gebhart/patrepeval huggingface dataset:
Erratum: Effect of evaporation and condensation on a thermoacoustic engine: A Lagrangian simulation approach [J. Acoust. Soc. Am. 141 (6), 4398-4407 (2017)] (2020)

In the original paper [Yasui and Izu, J. Acoust. Soc. Am. 141(6), 4398-4407 (2017)], the temperature gradient in Rott equations was assumed as zero by mistake as an author error, although temperature gradient was adequately taken into account in the numerical simulations of thermal conduction between a fluid parcel and the wall of a stack. In the present erratum, the results of the corrected numerical simulations are shown. The results show that the pV work done by a fluid parcel is larger in a wet stack compared to that in a dry stack not only in a traveling-wave thermoacoustic engine but also in a standing-wave thermoacoustic engine. The pV work is determined not only by the volume oscillation amplitude of a fluid parcel but also by the change in the mean volume of a fluid parcel.
Intra- and intersubject synthesis of cardiac MR images using a VAE and GAN (2023)

We propose a method for synthesizing cardiac MR images with plausible heart shape and realistic appearance. It breaks down the synthesis into labels deformation and label-to-image translation. The former is achieved via latent space interpolation in a VAE model, while the latter is accomplished via a conditional GAN model. We synthesize 32 short-axis slices within each subject (intrasubject), as well as eight intermediary generated subjects between two dissimilar real subjects (intersubject) that have different anatomies. Such method could provide a solution to enrich a database and to pave the way for the development of generalizable DL based algorithms.
Pseudotyped adeno‐associated viral vector tropism and transduction efficiencies in murine wound healing (2012)

Cell specific gene transfer and sustained transgene expression are goals of cutaneous gene therapy for tissue repair and regeneration. Adeno-associated virus serotype 2 (AAV2/2) mediated gene transfer to the skin results in stable transgene expression in the muscle fascicles of the panniculus carnosus in mice, with minimal gene transfer to the dermal or epidermal elements. We hypothesized that pseudotyped AAV vectors may have a unique and characteristic tropism and transduction efficiency profile for specific cells in the cutaneous wounds. We compared transduction efficiencies of cells in the epidermis, cells in the dermis, and the fascicles of the panniculus carnosus by AAV2/2 and three pseudotyped AAV vectors, AAV2/5, AAV2/7, and AAV2/8 in a murine excisional wound model. AAV2/5 and AAV2/8 result in significantly enhanced transduction of cells both in the epidermis and the dermis compared to AAV2/2. AAV2/5 transduces both the basilar and supra-basilar keratinocytes. In contrast, AAV2/8 transduces mainly supra-basilar keratinocytes. Both AAV2/7 and AAV2/8 result in more efficient gene transfer to the muscular panniculus carnosus compared to AAV2/2. The capsid of the different pseudotyped AAV vectors produces distinct tropism and efficiency profiles in the murine wound healing model. Both AAV2/5 and AAV2/8 administration result in significantly enhanced gene transfer. To further characterize cell specific transduction and tropism profiles of the AAV pseudotyped vectors, we performed in vitro experiments using human and mouse primary dermal fibroblasts. Our data demonstrate that pseudotyping strategy confers a differential transduction of dermal fibroblasts, with higher transduction of both human and murine cells by AAV2/5 and AAV2/8 at early and later time points. At later time points, AAV2/2 demonstrates increased transduction. Interestingly, AAV2/8 appears to be more efficacious in transducing human cells as compared to AAV2/5. The pseudotype-specific pattern of transduction and tropism observed both in vivo and in vitro suggests that choice of AAV vectors should be based on the desired target cell and the timing of transgene expression in wound healing for gene transfer therapy in dermal wounds.
Analyzing and Predicting Task Reminders (2016)

Automated personal assistants such as Siri, Cortana, and Google Now provide services to help users accomplish tasks, including tools to set reminders. We study how people specify and use reminders. Our study analyzes a sample of six months of logs of user-specified reminders from Cortana (Microsoft's intelligent personal assistant), the first large-scale analysis of such reminders. We focus our analyses on time-based reminders, the most common type of reminder found in the logs. We perform a data-driven analysis to identify common categories of tasks that give rise to these reminders across a large number of users, and we arrange these tasks into a taxonomy. We identify temporal patterns linked to the type of task, time of creation, and terms in the reminder text. Finally, we show that these patterns generalize by addressing a prediction task. Specifically, we show that a reminder's creation time is a strong feature in predicting the notification time, and that including the reminder text further improves prediction accuracy. The results have implications for the design of systems aimed at helping people to complete tasks and to plan future activities.
One-Step RT-qPCR for Viral RNA Detection Using Digital Analysis (2022)

