gebhart/patrepeval huggingface dataset:
Restoring redox balance enhances contractility in heart trabeculae from type 2 diabetic rats exposed to high glucose (2014)

Hearts from type 2 diabetic (T2DM) subjects are chronically subjected to hyperglycemia and hyperlipidemia, both thought to contribute to oxidizing conditions and contractile dysfunction. How redox alterations and contractility interrelate, ultimately diminishing T2DM heart function, remains poorly understood. Herein we tested whether the fatty acid palmitate (Palm), in addition to its energetic contribution, rescues function by improving redox [glutathione (GSH), NAD(P)H, less oxidative stress] in T2DM rat heart trabeculae subjected to high glucose. Using cardiac trabeculae from Zucker Diabetic Fatty (ZDF) rats, we assessed the impact of low glucose (EG) and high glucose (HG), in absence or presence of Palm or insulin, on force development, energetics, and redox responses. We found that in EG ZDF and lean trabeculae displayed similar contractile work, yield of contractile work (Ycw), representing the ratio of force time integral over rate of O2 consumption. Conversely, HG had a negative impact on Ycw, whereas Palm, but not insulin, completely prevented contractile loss. This effect was associated with higher GSH, less oxidative stress, and augmented matrix GSH/thioredoxin (Trx) in ZDF mitochondria. Restoration of myocardial redox with GSH ethyl ester also rescued ZDF contractile function in HG, independently from Palm. These results support the idea that maintained redox balance, via increased GSH and Trx antioxidant activities to resist oxidative stress, is an essential protective response of the diabetic heart to keep contractile function.
Topics in the phonology and morphology of San Francisco del Mar Huave (2008)

This dissertation is a study of the phonology and morphology of the Huave language as spoken in San Francisco del Mar, Oaxaca State, Mexico.Huave is a language isolate, and the San Francisco del Mar dialect (one of four) is severely endangered, with almost all of its approximately 100 remaining fluent speakers over 65 years of age.The present study represents the first in-depth linguistic research on this dialect and is based on the author's fieldwork in the village.The dissertation starts with a typological and sociolinguistic overview of Huave (Chapter 1).It then provides an analytical description of all phonological phenomena encountered in research to date (Chapter 2), paying special attention to the distribution and realization of palatalization, and to the fusion, dissimilation, and contextual deletion processes associated with glottal fricatives.The following chapters develop detailed and theoretically-oriented treatments of specific phonological phenomena.Chapter 3 proposes a unified analysis of various diphthongization processes and relates them to the realization of consonant palatalization, while also elaborating on the subsegmental representations of vowels and consonants.In Chapter 4, Correspondence theory is used to analyze unusual patterns of copy and blocking in the vowel harmony system.Chapter 5 gives a morphological overview of Huave word classes and basic morphological structure.Chapter 6 focuses on verbal morphology, including verbal person, number, and tense/aspect inflection, and a diverse array of valence alternations.Finally, Chapter 7 provides a comprehensive picture of verbal affix ordering, which is complicated by "mobile affixes" that surface as prefixes or suffixes depending on context.The abstract hierarchical structure of the verb is worked out, and the linear placement of mobile affixes within these hierarchical constraints is argued to be phonologically conditioned.
Achieving In-Depth Proteomics Profiling by Mass Spectrometry (2007)

Proteomics addresses the important goal of determining the chemistry and composition of proteins in biological samples. Mass-spectrometry-based strategies have been highly successful in identifying and profiling proteins in complex mixtures; however, although depth of sampling continues to improve, a general recognition exists that no study has yet achieved complete protein coverage in any tissue, cell type, subcellular component, or fluid. The development of new approaches for comprehensively surveying highly complex protein mixtures, distinguishing protein isoforms, quantifying changes in protein abundance between different samples, and mapping post-translational modifications are areas of active research. These will be needed to achieve the "systems-wide" protein profiling goals of defining molecular responses to cell perturbations and obtaining biomarker information for disease detection, prognosis, and responses to therapy. We review recent progress in approaching these problems and present examples of successful applications and the outlook for the future.
A randomized, phase II trial of oral azacitidine (CC-486) in patients with resected pancreatic adenocarcinoma at high risk for recurrence (2022)

