gebhart/patrepeval huggingface dataset:
Bioenergetic deficits in Huntington’s disease iPSC-derived neural cells and rescue with glycolytic metabolites (2019)

Altered cellular metabolism is believed to be an important contributor to pathogenesis of the neurodegenerative disorder Huntington's disease (HD). Research has primarily focused on mitochondrial toxicity, which can cause death of the vulnerable striatal neurons, but other aspects of metabolism have also been implicated. Most previous studies have been carried out using postmortem human brain or non-human cells. Here, we studied bioenergetics in an induced pluripotent stem cell-based model of the disease. We found decreased adenosine triphosphate (ATP) levels in HD cells compared to controls across differentiation stages and protocols. Proteomics data and multiomics network analysis revealed normal or increased levels of mitochondrial messages and proteins, but lowered expression of glycolytic enzymes. Metabolic experiments showed decreased spare glycolytic capacity in HD neurons, while maximal and spare respiratory capacities driven by oxidative phosphorylation were largely unchanged. ATP levels in HD neurons could be rescued with addition of pyruvate or late glycolytic metabolites, but not earlier glycolytic metabolites, suggesting a role for glycolytic deficits as part of the metabolic disturbance in HD neurons. Pyruvate or other related metabolic supplements could have therapeutic benefit in HD.
Regulation of pathways of extramitochondrial fatty acid oxidation and liver fatty acid-binding protein by long-chain monocarboxylic fatty acids in hepatocytes. Effect of inhibition of carnitine palmitoyltransferase I. (1993)

The regulation of the extramitochondrial fatty acid oxidation pathways located in the peroxisomes and the endoplasmic reticulum is not fully understood. Although both long-chain dicarboxylic fatty acids, which are poorly metabolized in hepatocytes, and non-beta-oxidizable fatty acid analogs induce peroxisomal beta-oxidation and liver fatty acid-binding protein (L-FABP) by a pretranslational mechanism, monocarboxylic long-chain fatty acids, which are rapidly esterified and oxidized, do not. To establish whether impaired utilization and, hence, sustained intracellular levels of monocarboxylic long-chain fatty acids increase their efficacy as inducers, the effect of oleic acid on cytochrome P-450 4A1, peroxisomal beta-oxidation, and L-FABP during inhibition of mitochondrial beta-oxidation was determined. In primary hepatocyte cultures, oleic acid had no inducing effect, but in the presence of 2-tetradecylglycidic acid (TDGA), an inhibitor of carnitine palmitoyltransferase I, it induced P-450 4A1, peroxisomal beta-oxidation, and L-FABP pretranslationally. An increase in peroxisomal beta-oxidation was also noted in the presence of etomoxir, another inhibitor of carnitine palmitoyltransferase I. Exposure of hepatocytes to TDGA for 1 h led to an expected decrease in incorporation of radiolabel from [1-14C]oleate into CO2 and water-soluble products. In contrast, long-term exposure to TDGA increased incorporation of [1-14C]oleate into oxidation products, most likely due to an adaptive induction of peroxisomal beta-oxidation. Both acute and long-term exposure of hepatocytes to TDGA decreased incorporation of oleic acid into triglycerides, an effect that may have contributed to the intracellular accumulation of fatty acids. These results provide support for a mechanism by which long-chain fatty acids or specific metabolites, including long-chain acyl-CoA esters and long-chain dicarboxylic acids, act as signals in the induction of P-450 4A1, peroxisomal beta-oxidation, and L-FABP under conditions in which long-chain fatty acids accumulate due to impaired entry into the mitochondrial beta-oxidation pathway.
Measuring Electric Fields Produced by MRI Gradient Coils Using a Patch Antenna Probe (2020)