The rapid detection of viruses is becoming increasingly important to prevent widespread infections. However, virus detection <i>via</i> reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is time-consuming, as it involves independent nucleic acid extraction and complementary DNA synthesis. This process limits the potential for rapid diagnosis and mass analysis, which are necessary to curtail viral spread. In this study, a simple and rapid thermolysis method was developed to circumvent the need for extraction and purification of viral RNA. The developed protocol was applied to one-chip digital PCR (OCdPCR), which allowed thermolysis, RT, and digital PCR in a single unit comprising 20,000 chambers of sub-nanoliter volume. Two viruses such as tobacco mosaic virus and cucumber mosaic virus were tested as model viral particles. First, the temperature, exposure time, and template concentration were optimized against tobacco mosaic viral particles, and the most efficient conditions were identified as 85°C, 5 min, and 0.01 μg/nL with a cycle threshold of approximately 33. Finally, the OCdPCR analysis yielded 1,130.2 copies/µL using 10<sup>-2</sup> μg/nL of viral particles in a 30 min thermolysis-RT reaction at 70°C. This novel protocol shows promise as a quick, accurate, and precise method for large-scale viral analysis in the future.
Continuous Remote Care Model Utilizing Nutritional Ketosis Improves Type 2 Diabetes Risk Factors in Patients with Prediabetes (2018)

Prediabetes (preT2D) is a major U.S. public health concern, as over 84 million adults are at greater risk of cardiovascular disease and progression to type 2 diabetes (T2D). Abnormal glucose, BMI, blood pressure, and blood lipids are risk factors for progression to T2D. The purpose of this single-arm prospective longitudinal investigation was to assess change in risk factors after one year of treatment with a continuous remote care model utilizing nutritional ketosis, behavior change, and support from a health coach, medical provider, and peers provided via an online clinic. Patients with preT2D enrolled (n=116); at 1 year, 95 participants (82%) remained active. Results are reported for participants with measurements completed at 1 year and baseline; n varied across measures (range: 77-95). Changes from baseline to 1 year included: weight -13.1±9.5 kg (from 110.6±23.5 kg, p&amp;lt;0.0001), BMI -5.0±3.5 kg/m2 (from 38.9 kg/m2, p&amp;lt;0.0001), HbA1c -0.3±0.3% (from 5.9±0.2%, p&amp;lt;0.0001), fasting glucose -9±14 mg/dL (from 110±15 mg/dL, p&amp;lt;0.0001), systolic BP -6±14 mmHg (from 130±13 mmHg, p=0.0003), diastolic BP -3±9 mmHg (from 83±8 mmHg, p=0.0032), triglycerides -43±55 mg/dL (from 148±67 mg/dL, p&amp;lt;0.0001), and HDL-C +7±9 mg/dL (from 52±14 mg/dL, p&amp;lt;0.0001). Seventy percent (54/77) of participants lost &amp;gt;7% body weight. At 1 year, 51.1% (45/88) participants achieved fasting glucose &amp;lt;100 mg/dL (up from 24/94, 25.5% at baseline). No completer progressed to T2D, and 60.7% (54/89) achieved HbA1c &amp;lt;5.7% (up from 14/94, 14.9% at baseline). Most participants (56.3%, 54/96) maintained mean blood beta-hydroxybutyrate concentrations ≥0.5 mmol/L, indicating moderate adherence to nutritional advice. These results demonstrate that patients with preT2D can be supported remotely with this continuous care model to improve risk factors associated with progression of preT2D to T2D. Ongoing research will evaluate the continued sustainability of this intervention and prevention of T2D. Disclosure A. McKenzie: Employee; Self; Virta Health Corp.. Stock/Shareholder; Self; Virta Health Corp. S. Hallberg: Board Member; Spouse/Partner; Atkins Nutritionals, Inc.. Employee; Self; Virta Health. Stock/Shareholder; Self; Virta Health. N.H. Bhanpuri: Employee; Self; Virta Health Corp.. Stock/Shareholder; Self; Virta Health Corp. S.J. Athinarayanan: Employee; Self; Virta Health Corp. J. McCue: Employee; Self; Virta Health Corp.. Stock/Shareholder; Self; Virta Health Corp. J.P. McCarter: Employee; Self; Virta Health Corp.. Stock/Shareholder; Self; Virta Health Corp. J. Volek: Stock/Shareholder; Self; Virta Health Corp.. Advisory Panel; Self; Atkins Nutritionals, Inc.. Other Relationship; Self; Beyond Obesity. S. Phinney: Employee; Self; Virta Health Corp.. Advisory Panel; Self; Atkins Nutritionals, Inc..
MicroRNAs in cancer: personalizing diagnosis and therapy (2010)

