gebhart/patrepeval huggingface dataset:
Constructing Dynamic Topic Models Based on Variational Autoencoder and Factor Graph (2018)

Topic models are widely used in various fields of machine learning and statistics. Among them, the dynamic topic model (DTM) is the most popular time-series topic model for the dynamic representations of text corpora. A major challenge is that the posterior distribution of DTM requires a complex reasoning process with the high cost of computing time in modeling, and even a tiny change of model requires restructuring. For these reasons, the variability and generality of DTM is so poor that DTM is difficult to be carried out. In this paper, we introduce a new method for constructing DTM based on variational autoencoder and factor graphs. This model uses re-parameterization of the variational lower bound to generate a lower bound estimator which is optimized by standard stochastic gradient descent method directly. At the same time, the optimization process is simplified by integrating the dynamic factor graph in the state space to achieve a better model. The experimental dataset uses a journal paper corpus that mainly focuses on natural language processing and spans twenty-five years (1984-2009) from DBLP. Experiment results indicate that the proposed method is effective and feasible by comparing several state-of-the-art baselines.
Three‐Dimensional Directed Self‐Assembly of Peptide Nanowires into Micrometer‐Sized Crystalline Cubes with Nanoparticle Joints (2010)

Micro construction sites: Engineered peptides and ligand-functionalized gold nanoparticles have been assembled into micrometer-scale 3D cube-shaped crystals (see picture), creating a physical framework for a biomimetic assembly strategy. The NPs join the peptide nanowires through streptavidin–biotin interactions to create cubic unit cells. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by 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.
Tissue preparation for immunocytochemistry. (1997)

There is no standard tissue preparation schedule for the optimal demonstration of all antigens. Factors involved in all aspects of tissue preparation can affect immunoreactivity, so it is important that precise details of the preparation schedule are given when reporting immunocytochemical studies, rather than using the general term "routinely fixed and processed".
Wearable, Redundant Fabric-Based Sensor Arrays for Reconstruction of Body Segment Posture (2004)

Posture and gesture analysis, together with the monitoring of body kinematics, is a field of increasing interest in bioengineering and several connected disciplines. In this paper, some typical features of distributed sensing systems are described, as well as a methodology to read signals from such systems. Theory, simulation, results, and some specific applications are shown. Strain gauges have been used as sensors and have been deposited directly onto textile fibers, demonstrating one way to realize a wearable sensor system.
Six-Degree-of-Freedom Localization With a 3-Axis Accelerometer and a 2-Axis Magnetometer for Magnetic Capsule Endoscopy (2022)

This letter presents a new localization method for magnetic capsule endoscopes that uses sensors internal to the capsule, but aims to relieve some of the previous limitations associated with this paradigm. The method estimates the six-degree-of-freedom capsule pose with no prior pose information other than the knowledge that it resides within a particular workspace. Internal to the capsule, it requires a 3-axis accelerometer, a 2-axis magnetometer (or 3-axis magnetometer with one axis saturated or disabled), a microcontroller capable of wireless communication, and a radio frequency antenna, all of which can be integrated into a single printed circuit board. The method is applicable to both of the common configurations of the internal permanent magnet. In a set of simulations and experiments, we show that the localization accuracy is comparable to what has been obtained with prior methods that have required more complexity.
Hormones in Human Pituitary Sinusoid Blood: Concentration of LH, GH and TSH1 (1969)

A technique is described for the collection of blood from the vasculature of the human pituitary gland and from pituitary tumors during stereotactic surgery. Twenty-five samples were obtained from 18 nonneoplastic pituitary glands (chiefly of postmenopausal women), and 7 samples from 1 chromophobe and 4 eosinophilic adenomas. The concentration of hormone in nonneoplastic pituitary sinusoid blood varied from 0.6 to 1250 ng/ml (mean 103 ng/ml) for LH, <1 to 3180 ng/ml (mean 384 ng/ml) for GH, and <0.4 to 2600 ng/ml (mean 140 ng/ml) for TSH. The average ratio of hormone concentration in pituitary sinusoidal to peripheral blood was 22.4, 87.3 and 87.5 for LH, GH and TSH, respectively. The data indicate there is a marked functional heterogeneity within the normal pituitary gland consistent with previous histological studies of topographical cell distribution within the human pituitary. In pituitary adenomas, there were extremely high concentrations of growth hormone in the effluent of the eosinophilic tumors. In addition, the effluent of these tumors and one chromophobe adenoma contained detectable and sometimes high levels of other trophic hormones. This indicates there may be mixed trophic hormone secretion by these tumors.
Spin reorientation inα-Fe2O3nanoparticles induced by interparticle exchange interactions inα-Fe2O3/NiO nanocomposites (2011)