Abstract Background Of the only 20% of patients with resectable pancreatic ductal adenocarcinoma (rPDA), cancer recurs in 80% of cases. Epigenetic dysregulation is an early hallmark of cancer cells acquiring metastatic potential, and epigenetic modulators may reactivate tumor suppressor genes, delay recurrence, and sensitize PDA to future chemotherapy. Methods This was a randomized phase II study (NCT01845805) of CC-486 (oral DNA methyltransferase inhibitor azacitidine) vs. observation (OBS) in rPDA patients harboring high-risk features (stage pN1-2, R1 margins, or elevated CA 19–9 level) with no evidence of disease following standard adjuvant therapy. Patients were randomized to oral CC-486 treatment (300 mg daily on days 1–21 on a 28-day cycle) or OBS for up to 12 cycles or until disease relapse/unacceptable toxicities. Following recurrence, records of next-line therapies, imaging, and survival were obtained. The primary endpoint was progression-free survival (PFS)—time from randomization to recurrence (imaging/biopsy confirmed or death). Secondary endpoints included OS and PFS and ORR and metastatic PFS with subsequent next-line systemic therapy in metastatic setting. Results Forty-nine patients (24 in CC-486 arm, 25 in OBS arm) were randomized: median age 66 (range 36–81), 53% male, 73% node positive, 49% elevated CA 19–9, 20% R1 resection, 63% and 100% received perioperative concurrent chemoradiation and chemotherapy, respectively. Median time from surgery to randomization was 9.6 mo (range 2.9–36.8). For the CC-486 arm, median treatment duration was 5.6 mo (range 1.3 to 12.8) with 14 treatment-related grade 3 or 4 AEs among 5 patients (22%) resulting in dose-reduction. Four patients (17%) discontinued therapy due to AEs. With median follow-up of 20.3mo (IQR 12.8, 41.4), 38 (79%) of evaluable patients recurred (34 imaging-confirmed, 4 clinically). Median PFS in imagining-confirmed cases was 9.2 and 8.9mo (HR 0.94, 95% CI 0.46–1.87, p = 0.85) for CC-486 and OBS patients, respectively. Median OS (2-yr OS%) was 33.8 (50%) and 26.4 mo (61%) in CC-486 and OBS patients, respectively. (HR 0.98, 95% CI 0.46–2.05, p = 0.96). ORR with subsequent chemotherapy in the metastatic setting was minimal in both arms. Conclusions Treatment with CC-486 following adjuvant therapy did not prolong time-to-relapse in patients with high-risk rPDA or improve disease response on 1st-line metastatic therapy.
An Analysis of MFCC-like Parametric Audio Features for Keyphrase Spotting Applications. (2010)

Paper 14
Neural Coding of Vibration Intensity (2021)

Vibrotactile feedback technology has become widely used in human-computer interaction due to its low cost, wearability, and expressiveness. Although neuroimaging studies have investigated neural processes associated with different types of vibrotactile feedback, encoding vibration intensity in the brain remains largely unknown. The aim of this study is to investigate neural processes associated with vibration intensity using electroencephalography. Twenty-nine healthy participants (aged 18-40 years, nine females) experienced vibrotactile feedback at the distal phalanx of the left index finger with three vibration intensity conditions: no vibration, low-intensity vibration (1.56 g), and high-intensity vibration (2.26 g). The alpha and beta band event-related desynchronization (ERD) as well as P2 and P3 event-related potential components for each of the three vibration intensity conditions are obtained. Results demonstrate that the ERD in the alpha band in the contralateral somatosensory and motor cortex areas is significantly associated with the vibration intensity. The average power spectral density (PSD) of the peak period of the ERD (400-600 ms) is significantly stronger for the high- and low-vibration intensity conditions compared to the no vibration condition. Furthermore, the average PSD of the ERD rebound (700-2,000 ms) is significantly maintained for the high-vibration intensity compared to low-intensity and no vibration conditions. Beta ERD signals the presence of vibration. These findings inform the development of quantitative measurements for vibration intensities based on neural signals.
Synthesis of Bacteriochlorins and Their Potential Utility in Photodynamic Therapy (PDT) (2004)