MicroRNAs (miRNAs) are 19-24nt noncoding RNAs that have been implicated in the pathogenesis of both solid and hematological malignancies. Frequently located in fragile chromosomal regions, miRNAs are essential to key biological functions, such as cellular differentiation, apoptosis, and growth. miRNAs may serve as either tumor suppressors or oncogenes. As a result, they have the potential to serve as both biomarkers and therapeutic agents in cancer. Based on our presentation at the recent Towards Personalized Cancer Medicine conference held in Barcelona, Spain, May 19-21, 2010, we provide an overview of the current knowledge of miRNA deregulation in solid and hematological malignancies and their application as biomarkers of disease.
A highly integrated GPS receiver for cellular handset (2002)

A highly integrated dual conversion heterodyne GPS receiver is reported. The receiver chip includes a 2.9 dB NF LNA, an image-reject mixer with 32 dB image rejection. The on-chip IF chain, which consists of a VGA, a 2nd mixer and filtering, has a maximum gain of 83 dB, a gain range of 45 dB and a 7 dB NF. A 4-bit ADC is integrated on chip for enhanced SNR. The PLL with its VCO are also integrated. The total NF is 3 dB with a total 121 dB voltage gain. The chip consumes 132 mW at 2.7 V.
Multimodal, Multidimensional Models of Mouse Brain (2007)

Naturally occurring mutants and genetically manipulated strains of mice are widely used to model a variety of human diseases. Atlases are an invaluable aid in understanding the impact of such manipulations by providing a standard for comparison and to facilitate the integration of anatomic, genetic, and physiologic observations from multiple subjects and experiments. We have developed digital atlases of the C57BL/6J mouse brain (adult and neonate) as comprehensive frameworks for storing and accessing the myriad types of information about the mouse brain. Along with raw and annotated images, these contain database management systems and a set of tools for comparing information from different techniques and different animals. Each atlas establishes a canonical representation of the mouse brain and provides the tools for the manipulation and analysis of new data. We describe both these atlases and discuss how they may be put to use in organizing and analyzing data from mouse models of epilepsy.
RASSF Family Proteins (2012)

1 JG Brown Cancer Center, University of Louisville, 417 CTR Building, 505 S. Hancock Street, Louisville, KY 40202, USA 2Division of Hematology/Oncology, Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, 3-055 Katz Group Centre for Pharmacy and Health Research, 113 Street 87 Avenue, Edmonton, AB, Canada T6G 2E1 3School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK 4National Creative Research Initiatives Center for Cell Division and Differentiation, Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 373-1 Guseoung-D, Yuseong-G, Daejeon 305-701, Republic of Korea
Exploiting pervasive enterprise chronicles using unstructured information management (2005)

Strides made in semiconductor technology and pervasive devices are fueling the ability to amass ever-increasing volumes of rich multimedia data chronicling the activities and experiences of enterprise employees. Rich content analytics are crucial to exploit the potential of such electronic chronicles, which represent a vital untapped resource in today's enterprises. This paper describes a system called Picasso that adds a new dimension to enterprise search and mining, by capturing and structuring information surrounding employee activities and making available vital insights from such information through our unstructured information management architecture (UIMA).
Partial Ossicular Replacement Versus Type II Tympanoplasty in Congenital Aural Atresia Surgery (2009)

POR can be a good surgical option in cases of a poor incudostapedial joint connection, ossicular anomaly, or ossicular fixation.
Lignin Biorefinery Optimization Through Machine Learning (2021)