As a part of this work a small patch antenna probe was developed to measure the variation in the electric field produced by gradient coils within an MRI in the presence of any active implantable medical devices (AIMDs). This probe was designed, fabricated, and tested within a gradient coil mimicking dB/dt exposure platform. A 2×1 cm small patch antenna followed by an instrumentational amplifier was chosen to measure the electric fields. Probe was fabricated using a 4-layer PCB. The fabricated probe was used to monitor the electric fields within the phantom in the gradient coil environment. To verify the observed behavior of the probe a simulation study was performed using Sim4Life. This study aims to assess the performance of this probe in a tissue mimicking environment within the coil.
Response Mechanism of Polymeric Liquid Junction-Free Reference Electrodes Based on Organic Electrolytes (2023)

To achieve a transition from conventional liquid-junction reference electrodes (LJF REs) to their all-solid-state alternatives, organic electrolytes are often introduced into the polymeric electrode membranes. In this article, we implement a theoretical approach to the explanation and quantification of the boundary potential stabilization phenomenon for the electrodes modified with organic electrolytes (Q<sup>+</sup>B<sup>-</sup>). For the first time, stabilization of the phase boundary potential due to the partition of lipophilic ions of the Q<sup>+</sup>B<sup>-</sup> electrolyte between the polymeric and aqueous phases is numerically simulated to predict the LJF electrodes behavior. The impact of the hydrophilic electrolyte on the potential stabilization is demonstrated both numerically and experimentally. The developed model predicted that the small additions of a traditional ion-exchanger enhance performance of the Q<sup>+</sup>B<sup>-</sup>-based reference electrodes. For some specific cases, the optimal concentrations of Q<sup>+</sup>B<sup>-</sup> and ion-exchanger in the polymeric phase are suggested to provide stable electrode potential in a broad range of aqueous electrolyte concentrations. In addition, the efficiency of the stabilization was shown to be dependent on the overall Q<sup>+</sup>B<sup>-</sup> load in the polymeric membrane rather than on the closeness of the partition coefficients of the Q<sup>+</sup> and B<sup>-</sup> ions; and on the volume of the aqueous phase. The model results are verified experimentally with poly(vinyl chloride) membranes containing ion-exchanger or hydrophilic electrolyte and Q<sup>+</sup>B<sup>-</sup> in various proportions. A good agreement between the measured electrode response and the theoretical results is observed in a broad range of solution concentrations. In particular, the cationic function of membranes containing KTpClPB is suppressed, and the electrodes begin to behave as REs starting from 50-60 mol. % of ETH500 electrolyte added to the membrane, relative to the total amount of salt.
Targeted Learning with Application to Health Care Research (2018)

Targeted learning (TL) is a paradigm for transforming data into reliable, actionable knowledge. The TL estimation roadmap describes a series of steps for expressing the substantive goal in terms of a parameter of the distribution of the data, and then estimating that statistical parameter from data. TL relies on two core analytic estimation methodologies. Super learning (SL) is a data-adaptive ensemble machine learning algorithm for predictive modeling. Targeted minimum loss-based estimation (TMLE) is an efficient double-robust semi-parametric substitution estimator. TL is built upon a theoretical foundation that incorporates machine learning into statistical analysis while preserving the ability to quantify uncertainty in the parameter estimate. TL has been applied in a broad range of health care settings that include risk prediction and estimation of causal and non-causal effects. This chapter describes the roadmap and offers a primer on SL and TMLE in the context of point treatment and longitudinal data analyses. Applications to mortality risk prediction, variable importance ranking, estimating the effects of point treatments, and parameters of a marginal structural model for longitudinal data analyses illustrate how TL is currently being used in practice. Promising directions for future research are also described.
Optimized multistandard RF subsampling radio receiver design (2005)

This paper presents an improved topology design at RF system architecture level for multi-standard radio receiver based on RF subsampling technique. By limiting downconversion to IF domain, a single path for RF signal analogue processing is used avoiding circuit complexities and allowing software-based IF processing in DSP stage. This ensures required configurability for multimode operation with high-level integration. This work is also addressing the choice of sampling frequency for the track and hold circuit control by considering aliasing and noise constraints. Simulation results of optimized sampling frequency are presented for a multi-standard radio receiver designed for GSM, UMTS and IEEE-802.11g.
Front Cover: Optimization of Pyrazoles as Phenol Surrogates to Yield Potent Inhibitors of Macrophage Migration Inhibitory Factor (ChemMedChem 11/2018) (2018)

