gebhart/patrepeval huggingface dataset:
Bumpy Road to Vaccination Policies (2007)

State of Immunity . The Politics of Vaccination in Twentieth-Century America. By James Colgrove . University of California Press, Berkeley, 2006. 346 pp. $39.95 £26.95. ISBN 9780520247499. California/Milbank Books on Health and the Public. Colgrove explores the social and political facets of vaccination as a public health measure in 20th-century United States.
Severe Charcot-Marie-Tooth neuropathy type 1A with 1-base pair deletion and frameshift mutation in the peripheral myelin protein 22 gene (1997)

A 27-year-old man with negative family history and both parents with normal neurological evaluation and motor nerve conduction velocities (MNCVs) showed onset of severe weakness of feet at 4 years of age. Subsequently he developed left equinovarus deformity, thoracic scoliosis, ulnar nerve enlargement, areflexia, distal hypesthesia and slowing of MNCVs for median and ulnar nerves (15-25 m/sec). Molecular genetic studies showed deletion of one nucleotide (G330) (codon 94) in exon 3 of the PMP22 gene associated with frameshift mutation.
Hemoglobin Conjugates with Antioxidant Enzymes (Hemoglobin-Superoxide Dismutase-Catalase) via Poly(Ethylene Glycol) Crosslinker for Protection of Pancreatic Beta RINm5F Cells in Hypoxia (2011)

A low p50 hemoglobin (Hb) (p50 indicates O(2) tension at which Hb is half-saturated)-based oxygen carrier conjugated to antioxidant enzymes via dicarboxymethylated poly(ethylene glycol) (PEG) linker may have the beneficial effect in protecting pancreatic beta cells from severe hypoxia at transplantation sites. In this study, the oxygen dissociation curves, Hill plots, Bohr Effect, and oxygen content of Hb conjugates were measured. The protective effect due to incubation of Hb-conjugates (Hb/PEG molar ratio 1:10) with pancreatic beta cells (RINm5F) against hypoxia (6%, 3%, and 1% oxygen) was evaluated by an MTT assay and confocal microscopy. Quantitatively, Hb conjugates with antioxidant enzymes offered statistically significant protection (p<0.01, increased viability ∼80%) from hypoxia compared to control cells in 1% oxygen environment. Confocal images also showed that the low p50 Hb conjugates with antioxidants protected RINm5F cells from hypoxia.
Basic Properties of Rotary Dynamics of the Molecular Motor Enterococcus hirae V1-ATPase (2013)

V-ATPases are rotary molecular motors that generally function as proton pumps. We recently solved the crystal structures of the V1 moiety of Enterococcus hirae V-ATPase (EhV1) and proposed a model for its rotation mechanism. Here, we characterized the rotary dynamics of EhV1 using single-molecule analysis employing a load-free probe. EhV1 rotated in a counterclockwise direction, exhibiting two distinct rotational states, namely clear and unclear, suggesting unstable interactions between the rotor and stator. The clear state was analyzed in detail to obtain kinetic parameters. The rotation rates obeyed Michaelis-Menten kinetics with a maximal rotation rate (Vmax) of 107 revolutions/s and a Michaelis constant (Km) of 154 μM at 26 °C. At all ATP concentrations tested, EhV1 showed only three pauses separated by 120°/turn, and no substeps were resolved, as was the case with Thermus thermophilus V1-ATPase (TtV1). At 10 μM ATP (<<Km), the distribution of the durations of the ATP-waiting pause fit well with a single-exponential decay function. The second-order binding rate constant for ATP was 2.3 × 10(6) M(-1) s(-1). At 40 mM ATP (>>Km), the distribution of the durations of the catalytic pause was reproduced by a consecutive reaction with two time constants of 2.6 and 0.5 ms. These kinetic parameters were similar to those of TtV1. Our results identify the common properties of rotary catalysis of V1-ATPases that are distinct from those of F1-ATPases and will further our understanding of the general mechanisms of rotary molecular motors.
Predictive Guardbanding: Program-Driven Timing Margin Reduction for GPUs (2020)