Lignin is an abundant biomaterial that currently emerges as a low value by-product in the pulp and paper industry but could be repurposed for high-value products as part of the ongoing global transition to a sustainable society. To increase lignins value, rational and efficient approaches to optimizing lignin biorefineries to produce high value bioproducts are required. Here, we report the optimization of the AquaSolv Omni (AqSO) Biorefinery, a newly introduced biorefinery concept based on hydrothermal pretreatment and solvent extraction. We employ a machine-learning framework based on Bayesian optimization, to provide sample-efficient and guided data collection as well as surrogate model building. The surrogate models allow us to map multiple experimental outputs, including the extracted lignin yield and main structural properties obtained by 2D NMR, as functions of the hydrothermal pretreatment reaction severity and temperature. Our results show that with Bayesian optimization, predictive models can be converged with only 21 data points to within a margin of error comparable to the underlying experimental error. By applying a Pareto point analysis, we demonstrate how the predictive models can be used in tandem to identify optimal extraction conditions for concrete applications in lignin valorization.
Bidirectional Forwarding Detection (BFD) for the Pseudowire Virtual Circuit Connectivity Verification (VCCV) (2010)

This document describes Connectivity Verification (CV) Types using
Bidirectional Forwarding Detection (BFD) with Virtual Circuit
Connectivity Verification (VCCV). VCCV provides a control channel that
is associated with a pseudowire (PW), as well as the corresponding
operations and management functions such as connectivity verification
to be used over that control channel. [STANDARDS-TRACK]
Cell phone based balance trainer (2012)

The results suggest that the real-time feedback provided by this system can be used to reduce body sway. Its advantages over more complex laboratory-based and commercial balance training systems in terms of cost, size, weight, functionality, flexibility, and accessibility make it a good candidate for further home-based balance training evaluation.
In Vivo Dynamic Strains of the Mitral Valve Annulus (2007)

The mitral valve apparatus is a complex structure with multiple components that require seamless, integrated operation for normal valve function. One of these components is the annulus, a fibrous ring of tissue that defines the boundary between the mitral valve leaflets and the surrounding superstructure of the heart. During the cardiac cycle the annulus undergoes large deformations and dramatic shape changes. Moreover, the annulus motion represents a key boundary condition for mitral valve leaflet deformation. Yet, to date our knowledge of the subtle deformations this structure undergoes during the cardiac cycle remains very limited. In the present study, an array of 1 mm diameter piezoelectric sonocrystals was implanted in 5 sheep to quantify annular deformation over the complete cardiac cycle. These crystals act as fiducial markers for the mitral annulus with a temporal resolution of ∼1ms and a special resolution of .01mm in a calibrated three dimensional space. A quintic order generalized 3D spline was developed to reconstruct the annular geometry.
An Architecture with Planning for Autonomic Systems (2011)

Autonomic systems aim to reduce the configuration, operational, and maintenance tasks of large distributed applications. In order to implement autonomic systems, several approaches, such as Self-managed system and Autonomic Computing, have been proposed. This paper describes an architectural approach for autonomic systems, which is based on a three-layered model. In the uppermost layer, the planning function, which is an important part of this model, has to efficiently make an effective sequence of operational services to satisfy goals. In this paper, we propose an automated planning algorithm using hierarchy planning technique. Our planner composes the sequence of operational services in the most abstract space, and then it successively embodies the detail of them. The critical values, which determine the abstract space, are automatically discovered from the knowledge of operational services. We also present the experimental results to show the effectiveness of our method.
Targeted disruption of GPR7, the endogenous receptor for neuropeptides B and W, leads to metabolic defects and adult-onset obesity (2003)