The Front Cover reflects the optimization of inhibitors of the tautomerase activity of macrophage migration inhibitory factor (MIF) that feature a 4-phenylpyrazole core. Starting from a weak docking hit (113 μM) at the bottom left of the gauge, structure-based and computer-aided design led to inhibitors of increasing potency, finally yielding the 67 nM biphenyl analog on the far right. Four crystal structures of complexes are reported, including the illustrated one for the 2-naphthyl analog. Cover artwork by V. Trivedi-Parmar and M. J. Robertson. More information can be found in the Communication by William L. Jorgensen et al. on page 1092 in Issue 11, 2018 (DOI: 10.1002/cmdc.201800158).
Restricting the Solubility of Polysulfides in Li‐S Batteries Via Electrolyte Salt Selection (2016)

Lithium 2-trifluoromethyl-4,5-dicyanoimidazole as a supporting salt in electrolytes achieves a reduced Li2S8 solubility by tuning the chemical production to Li4S8 dimer. Ab initio molecular dynamics and nuclear magnetic resonance calculation confirms the solvation structure radius increase by 20%. Combined with Li2S8 and LiNO3, the electrolyte can demonstrate a stable 300 cycling battery of practical sulfur loading. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Gibbs Sampler Based Control of Autonomous Vehicle Swarms in the Presence of Sensor Errors (2006)

In earlier work of the authors (Baras and Tan, 2004 and Xi et al., 2005) it was shown that Gibbs sampler based annealing algorithms could be used for vehicle swarms to achieve self-organization. Nevertheless, the earlier convergence analyses were based on the assumption that the Gibbs potential can be precisely evaluated. In practice, Gibbs potentials have to be measured via sensors, which usually introduce errors. The robustness of the stochastic algorithm under sensor errors is studied in this paper. Two types of sensor error, range-error and random-error, are investigated. Analytical results on convergence are derived for sensor errors with limited support, and are further validated through simulations
Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children (2018)

The cystic fibrosis (CF) lung microbiome has been studied in children and adults; however, little is known about its relationship to early disease progression. To better understand the relationship between the lung microbiome and early respiratory disease, we characterized the lower airways microbiome using bronchoalveolar lavage (BAL) samples obtained from clinically stable CF infants and preschoolers who underwent bronchoscopy and chest computed tomography (CT). Cross-sectional samples suggested a progression of the lower airways microbiome with age, beginning with relatively sterile airways in infancy. By age two, bacterial sequences typically associated with the oral cavity dominated lower airways samples in many CF subjects. The presence of an oral-like lower airways microbiome correlated with a significant increase in bacterial density and inflammation. These early changes occurred in many patients, despite the use of antibiotic prophylaxis in our cohort during the first two years of life. The majority of CF subjects older than four harbored a pathogen dominated airway microbiome, which was associated with a further increase in inflammation and the onset of structural lung disease, despite a negligible increase in bacterial density compared to younger patients with an oral-like airway microbiome. Our findings suggest that changes within the CF lower airways microbiome occur during the first years of life and that distinct microbial signatures are associated with the progression of early CF lung disease.
Routing-aware scan chain ordering (2003)

Scan chain insertion can have a large impact on routability, wirelength and timing of the design. We present a routing-driven methodology for scan chain ordering with minimum wirelength objective. A routing-based approach to scan chain ordering, while potentially more accurate, can result in TSP (Traveling Salesman Problem) instances which are asymmetric and highly non-metric; this may require a careful choice of solvers. We evaluate our new methodology on recent industry place-and-route blocks with 1200 to 5000 scan cells. We show substantial wirelength reductions for the routing-based flow, versus the traditional placement-based flow: in a number of our test cases, over 86% of scan routing overhead is saved. Even though our experiments are so far timing-oblivious, the routing-based flow does also improve evaluated timing, and practical timing-driven extensions appear feasible.
DOMESTIC CONSUMER AWARENESS OF ENERGY CONSUMPTION PRACTICES IN PAKISTAN (2021)