The energy efficiency of GPU architectures has emerged as an essential aspect of computer system design. In this article, we explore the energy benefits of reducing the GPU chip's voltage to the safe limit, i.e., V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">min</sub> point, using predictive software techniques. We perform such a study on several commercial off-the-shelf GPU cards. We find that there exists about 20% voltage guardband on those GPUs spanning two architectural generations, which, if “eliminated” entirely, can result in up to 25% energy savings on one of the studied GPU cards. Our measurement results unveil a program dependent V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">min</sub> behavior across the studied applications, and the exact improvement magnitude depends on the program's available guardband. We make fundamental observations about the program-dependent V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">min</sub> behavior. We experimentally determine that the voltage noise has a more substantial impact on V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">min</sub> compared to the process and temperature variation, and the activities during the kernel execution cause large voltage droops. From these findings, we show how to use kernels' microarchitectural performance counters to predict its V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">min</sub> value accurately. The average and maximum prediction errors are 0.5% and 3%, respectively. The accurate V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">min</sub> prediction opens up new possibilities of a crosslayer dynamic guardbanding scheme for GPUs, in which software predicts and manages the voltage guardband, while the functional correctness is ensured by a hardware safety net mechanism.
A Cryo-CMOS Low-Power Semi-Autonomous Qubit State Controller in 14nm FinFET Technology (2022)

Error-corrected quantum computing is expected to require at least 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> to 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> physical qubits. Superconducting transmons, which are promising qubit candidates for scaled quantum computing systems, typically require individually tailored RF pulses in the 4-to-6 GHz range to manipulate their states, so scaling to 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> qubits presents an enormous challenge. Providing a control line for every qubit from room temperature (RT) to the 10mK environment does not appear to be viable for a 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> qubit system due to multiple factors, including RF loss, mechanical congestion, heat load, and connector unreliability. TDM cannot be used to reduce the number of control lines since all of the qubits may need to be activated at once (e.g., during quantum error correction (QEC) cycles). FDM has been proposed but is undesirable because extra tones can give rise to unwanted qubit excitations.
Spatiotemporal Distribution of the Glassy-Winged Sharpshooter, Homalodisca vitripennis (Hemiptera: Cicadellidae), in a Southeastern Agroecosystem (2023)

La chicharrita de alas cristalinas, Homalodisca vitripennis (Germar) (Hemiptera: Cicadellidae), es una especie de insecto generalista que se alimenta del xilema y es una plaga agrícola. En los agroecosistemas, los adultos se dispersan entre hábitats, alimentándose de hospederos cultivados y no cultivados, a menudo es un vector de un patógeno dañino para las plantas, Xylella fastidiosa Wells et al. (Xanthomonadales: Xanthomonadaceae). Al entender la dinámica espaciotemporal de esta especie en los cultivos y su hábitat no agrícola alrededor del campo puede conducir a mejores programas de manejo de plagas que reduzcan la transmisión de patógenos. Aquí, usamos 3 años de datos de captura en un agroecosistema del sureste de los EE. UU. para caracterizar los patrones de distribución espaciotemporal de la chicharrita de alas cristalinas en una variedad de hábitats. Se capturaron los adultos de la chicharrita de alas cristalinas en trampas cilíndricas adhesivas amarillas. Se utilizó el análisis espacial por índices de distancia (SADIE) para identificar agregaciones significativas y se generaron mapas interpolados para caracterizar los patrones de distribución de adultos dentro de la temporada y entre años. En general, la distribución de las chicharritas de alas cristalinas varió según la estación, y los individuos fueron capturados principalmente en bosques y campos en barbecho durante el mes de comienzo de la temporada. Más adelante en la temporada de crecimiento y a medida que aumentaban los niveles de población, las chicharritas se capturaban más comúnmente en el hábitat de cultivos, incluidos los campos de trigo y maíz. Mediante la evaluación de los patrones de distribución espaciotemporal, identificamos fuentes probables de migración primaveral hacia los sistemas de cultivo. Por lo tanto, las estrategias de manejo de plagas para la chicharrita de alas cristalinas deben tratar de limitar la migración temprana de la primavera desde el hábitat sin cultivos a los campos de cultivo.
Leukocyte Recruitment Alters Pathological Angiogenesis Gene Expression During DSS Colitis (2012)