The porphyrins and related tetrapyrrole systems are among the most widely studied of all macrocyclic compounds. In fact, in one capacity or another these versatile molecules have influenced nearly all disciplines in chemistry. In recent years, efforts are underway to develop tetrahydroporphyrin-based (bacteriochlorin) compounds with long wavelength absorption in the range of 700-800 nm as photosensitizers for photodynamic therapy (PDT). This review article summarizes the synthetic methodologies that have been developed for the preparation of a variety of bacteriochlorins, either from porphyrins or chlorin systems.
The influence of the host cell on standardisation of influenza vaccine potency. (1999)

Conventional influenza vaccines are standardised using the single-radial-immunodiffusion (SRD) test where reagents are produced from egg-grown viruses. It is important to ensure homology between SRD antigen reagents and test vaccines. There was concern that cell-grown vaccines may differ antigenically from corresponding egg-grown vaccines, which may in turn affect vaccine standardisation. In an examination of five cell-grown vaccines from two companies, only one vaccine was affected by the specificity of the SRD test. Options for standardisation of cell-grown vaccines are considered and recommendations are made for further studies.
Ultrastructural Features of Skeletal Muscle Differentiation and Development (1974)

It is obvious from even this cursory review that ultrastructural studies have provided the basis for much of our existing knowledge about differentiation and development of muscle. It is also evident that a great deal is known about differentiation of muscle cells. Because the major myofibrillar proteins of muscle are well characterized and possess unique features that permit their isolation and identification from very small amounts of tissue, muscle tissue may well constitute a very favorable system for the study of cell differentiation in general. It seems probable that future progress in the study of muscle differentiation will rely on an integrated application of biochemical, immunological, and ultrastructural techniques. Information from such efforts should eventually lead to the ability to control the rate of synthesis of myofibrillar proteins, and the rates and times at which myoblasts fuse to form muscle cells. Possession of this ability will make it possible to achieve extraordinary increases in feed efficiency and muscling in our domestic animals, and indeed, may usher in an entirely new era in animal science.
Unusual Antioxidant Properties of 26S Proteasome Isolated from Cold-Adapted Organisms (2017)

The oxidative challenge represents an important factor affecting the adaptive strategies in Antarctic fish, but their impact on the protein degradation machinery still remains unclear. The previous analysis of the first 26S proteasome from the Antarctic red-blooded fish <i>Trematomus bernacchii</i>, evidenced improved antioxidant functions necessary to counteract the environmental pro-oxidant conditions. The purpose of this work was to carry out a study on 26S proteasomes from the temperate red-blooded <i>Dicenthrarcus labrax</i> and the icefish <i>Chionodraco hamatus</i> in comparison with the isoform already described from <i>T. bernacchii</i>, to better elucidate the cold-adapted physiological functions of this complex. Therefore, the 26S isoforms were isolated and the complementary DNAs (cDNAs) codifying the catalytic subunits were cloned. The biochemical characterization of Antarctic 26S proteasomes revealed their significantly higher structural stability and resistance to H₂O₂ with respect to that of the temperate counterpart, as also suggested by a comparative modeling analysis of the catalytic subunits. Moreover, in contrast to that observed in <i>T. bernacchii</i>, the 26S systems from <i>C. hamatus</i> and <i>D. labrax</i> were incapable to hydrolyze oxidized proteins in a ubiquitin-independent manner. Therefore, the 'uncommon' properties displayed by the Antarctic 26S proteasomes can mirror the impact exercised by evolutionary pressure in response to richly oxygenated environments.
Robust real‐time robot–world calibration for robotized transcranial magnetic stimulation (2011)

This robust online calibration greatly enhances the system's user-friendliness and safety.
Structured State Space Models for In-Context Reinforcement Learning (2023)