Electricity waste is a bottleneck in availing clean, green, uninterrupted, and sustainable electricity supply. The synthesis of the studied literature portrays that irresponsible behavior indulges consumers to take irresponsible action, which leads to electricity waste and crisis. Therefore, to get the know-how of irresponsible behavior, this study aims to investigate the role of awareness concerning electricity consumption, wastage, gadget efficiency, and conservation. A questionnaire-focused survey was carried out to collect data and performed descriptive analysis to critically evaluate the data. The results explicate that consumers possess a low level of wasteful consumption awareness and “lack-of-information” is a big issue in waste management. Thus, the study concludes that unawareness is the key determinant that creates and strengthens a sense of irresponsibility in consumer behavior. The academician and practitioners need dire attention to take precautionary measures for developing prominent awareness campaigns and strategic policy guidelines to distort irresponsible human nature by including fearful promotional contents in marketing campaigns. Keywords: Electricity Awareness, Electricity Conservation, Electricity Efficiency, Electricity Waste, Irresponsible Behavior, Electricity Crisis JEL Classifications: Q4, Q40, D1 DOI: https://doi.org/10.32479/ijeep.11441
A Figure of Merit Based Transmitter Link Penalty Calculation for CMOS-Compatible Plasma-Dispersion Electro-Optic Mach-Zehnder Modulators (2012)

We derive equations that quantify silicon Mach-Zehnder Interferometer (MZI) modulator impact upon optical link budget for NRZ transmissions based solely upon modulator extinction ratio (ER), the efficiency-loss figure of merit (FOM), and peak-to-peak drive voltage (Vpp). Our modulator link penalty equations transform the modulator efficiency-loss FOM from a simple device quality metric into a means of predicting how design and technology choices impact system margin. Our results indicate that, with a 17.8 V-cm FOM and 1 Vpp drive, designing an MZI to have an ER anywhere within the large range from 3.5-10 dB leads to nearly constant link margins, identical to within 0.5 dB.
PET Amyloid Imaging with Florbetapir Predicts Cognitive Decline in the Oldest-Old (P4.011) (2014)

OBJECTIVE: To determine if amyloid burden measured by florbetapir-PET predicts cognitive decline in oldest-old participants. BACKGROUND: PET Amyloid imaging has shown to identify younger elderly individuals at higher risk of cognitive decline, but it is unknown if this relationship persists in the oldest-old, people aged 90 and over, where the correlation between cerebral amyloid and cognition is poor. DESIGN/METHODS: The study included 33 participants from the 90+ Study, a longitudinal investigation of the oldest-old. Participants underwent florbetapir-PET imaging within 3 months of baseline neuropsychological testing including the Modified Mini-Mental State exam, California Verbal Learning Test 10-minute delay, animal fluency, and Trails A and B. Test scores were z-transformed using age-specific norms and a composite neuropsychological score was computed by averaging the z-scores. Neuropsychological testing was repeated every 6 months. Amyloid load was measured as a semi-automated quantitative analysis of cortical-to-cerebellar standardized uptake value ratio (SUVr) averaged over 6 cortical brain regions (frontal, temporal, parietal, anterior and posterior cingulate, and precuneus). SUVrs were dichotomized as Aβ+ and Aβ− (cut-point=1.2). Average rate of change in the composite neuropsychological score was compared in participants with Aβ+ and Aβ− scans using t-test and Wilcoxon rank test. RESULTS: At scanning time, participants were on average 95 years (range: 91-101) and 67% were women. There were 19 normal, 13 cognitively impaired, and 1 participant with dementia. Thirty percent of participants had Aβ+ scans. Median follow-up was one year (range=0.5-1.6 years). Rate of decline in the composite neuropsychological score was faster in individuals with Aβ+ scans (-0.32 SD/year) compared to those with Aβ− scans (+0.21 SD/year) [t=1.99, p=0.06; Wilcoxon rank p=0.02]. CONCLUSIONS: Despite advanced age of our participants, these results support previous observations from younger elderly that high amyloid burden on florbetapir-PET can identify oldest-old individuals at high risk of cognitive decline. Study Supported by: NIH-NIA grant R01AG21055 and AVID Radiopharmaceuticals, a wholly-owned subsidiary of Eli Lilly and Company.
Trends in prescribing of psychotropic medications for inpatient adolescents in Israel: A 10 years retrospective analysis (2011)