Experimental models of colitis in mice have been extensively used to study molecular events that occur during inflammatory bowel disease (IBD) development. However, direct and comprehensive comparison of mouse and human inflamed colon tissue at the genome level remains largely unknown and to what extent such differences reflect changes associated with human IBD. Here we report comparative functional genomic analysis between experimental colitis models and pediatric IBD. Two sets of pediatric IBD microarray data (GEO accession number GSE9686 and GSE10616) and experimental colitis microarray data (DSS colitis model GEO number GSE22307 and T-cell transfer colitis model GEO number 27302) were used for comparative functional genome expression pattern analysis. All microarray data were obtained using Affymetrix GeneChip arrays providing the most comprehensive coverage of transcribed genomes of human or mouse. Microarray data were input into Genesifter software and normalized for comparison using the Robust Multichip Averaging (RMA) method. Threshold value for significant differences in gene expression was set at 2 fold and the Benjamini-Hochberg test used to diminish false discovery rates. Identified genes were uploaded into Ingenuity software for network analysis, and cREMaG (cis-Regulatory Elements in the Mammalian Genome) software for transcription factor/promoter analysis. Microarray analysis revealed that chitinase 3-like 1(cartilage glycoprotein-39, CHI3L1), Cysteine-rich, angiogenic inducer 61 (CYR61, or CCN1), and Chemokine (C-C motif) ligand 2 (CCL2) were up regulated in both pediatric CD and UC. Ingenuity network analysis of differentially expressed genes from pediatric CD was clustered into 8 networks and pediatric UC into 25 networks. By comparison of pediatric IBD and experimental colitis microarray data, we found the following common features: 1) CXCL9 and S100A8 were abundantly up regulated; 2) cytokine-cytokine receptor networks were dysregulated; and 3) IRF-1 transcription binding sites were over represented in the promoter region of up regulated genes, while HNF1A and Lhx3 binding sites were over represented in the promoter region of the down regulated genes. Together, our study provides a comprehensive comparative view of genome expression and transcription factor profile changes between pediatric IBD and experimental colitis models revealing common pathways that may be useful for future therapeutics.
Design of force compensator with variable gain for bilateral control system under time delay (2013)

This study deals with a bilateral control system under communication delay. Control structure is designed to be symmetric among master and slave devices in proposed system, in order to realize the same performance as much as possible even though master and slave side is replaced. Then, this research aims to improve the performance of position tracking in free motion and aims to ensure zero steady state errors of both position and force control in contact motion. The time delay is compensated at force controller section and its gain is varied according to the force responses of master and slave motors. By the proposed method, haptic communication with enhanced performance under communication delay is expected. The validity of proposal is shown by experimental results.
Feasibility of Bluetooth Low Energy for motion capturing with Inertial Measurement Units (2022)

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Scalability study of SOA based optical switch for optical packet networks (2009)

We investigate the scalability of a SOA based optical switch for optical packet-switched system. By extensive simulations, based on the expected switch parameters, a consecutive switch limit of 14 or 9 is demonstrated.
Surface-Enhanced Raman Spectroscopy Biosensing:In VivoDiagnostics and Multimodal Imaging (2016)

This perspective presents recent developments in the application of surface-enhanced Raman spectroscopy (SERS) to biosensing, with a focus on in vivo diagnostics. We describe the concepts and methodologies developed to date and the target analytes that can be detected. We also discuss how SERS has evolved from a "point-and-shoot" stand-alone technique in an analytical chemistry laboratory to an integrated quantitative analytical tool for multimodal imaging diagnostics. Finally, we offer a guide to the future of SERS in the context of clinical diagnostics.
The Effects of Lingual Exercise on Swallowing in Older Adults (2005)