We report that the spin structure of $\ensuremath{\alpha}$-Fe${}_{2}$O${}_{3}$ nanoparticles rotates coherently out of the basal (001) plane at low temperatures when interacting with thin plate-shaped NiO nanoparticles. The observed spin reorientation (up to \ensuremath{\sim}70${}^{\ensuremath{\circ}}$) in $\ensuremath{\alpha}$-Fe${}_{2}$O${}_{3}$ nanoparticles has, in appearance, similarities to the Morin transition in bulk $\ensuremath{\alpha}$-Fe${}_{2}$O${}_{3}$, but its origin is different---it is caused by exchange coupling between aggregated nanoparticles of $\ensuremath{\alpha}$-Fe${}_{2}$O${}_{3}$ and NiO with different directions of easy axes of magnetization.
A guide to the measurement and interpretation of fMRI test-retest reliability (2021)

The test-retest reliability of functional neuroimaging data has recently been a topic of much discussion. Despite early conflicting reports, converging reports now suggest that test-retest reliability is poor for standard univariate measures-namely, voxel- and region-level task-based activation and edge-level functional connectivity. To better understand the implications of these recent studies requires understanding the nuances of test-retest reliability as commonly measured by the intraclass correlation coefficient (ICC). Here we provide a guide to the measurement and interpretation of test-retest reliability in functional neuroimaging and review major findings in the literature. We highlight the importance of making choices that improve reliability so long as they do not diminish validity, pointing to the potential of multivariate approaches that improve both. Finally, we discuss the implications of recent reports of low test-retest reliability in the context of ongoing work in the field.
Evaluation and optimization of silicon sheet solar cells (1980)

This paper describes the results and procedures to evaluate and improve the efficiency of solar cells made from various unconventional silicon sheets. The performance parameters included photovoltaic characteristics, spectral response, dark I-V characteristics, and diffusion length. The evaluation techniques used provided accurate and reliable information on sheet performance, and self-consistent results were obtained from the various measurement techniques used. Minority carrier diffusion length (L) was shown to be the ultimate limiting factor for the sheet cell performance (efficiency) and other back-up measurements confirmed this L-dependence. Limited efforts were made to identify defects which influence cell performance, and to use some improved process methods to increase cell efficiency.
The Development of Diets to Induce Atherogenic Lipid Profiles for Cynomolgus Monkeys in Their Country of Origin (2014)

Understanding the process of atherosclerosis progress can be studied in laboratory animals, such as nonhuman primate (NHP)<i>.</i> Investigators at Bogor Agricultural University Indonesia, Primate Research Center (IPB) reported to develop an atherogenic diet (IPB 1) by using fresh egg yolk and coconut oil as source of cholesterol and fat. The aims of the research were to correct nutritional inadequacy in the initial IPB 1 atherogenic diet by supplementation with corn oil (IPB 1+CO); to use dry powdered egg yolk (PEY) instead of fresh egg yolk (IPB 1+CO+PEY); to use concentrated source of protein (43%) pupae meal (PM) instead of soya meal (IPB 1+CO+PM) ; and to use crystalline cholesterol (CC) instead of egg yolk (IPB 1+CO+CC). Twenty four <i>Macaca fascicularis</i> were used as animal model for three months adaptation followed by 12 months for four diet treatments. Parameters measured such body weight, waist circumference, trunk length, adiposity index, nutrient utilization, and plasma lipid profile every three months. This experiment used Completely Randomized Design with four treatments and six replications. Result showed that there were no significant differences found in morphometric parameters among the diet groups compared to one another or change from baseline. The nutrient (protein, fat and carbohydrate) consumption and the absorption were essentially the same for all four diet groups. The IPB 1+CO diet, the IPB 1+CO+PM diet and the IPB 1+CO+CC induced a similar atherogenic plasma lipid profile, with marked increases in total plasma cholesterol concentrations.
Fatigue fracture of nearly elastic hydrogels (2018)

Polyacrylamide hydrogels are highly stretchable and nearly elastic. Their stress-stretch curves exhibit small hysteresis, and change negligibly after many loading cycles. Polyacrylamide is used extensively in applications, and is the primary network for many types of tough hydrogels. Recent experiments have shown that polyacrylamide hydrogels are susceptible to fatigue fracture, but available data are limited. Here we study fatigue fracture of polyacrylamide hydrogels of various water contents. We form polymer networks in all samples under the same conditions, and then obtain hydrogels of 96, 87, 78, and 69 wt% of water by solvent exchange. We measure the crack extension under cyclic loads, and the fracture energy under monotonic loading. For the hydrogels of the four water contents, the fatigue thresholds are 4.3, 8.4, 20.5, and 64.5 J m-2, and the fracture energies are 18.9, 71.2, 289, and 611 J m-2. The measured thresholds agree well with the predictions of the Lake-Thomas model for hydrogels of high water content, but not in the case of low water content. It is hoped that further basic studies will soon follow to aid the development of fatigue-resistant hydrogels.
Review of Optimization Problems in Wireless Sensor Networks (2012)