Gold-thioglucose (GTG) induces lesions in the ventromedial nucleus of the hypothalamus, resulting in hyperphagia and obesity. To identify genes involved in the hypothalamic regulation of energy homeostasis, we used a screen for genes that are dysregulated in GTG-induced obese mice. We found that GPR7, the endogenous G protein-coupled receptor for the recently identified ligands neuropeptide B and neuropeptide W, was down-regulated in hypothalamus after GTG treatment. Here we show that male GPR7-/- mice develop an adult-onset obese phenotype that progressively worsens with age and was greatly exacerbated when animals are fed a high-fat diet. GPR7-/- male mice were hyperphagic and had decreased energy expenditure and locomotor activity. Plasma levels of glucose, leptin, and insulin were also elevated in these mice. GPR7-/- male mice had decreased hypothalamic neuropeptide Y RNA levels and increased proopiomelanocortin RNA levels, a set of effects opposite to those evident in ob/ob mice. Furthermore, ob/ob GPR7-/- and Ay/a GPR7-/- double mutant male mice had an increased body weight compared with normal ob/ob or Ay/a male mice, suggesting that the obesity of GPR7-/- mice is independent of leptin and melanocortin signaling. Female mice did not show any significant weight increase or associated metabolic defects. These data suggest a potential role for GPR7 and its endogenous ligands, neuropeptide B and neuropeptide W, in regulating energy homeostasis independent of leptin and melanocortin signaling in a sexually dimorphic manner.
Endoscopically directed single-port intragastric fundoplication, sleeve gastroplasty, and myotomy: a preclinical study in a porcine model (2022)

Video 1Endoscopically directed single-port intragastric procedures in a porcine model.
Lectin Fingerprinting Distinguishes Antibody Neutralization in SARS-CoV-2 (2023)

Enveloped viruses co-opt host glycosylation pathways to decorate their surface proteins. As viruses evolve, emerging strains can modify their glycosylation patterns to influence host interactions and subvert immune recognition. Still, changes in viral glycosylation or their impact on antibody protection cannot be predicted from genomic sequences alone. Using the highly glycosylated SARS-CoV-2 Spike protein as a model system, we present a lectin fingerprinting method that rapidly reports on changes in variant glycosylation state, which are linked to antibody neutralization. In the presence of antibodies or convalescent and vaccinated patient sera, unique lectin fingerprints emerge that distinguish neutralizing versus non-neutralizing antibodies. This information could not be inferred from direct binding interactions between antibodies and the Spike receptor-binding domain (RBD) binding data alone. Comparative glycoproteomics of the Spike RBD of wild-type (Wuhan-Hu-1) and Delta (B.1.617.2) variants reveal O-glycosylation differences as a key determinant of immune recognition differences. These data underscore the interplay between viral glycosylation and immune recognition and reveal lectin fingerprinting to be a rapid, sensitive, and high-throughput assay to distinguish the neutralization potential of antibodies that target critical viral glycoproteins.
In vivo transfer of nitric oxide between a plasma protein-bound reservoir and low molecular weight thiols. (1994)

Plasma albumin reacts with nitric oxide (NO) to form the bioactive adduct, S-nitroso-albumin (S-NO-albumin). The limited intracellular access of S-NO-albumin suggests the need for a vascular transfer mechanism of NO from a large plasma S-NO-albumin pool to effect biologic function. To study the role of low molecular weight (LMW) thiols in NO transfer in vivo, we administered intravenous S-NO-albumin (1-300 nmol/kg) to rabbits before and after an intravenous infusion of L-cysteine or N-acetyl-L-cysteine. S-NO-albumin produced dose-dependent hypotension that was significantly augmented by prior infusion of either LMW thiol. LMW thiol infusion significantly accelerated the rate of onset and reduced the duration of action of the hypotension induced by S-NO-albumin. The hemodynamic effects of S-NO-albumin after pretreatment with LMW thiols were mimicked by administration of the corresponding LMW S-nitrosothiol. The transfer of NO from albumin to L-cysteine was directly measured in rabbit plasma using a novel technique that couples high performance liquid chromatography to electrochemical detection. These data demonstrate that NO exchange between plasma protein thiol-bound NO and available LMW thiol pools (transnitrosation) occurs in vivo.
ISA: An Intelligent Shopping Assistant (2020)

Despite the growth of e-commerce, brick-and-mortar stores are still the preferred destinations for many people. In this paper, we present ISA, a mobile-based intelligent shopping assistant that is designed to improve shopping experience in physical stores. ISA assists users by leveraging advanced techniques in computer vision, speech processing, and natural language processing. An in-store user only needs to take a picture or scan the barcode of the product of interest, and then the user can talk to the assistant about the product. The assistant can also guide the user through the purchase process or recommend other similar products to the user. We take a data-driven approach in building the engines of ISA's natural language processing component, and the engines achieve good performance.