The findings indicate that lingual resistance exercise is promising not only for preventing dysphagia due to sarcopenia, but also as a treatment strategy for patients with lingual weakness and swallowing disability due to frailty or other age-related conditions. The potential effect of lingual exercise on reducing dysphagia-related comorbidities (pneumonia, malnutrition, and dehydration) and healthcare costs while improving quality of life is encouraging.
Immediate Impact of Yogic Breathing on Pulsatile Cerebrospinal Fluid Dynamics (2021)

Abstract Cerebrospinal fluid (CSF), a clear fluid bathing the central nervous system (CNS), undergoes pulsatile movements, and plays a critical role for the removal of waste products from the brain including amyloid beta, a protein associated with Alzheimer’s disease. Regulation of CSF dynamics is critical for maintaining CNS health, and increased pulsatile CSF dynamics may alter brain’s waste clearance due to increased mixing and diffusion. As such, understanding the mechanisms driving CSF movement, and interventions that influence its resultant removal of wastes from the brain is of high scientific and clinical impact. Since pulsatile CSF dynamics is sensitive and synchronous to respiratory movements, we are interested in identifying potential integrative therapies such as yogic breathing to regulate and enhance CSF dynamics, which has not been reported before. Here, we investigated the pre-intervention baseline data from our ongoing randomized controlled trial, and examined whether yogic breathing immediately impacts pulsatile CSF dynamics compared to spontaneous breathing. We utilized our previously established non-invasive real-time phase contrast magnetic resonance imaging (RT-PCMRI) approach using a 3T MRI instrument, and computed and rigorously tested differences in CSF velocities (instantaneous, respiratory, cardiac 1 st and 2 nd harmonics) at the level of foramen magnum during spontaneous versus four yogic breathing patterns. In examinations of 18 healthy participants (eight females, ten males; mean age 34.9 ± 14 (SD) years; age range: 18-61 years), we discovered immediate increase in cranially-directed velocities of instantaneous-CSF 16% - 28% and respiratory-CSF 60% - 118% during yogic versus spontaneous breathing, with most statistically significant changes during deep abdominal breathing (28%, p=0.0008, and 118%, p=0.0001, respectively). Further, cardiac pulsation was the primary source of pulsatile CSF during all breathing conditions except during deep abdominal breathing, when there was a comparable contribution of respiratory and cardiac 1st harmonic power [0.59 ± 0.78], demonstrating respiration can be the primary regulator of CSF depending on individual differences in breath depth and location. Further work is needed to investigate the impact of sustained training yogic breathing on increased pulsatile CSF dynamics and brain waste clearance for CNS health.
Irreducibility to the One-More Evaluation Problems: More May Be Less. (2007)

For a random-self-reducible function, the evaluation problem is irreducible to the one-more evaluation problem, in the following sense. An irreduction algorithm exists that, given a reduction algorithm from the evaluation to the one-more evaluation problem, solves a separator problem: the evaluation problem itself. Another irreduction shows that if the computational Diffie-Hellman problem is reduced to the gap Diffie-Hellman problem, then the decision Diffie-Hellman problem is easy. Irreductions are primarily of theoretical interest, because they do not actually prove inequivalence between problems. What these irreductions suggest, though, is that one-more variants of the RSA and discrete logarithm problems may be easier than the standard variants, and that the gap Diffie-Hellman problem may be easier than the standard Diffie-Hellman problem. 1
Ambient-temperature co-digestion of low-solids municipal and industrial waste mixtures: Insights from molecular analyses (2018)

The performance of ambient temperature anaerobic co-digestion was investigated for mixtures of six substrates: canned tomato and salsa waste, portable toilet waste, septic tank waste, winery waste, beer and cider waste, and fats, oils, and grease (FOG). Laboratory semi-continuous reactor studies and molecular biological analyses revealed that beer/winery, and tomato/FOG/winery/beer mixtures resulted in the best performance in terms of biogas production (515 and 371 mL CH4/g VS, respectively) and methanogenic populations. A portable toilet/septage mixture resulted in the overall poorest performance and inhibition of microbial activity was evident. Average methane content was ~70% for all mixtures tested. The findings of this study reveal that healthy methanogen populations were present, further supporting the feasibility of biogas production via the novel feedstock mixtures in ambient temperature lagoons. Implications: Disposal of septic tank waste and other high chemical oxygen demand (COD) 10 industrial food processing waste at a small wastewater treatment plant is uncommon, because it can upset the treatment process and requires additional power for treatment. Ambient-temperature covered lagoon digesters can be an alternative low-cost technology for co-digestion of these recalcitrant waste streams while generating bioenergy. The results of this study demonstrated that there is potential for implementation of unheated covered lagoon digester systems 15 for conversion of liquid wastes for production of renewable biomethane while eliminating the need to treat these wastes at a wastewater treatment plant.
Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin (2023)