Abstract—The Wireless Sensor Networks (WSNs) design related questions give rise to new complex and difficult the-oretical problems and challenges in operations research and optimization areas. As WSNs become increasingly pervasive, a good understanding of these problems in terms of theoretical complexity is of great help in designing appropriate algorithms. In this paper, we examine some of the most fundamental optimization problems related to coverage, topology control, scheduling, routing and mobility in WSNs. Then we focus on their complexity and analyze the differences that exist with the counter part conventional theoritical problems or those already studied in traditional networks. We present as well some of the main methods proposed in the literature and report some open issues regarding these problems. Keywords-WSN, Optimization problems, Complexity. I.
Unique Fluorescent Imaging Probe for Bacterial Surface Localization and Resistant Enzyme Imaging (2018)

Emergence of antibiotic bacterial resistance has caused serious clinical issues worldwide due to increasingly difficult treatment. Development of a specific approach for selective visualization of resistant bacteria will be highly significant for clinical investigations to promote timely diagnosis and treatment of bacterial infections. In this article, we present an effective method that not only is able to selectively recognize drug resistant AmpC β-lactamases enzyme but, more importantly, is able to interact with bacterial cell wall components, resulting in a desired localization effect on the bacterial surface. A unique and specific enzyme-responsive cephalosporin probe (DFD-1) has been developed for the selective recognition of resistance bacteria AmpC β-lactamase, by employing fluorescence resonance energy transfer with an "off-on" bioimaging. To achieve the desired localization, a lipid-azide conjugate (LA-12) was utilized to facilitate its penetration into the bacterial surface, followed by copper-free click chemistry. This enables the probe DFD-1 to be anchored onto the cell surface. In the presence of AmpC enzymes, the cephalosporin β-lactam ring on DFD-1 will be hydrolyzed, leading to the quencher release, thus generating fluorescence for real-time resistant bacterial screening. More importantly, the bulky dibenzocyclooctyne group in DFD-1 allowed selective recognition toward the AmpC bacterial enzyme instead of its counterpart ( e.g., TEM-1 β-lactamase). Both live cell imaging and cell cytometry assays showed the great selectivity of DFD-1 to drug resistant bacterial pathogens containing the AmpC enzyme with significant fluorescence enhancement (∼67-fold). This probe presented promising capability to selectively localize and screen for AmpC resistance bacteria, providing great promise for clinical microbiological applications.
PPARs and Bone Metabolism (2006)

Welcome to the inaugural special issue of PPAR Research: PPARs and Bone Metabolism. In addition to the key roles PPARs play in numerous processes including glucose and fat metabolism, inflammation, cancer, and central nervous system maintenance, a new role for PPAR-γ has recently emerged: the maintenance of bone homeostasis during aging and disease. In this premier issue we have assembled what is close to a comprehensive overview of the role of PPAR-γ in the control of bone maintenance. This takes into account PPAR-γ's role in mesenchymal stem cell lineage allocation, possible cross-talk with relevant nuclear receptors, examination of PPAR-γ gene polymorphisms and bone mineral density in humans, a role of PPAR-γ in bone loss due to skeletal disuse, evidence that human bone is vulnerable to antidiabetic therapies with PPAR-γ agonists, the thiazolidinediones, and evidence that the antiosteoblastic activity of PPAR-γ can be separated from its proadipocytic and antidiabetic activities by using selective modulators. We also present a novel hypothesis that PPAR-γ acts as a regulator of chondrocyte development and cartilage homeostasis. We realize that we have not covered all aspects of PPARs involvement in the control of bone maintenance; however, this introduction should serve as a competent first attempt to present these new aspects of bone biology to the broader audience of our readers.


Beata Lecka-Czernik
Sinus Histiocytosis with Massive Lymphadenopathy: Virological, Immunological and Morphological Studies (1980)

The histiocytes from a patient with sinus histiocytosis were tested for the presence of Epstein-Barr viral nuclear antigen (EBNA) before and after in vitro growth. On both occasions the histiocytes as well as the lymphocytes were EBNA negative. Likewise the profile of EBV viral capsid antibody (VCA) suggests that this virus is unlikely to be directly involved in the development of the disease. The maintenance of an unusually high level of antibodies to EBV and measles, both viruses which produce persistent infections, indicates that the humoral immune response is active. That a normal humoral response occurred in response to mumps virus during the same period suggests that a deficiency in the cell mediated immune response to the persistent viruses might be the reason for the abnormally high antibody levels. The fresh as well as the cultured histiocytes had only Fc receptors. The affected lymph node lymphocytes developed unusual large inclusion bodies following in vitro culture.
Deep Active Learning for Dialogue Generation (2016)

