide the development of this novel field, quantitative estimates of the light fluence rate of Cherenkov radiation from both radionuclides and radiotherapy beams in a biological tissue are presented for the first time. Using Monte Carlo simulations, these values were found to be on the order of 0.01-1 nW cm(-2) per MBq g(-1) for radionuclides, and 1-100 μW cm(-2) per Gy s(-1) for external radiotherapy beams, dependent on the given waveband, optical properties, and radiation source. For phototherapy applications, the total light fluence was found to be on the order of nJ cm(-2) for radionuclides, and mJ cm(-2) for radiotherapy beams. The results indicate that diagnostic potential is reasonable for Cherenkov excitation of molecular probes, but phototherapy may remain elusive at such exceedingly low fluence values. The results of this study are publicly available for distribution online at www.dartmouth.edu/optmed/.
Structure-Function Studies of the Lustrin A Polyelectrolyte Domains, RKSY and D4 (2003)

The lustrin superfamily represents a unique group of biomineralization proteins localized between layered aragonite mineral plates (i.e., nacre layers) in mollusk shell. These proteins not only exhibit elastomeric behavior within the mineralized matrix, but also adhesion to the aragonite-containing composite layer. One member of the lustrin superfamily, Lustrin A, has been sequenced; the protein is organized into defined, modular sequence domains that are hypothesized to perform separate functions (i.e., force unfolding, mineral adhesion, intermolecular binding) within the Lustrin A protein. Using nuclear magnetic resonance (NMR) and in vitro mineralization assays, we investigated structure-function relationships for two Lustrin A putative mineral binding domains, the 30 AA Arg, Lys, Tyr, Ser-rich (RKSY) and the 24 AA Asp-rich (D4) sequence regions domain of the Lustrin A protein. The results indicate that both sequences adopt open, unfolded structures that represent either extended or random coil states. Using geologic calcite overgrowth assays and scanning electron microscopic analyses, we observe that the RKSY polypeptide does not significantly perturb calcium carbonate growth. However, the D4 domain does influence crystal growth in a concentration-dependent manner. Collectively, our data indicate that D4, and not the RKSY domain, exhibits structure-function activity consistent with a mineral binding region.
Outdoor Measurements Using an Optical Wireless Link for Fixed-Access Applications (2018)

In this paper, results are presented from a long-term outdoor field trial using a rate-adaptive, LED-based optical wireless link over 100 m rooftop-to-rooftop distance. The optical link is installed in parallel to a 60 GHz link, enabling a direct comparison of both technologies for the same conditions by logging signal-to-noise ratios, data rates, and weather conditions. A model for the optical link has been developed for performance prediction based on weather data. Besides studying particular weather events, an analysis was conducted for the whole statistics. Results indicate that availability of the optical link was higher than 99.99%, despite severe weather conditions due to fog, rain, and snow. Although both links offer several hundred megabit per second, the optical link has a higher data rate 99.8% of the time while the 60 GHz link has a more consistent performance. Correlation is weak in bad weather conditions, e.g., if the SNR is low for the 60 GHz link due to heavy rain, the SNR in the optical link is high as the fog is light at the same time. Further measurements verify low latencies in the millisecond to sub-millisecond range for the optical link. Results indicate that the optical link is a promising low-cost solution for fixed access applications such as the replacement of fiber on the last 100 m to the end user, also denoted as wireless-to-the-home, and as a backhaul for Wi-Fi and small mobile radio cells.
Longitudinal Resting State Functional Connectivity Predicts Clinical Outcome in Mild Traumatic Brain Injury (2018)

Mild traumatic brain injury (mTBI) affects about 42 million people worldwide. It is often associated with headache, cognitive deficits, and balance difficulties but rarely shows any abnormalities on conventional computed tomography (CT) or magnetic resonance imaging (MRI). Although in most mTBI patients the symptoms resolve within 3 months, 10-15% of patients continue to exhibit symptoms beyond a year. Also, it is known that there exists a vulnerable period post-injury, when a second injury may exacerbate clinical prognosis. Identifying this vulnerable period may be critical for patient outcome, but very little is known about the neural underpinnings of mTBI and its recovery. In this work, we used advanced functional neuroimaging to study longitudinal changes in functional organization of the brain during the 3-month recovery period post-mTBI. Fractional amplitude of low frequency fluctuations (fALFF) measured from resting state functional MRI (rs-fMRI) was found to be associated with symptom severity score (SSS, r = -0.28, p = 0.002). Decreased fALFF was observed in specific functional networks for patients with higher SSS, and fALFF returned to higher values when the patient recovered (lower SSS). In addition, functional connectivity of the same networks was found to be associated with concurrent SSS, and connectivity immediately after injury (<10 days) was capable of predicting SSS at a later time-point (3 weeks to 3 months, p < 0.05). Specific networks including motor, default-mode, and visual networks were found to be associated with SSS (p < 0.001), and connectivity between these networks predicted 3-month clinical outcome (motor and visual: p < 0.001, default-mode: p < 0.006). Our results suggest that functional connectivity in these networks comprise potential biomarkers for predicting mTBI recovery profiles and clinical outcome.