We examined the trends in prescribing psychotropic drugs to children and adolescents within an inpatients adolescent psychiatric ward in Israel. Data of 414 subjects, ranging from 12- to 22-year-old, covering the years 1997, 2002 and 2007, was examined retrospectively. Analyzed variables included the number and type of drug prescriptions per patient at discharge, the subjects' age at discharge and the number of diagnoses per patient at discharge. Analysis of variance (ANOVA) with repeated measures was used to evaluate changes between the three calendar years, along the 10-year study period, while Pearson χ(2) test was performed for categorical variables. Over the study period the mean age at discharge decreased significantly, by about a year and a half, the mean number of diagnoses increased significantly, from 1.6 to 2.4 diagnoses per patient and the total number of drugs prescribed at discharge increased significantly from 1.48 to 1.93 per patient. Overall, the number of patients who were prescribed mood stabilizers increased by 14%, those who were prescribed antidepressants increased by almost 24%, almost 16% in antipsychotics prescriptions and 51.5% in prescriptions of atypical antipsychotics. Typical antipsychotic prescriptions decreased by 35.5% and accordingly, the number of patients who were prescribed agents for the treatment of extra-pyramidal side effects decreased by almost 24%. Due to a low number of inpatients with attention deficit and hyperactivity disorder (ADHD), no significant statistical conclusion could be drawn regarding trends in psychostimulant prescriptions. Our findings agree with other published studies from the last two decades. The growing use of psychotropic agents in children and adolescents merit a continuous concern with regard to their effects on the developing brain and impact on quality of life and to authorizing these drugs for use in specific young age subgroups.
Estimation of the velocity and trajectory of three-dimensional reaching movements from non-invasive magnetoencephalography signals (2013)

These results imply that disabled people will be able to control prosthetic devices without surgery in the near future.
Optimization and Dose Reduction in Hybrid Imaging: PET/CT and SPECT/CT (2018)

Hybrid imaging with PET/CT or SPECT/CT systems is performed for a variety of tasks from diagnosis to treatment monitoring over a wide range of clinical applications including oncology, neurology, cardiology, and musculoskeletal imaging. With these systems, the patient is exposed to ionizing radiation from both the administered radiopharmaceutical and the CT component. This work describes the radiation dosimetry aspects of PET/CT and SPECT/CT systems in an effort to inform appropriate protocol design. In general, acquisition protocols should be task-, application-, and patient-specific in order to generate clinical information with sufficient performance at a minimal level of risk.
Bicyclononynes: New Ring-Strained Alkynes for Bioorthogonal Labeling (2011)

New bicyclo[6.1.0]nonyne (BCN) ring-strained alkynes (e.g. endo- 2) are readily ­accessible, stable, and exhibit excellent kinetics in metal-free alkyne-azide and alkyne-nitrone ­cycloadditions (3, 4). The C s symmetry of BCN simplifies NMR analysis and produces a single ­regioisomer upon cycloaddition.
Configurable spectral filter with an array of diffraction grating (2004)

This paper presents the design, fabrication, and characterization of a configurable diffractive filter capable of high optical resolution within a narrow spectral range. Based on measurements of spectral reflectance from this device, and from corresponding set of fixed diffractive elements, this type of spectral filter is well suited for spectroscopy applications.
Differential Association of Serum Lipids with Diabetic Retinopathy and Diabetic Macular Edema (2011)

Serum lipids are independently associated with the CSME, but not with DR, mild or moderate DME, or macular thickness. These data reflect the different impact of hyperlipidemia in the pathogenesis of DR and DME and may explain the discrepancies in previous studies.