Structured state space sequence (S4) models have recently achieved state-of-the-art performance on long-range sequence modeling tasks. These models also have fast inference speeds and parallelisable training, making them potentially useful in many reinforcement learning settings. We propose a modification to a variant of S4 that enables us to initialise and reset the hidden state in parallel, allowing us to tackle reinforcement learning tasks. We show that our modified architecture runs asymptotically faster than Transformers in sequence length and performs better than RNN's on a simple memory-based task. We evaluate our modified architecture on a set of partially-observable environments and find that, in practice, our model outperforms RNN's while also running over five times faster. Then, by leveraging the model's ability to handle long-range sequences, we achieve strong performance on a challenging meta-learning task in which the agent is given a randomly-sampled continuous control environment, combined with a randomly-sampled linear projection of the environment's observations and actions. Furthermore, we show the resulting model can adapt to out-of-distribution held-out tasks. Overall, the results presented in this paper show that structured state space models are fast and performant for in-context reinforcement learning tasks. We provide code at https://github.com/luchris429/popjaxrl.
An Agent-Based Model Approach for Simulating Interactions between Occupants and Building Systems (2017)

Building occupants are one of the most dominant variable factors in building energy consumption. However, current building performance simulation engines incorporate occupant information as simple, static profiles, which lead to discrepancy in actual energy use as occupants interact with building systems in an active manner, i.e., occupant behavior over time is not captured by simulation algorithms. The need for modeling energy-related occupant behavior dynamically in energy simulation tools to increase prediction capability cannot be understated. This paper proposes a possible solution by discussing the use of a Performance Moderator Functions testbed (PMFserv) - a well-tested Agent-Based Modeling (ABM) tool, for occupant behavior modeling and its potential integration with energy simulation engine, EnergyPlus™. In order to extend PMFserv to buildings for improving energy estimation, a thermal zone in an educational building is tested and observed using sensing technologies. The study explores the interactions between occupants and building using cognitively detailed ABM, as well as the impact of occupant behavior on building energy use.
Vapor–Liquid Equilibrium Data for Binary Systems of n-Dodecane + {Propan-1-ol, Butan-1-ol, 2-Methylpropan-1-ol} at 40 kPa (2014)

Isobaric (T–x–y) binary vapor–liquid equilibrium (VLE) data were measured and modeled for the n-dodecane + {propan-1-ol, butan-1-ol, or 2-methylpropan-1-ol} systems at 40 kPa. A low pressure dynamic still, capable of measuring systems of high relative volatility, was used for the measurements. The vapor and liquid equilibrium compositions were determined using a gas chromatograph with a thermal conductivity detector. The experimental data were regressed using the combined method (γ–φ approach). The nonrandom two-liquid (NRTL) activity coefficient model was used to describe the liquid phase nonideality, and the vapor phase was assumed to be ideal. The NRTL model parameters were determined using nonlinear least-squares regression. The experimental data were found to be well correlated with the thermodynamic modeling. No azeotropic behavior has been observed. The three investigated systems show a large positive deviation from Raoult’s law.
All-Polarization-Maintaining Erbium-doped Mode-locked Fibre Laser Using CNT-coated PANDA Microfibre (2020)

An all-polarization-maintaining Er-doped fibre laser was demonstrated using PANDA microfibre embedded in a CNT-PDMS composite. The PANDA microfibre had good extinction ratio and low insertion loss. Robust and efficient saturable absorption was confirmed. © 2020 The Author(s)
Confidence measures of optical flow estimation suitable for multiframe superresolution (2012)

Multi-frame super-resolution of images containing complex motion fields remains an elusive target requiring precise estimation of such motion between the frames. Although accuracy of optical flow algorithms has been increasing steadily it is not yet sufficient to provide confident subpixel resolution enhancement during super-resolution reconstruction. One way to approach the problem is to augment optical flow estimation input into super-resolution procedure by reliable confidence measure. Numerous optical flow confidence or conversely uncertainty measures have been developed recently. However, their performance has been studied and evaluated with respect to error metric involving optical flow vectors, namely angular and end point errors averaged over the entire image. Super-resolution processing requires consideration of interpolation error i.e. the difference between the reference image and the motion compensated image. This work presents comparative evaluation of optical flow confidence measures and makes conclusions of their usefulness to applications utilizing image compensation.
Evaluation of Presumably Disease Causing SCN1A Variants in a Cohort of Common Epilepsy Syndromes (2016)