The peptide antibiotic albicidin is a DNA topoisomerase inhibitor with low-nanomolar bactericidal activity towards fluoroquinolone-resistant Gram-negative pathogens. However, its mode of action is poorly understood. We determined a 2.6 Å resolution cryoelectron microscopy structure of a ternary complex between <i>Escherichia coli</i> topoisomerase DNA gyrase, a 217 bp double-stranded DNA fragment and albicidin. Albicidin employs a dual binding mechanism where one end of the molecule obstructs the crucial gyrase dimer interface, while the other intercalates between the fragments of cleaved DNA substrate. Thus, albicidin efficiently locks DNA gyrase, preventing it from religating DNA and completing its catalytic cycle. Two additional structures of this trapped state were determined using synthetic albicidin analogues that demonstrate improved solubility, and activity against a range of gyrase variants and <i>E. coli</i> topoisomerase IV. The extraordinary promiscuity of the DNA-intercalating region of albicidins and their excellent performance against fluoroquinolone-resistant bacteria holds great promise for the development of last-resort antibiotics.
Combination of CT scanning and fluoroscopy imaging on a flat-panel CT scanner (2006)

We developed and evaluated a prototype flat-panel detector based Volume CT (fpVCT) scanner. The fpVCT scanner consists of a Varian 4030CB a-Si flat-panel detector mounted in a multi slice CT-gantry (Siemens Medical Solutions). It provides a 25 cm field of view with 18 cm z-coverage at the isocenter. In addition to the standard tomographic scanning, fpVCT allows two new scan modes: (1) fluoroscopic imaging from any arbitrary rotation angle, and (2) continuous, time-resolved tomographic scanning of a dynamically changing viewing volume. Fluoroscopic imaging is feasible by modifying the standard CT gantry so that the imaging chain can be oriented along any user-selected rotation angle. Scanning with a stationary gantry, after it has been oriented, is equivalent to a conventional fluoroscopic examination. This scan mode enables combined use of high-resolution tomography and real-time fluoroscopy with a clinically usable field of view in the z direction. The second scan mode allows continuous observation of a timeevolving process such as perfusion. The gantry can be continuously rotated for up to 80 sec, with the rotation time ranging from 3 to 20 sec, to gather projection images of a dynamic process. The projection data, that provides a temporal log of the viewing volume, is then converted into multiple image stacks that capture the temporal evolution of a dynamic process. Studies using phantoms, ex vivo specimens, and live animals have confirmed that these new scanning modes are clinically usable and offer a unique view of the anatomy and physiology that heretofore has not been feasible using static CT scanning. At the current level of image quality and temporal resolution, several clinical applications such a dynamic angiography, tumor enhancement pattern and vascularity studies, organ perfusion, and interventional applications are in reach.
Future considerations for dendritic cell immunotherapy against chronic viral infections (2014)

Dendritic cells (DCs) are multifunctional cells that are pivotal in immune defense. As such they have been explored as vaccine carriers, largely in cancer immunotherapy and against some infectious diseases including HIV and viral hepatitis. However, while the use of DCs as vaccine carrier has shown some promise in cancer immunotherapy, this approach is laborious and is subject to strict quality control, which makes it expensive. Furthermore, in some individuals chronically infected with HIV, HCV and/or HBV the numbers of circulating DCs are reduced and/or their functions impaired. In vivo expansion and mobilization of DCs with Flt3L in combination with antigen and/or adjuvant targeting to critical DC receptors may be a more effective approach to control viral replication in chronically infected HIV, HBV and/or HCV patients than current DC immunotherapy approaches.