We identified 8 known missense mutations, previously reported as pathogenic, in a total of 17 unrelated epilepsy patients (17/448; 3.80%). Our re-evaluation indicates that 7 out of these 8 variants (p.R27T; p.R28C; p.R542Q; p.R604H; p.T1250M; p.E1308D; p.R1928G; NP_001159435.1) are not pathogenic. Only the p.T1174S mutation may be considered as a genetic risk factor for epilepsy of small effect size based on the enrichment in patients (P = 6.60 x 10-4; OR = 0.32, fishers exact test), previous functional studies but incomplete penetrance. Thus, incorporation of previous studies in genetic counseling of SCN1A sequencing results is challenging and may produce incorrect conclusions.
Frequency Adaptive CDSC-PLL Using Axis Drift Control Under Adverse Grid Condition (2016)

This paper presents a new technique to adapt the cascaded delayed signal cancellation phase-locked loop (CDSC-PLL) using a proposed axis drift control (ADC). When grid frequency changes, the estimated grid angle by PLL drifts with a residual error proportional to the frequency change value thus, the accuracy and performance of the conventional CDSC-PLL is deteriorated which can lead to malfunction of the connected applications. Accordingly, CDSC-PLL type has to be adaptable to frequency changes with high immunity to grid disturbances. Designing frequency adapted CDSC-PLL is complex and needs a dedicated design due to the high nonlinearity introduced by adaptive loops. The ADC is proposed as an online adaptive technique that contains a self-tuned DSC operator to mitigate the grid disturbances and a PI controller to perform the adaptation task. The proposed technique is mathematically analyzed and systematic tuning methods are presented. A new analysis for CDSC under off-nominal sample parameter is presented and verified. The robustness of proposed adaptive controller is investigated under parameters uncertainty and various grid disturbances. The proposed technique is numerically and experimentally verified.
A Phased Array Antenna for Deep Space Communications (2008)

This paper describes a phased array antenna that has been studied for use as the next generation deep space network (DSN) for NASA. The DSN currently consists of large reflector antennas located approximately equidistant around the earth and provides communications and navigation services to the NASA science missions to the solar system planets. These individual antennas range in size from 34-m to 70-m. In the future, there have been proposals to replace these antennas with a phased array, each element of which would consist of smaller reflector antennas than currently used. The total aperture could be increased as required by future missions, with total future aperture up to or more than 10 times that of the current DSN total aperture. One possible architecture for this phased array antenna is described. A breadboard phased array was constructed to demonstrate this concept. The performance of the individual antenna elements and their corresponding subsystems, and the performance of the phased array signal combiner developed for this breadboard phased array is described.
Robust Planning over Restless Groups: Engagement Interventions for a Large-Scale Maternal Telehealth Program (2023)

In 2020, maternal mortality in India was estimated to be as high as 130 deaths per 100K live births, nearly twice the UN's target. To improve health outcomes, the non-profit ARMMAN sends automated voice messages to expecting and new mothers across India. However, 38% of mothers stop listening to these calls, missing critical preventative care information. To improve engagement, ARMMAN employs health workers to intervene by making service calls, but workers can only call a fraction of the 100K enrolled mothers. Partnering with ARMMAN, we model the problem of allocating limited interventions across mothers as a restless multi-armed bandit (RMAB), where the realities of large scale and model uncertainty present key new technical challenges. We address these with GROUPS, a double oracle–based algorithm for robust planning in RMABs with scalable grouped arms. Robustness over grouped arms requires several methodological advances. First, to adversarially select stochastic group dynamics, we develop a new method to optimize Whittle indices over transition probability intervals. Second, to learn group-level RMAB policy best responses to these adversarial environments, we introduce a weighted index heuristic. Third, we prove a key theoretical result that planning over grouped arms achieves the same minimax regret--optimal strategy as planning over individual arms, under a technical condition. Finally, using real-world data from ARMMAN, we show that GROUPS produces robust policies that reduce minimax regret by up to 50%, halving the number of preventable missed voice messages to connect more mothers with life-saving maternal health information.