We propose an online, end-to-end, neural generative conversational model for open-domain dialogue. It is trained using a unique combination of offline two-phase supervised learning and online human-in-the-loop active learning. While most existing research proposes offline supervision or hand-crafted reward functions for online reinforcement, we devise a novel interactive learning mechanism based on hamming-diverse beam search for response generation and one-character user-feedback at each step. Experiments show that our model inherently promotes the generation of semantically relevant and interesting responses, and can be used to train agents with customized personas, moods and conversational styles.
Localising Faster: Efficient and precise lidar-based robot localisation in large-scale environments (2020)

This paper proposes a novel approach for global localisation of mobile robots in large-scale environments. Our method leverages learning-based localisation and filtering-based localisation, to localise the robot efficiently and precisely through seeding Monte Carlo Localisation (MCL) with a deeplearned distribution. In particular, a fast localisation system rapidly estimates the 6-DOF pose through a deep-probabilistic model (Gaussian Process Regression with a deep kernel), then a precise recursive estimator refines the estimated robot pose according to the geometric alignment. More importantly, the Gaussian method (i.e. deep probabilistic localisation) and nonGaussian method (i.e. MCL) can be integrated naturally via importance sampling. Consequently, the two systems can be integrated seamlessly and mutually benefit from each other. To verify the proposed framework, we provide a case study in large-scale localisation with a 3D lidar sensor. Our experiments on the Michigan NCLT long-term dataset show that the proposed method is able to localise the robot in 1.94 s on average (median of 0.8 s) with precision 0.75 m in a largescale environment of approximately 0.5 km <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Automated Contextual Annotation of B-Rep Cad Mechanical Components Deriving Technology and Symmetry Information to Support Partial Retrieval (2012)

Mechanical components are often related to technological meaning: it is a screw, a ball bearing, . . . Technological meaning relates to the notion of function which, in turn, refers to the environment of a component. Here, it is shown how a digital mock-up contextualizing a set of components is used to annotate its components with technological information. This information is derived from the interfaces between components. Interfaces together with the concept of state of a digital mock-up initiate annotations of components with functional information. Symmetries of components is a complementary information that can contribute to a query. Local rotational symmetry is analyzed and adapted to the context of mechanical components. Then, combining these two categories of information enables the generation of high level queries addressing a subset of a component boundary. Technological as well as symmetry informations are component annotations automatically derived from the digital mock-up analysis and from components analyzed separately.
Kidney Transplantation 2: Care of the Kidney Transplant Recipient (2021)

Renal transplantation is the preferred therapy for patients with end-stage kidney disease, leading to increased life expectancy, improved quality of life, and reduced health care resource use. Owing to their preexisting burden of disease, caring for renal transplant recipients is complex. Patient management following successful renal transplantation involves a multifactorial approach to cardiovascular risk factor management, along with titration of immunosuppression, management of complications related to immunosuppression, and active monitoring of allograft function. Recent advances in immunosuppressive management hold promise for improved long-term allograft survival. Finally, immune monitoring of transplant recipients is an area of considerable research, with the ultimate aim of individualized management of immunosuppression and the ability to induce transplant-specific tolerance. This review contains 7 figures, 11 tables, and 119 references. Key words: cardiovascular disease, drug interactions, immunosuppression, infection, interstitial fibrosis and tubular atrophy, malignancy, rejection, tolerance
Comprehensive alternative splicing recovery needs 200 million reads (2023)

<strong>A key parameter in the experimental design of poly(A) RNA-seq projects is the choice of sequencing depth. Considering a limited budget, one needs to find a tradeoff between the number of samples and the sensitivity of the analysis, in particular with respect to lowly expressed genes. While previous studies have proposed a lower bound for the comprehensive analysis of differential gene expression, for the analysis of alternative splicing has only been proposed for human adipose tissue. Alternative splicing, however, differs across tissues and conditions. We analyzed deeply sequenced paired-end RNA-seq samples (between 150 and &gt;500 million reads, read length 50-150 bp) from human buffy coat cells and diverse tissues, including gluteal subcutaneous fat, heart, and hypothalamus. We provide evidence that for genes with moderate and high expression, 200 million reads is the lower bound for comprehensive analysis of alternative splicing. Hence, given the current state of methodology, integrating splicing into the systems biology landscape requires much deeper sequencing than in most published cohorts.</strong>
Orbital Ordering in Orthorhombic Perovskites (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
The theoretical basis of the isoinversion principle (1997)

The theoretical basis of the isoinversion principle is discussed in terms of the temperature dependence of absolute rate constants. This description gives an insight into the origin and physical meaning of the terms ‘inversion temperature’ and ‘transition region’. The consequences of quantitative interpretation of non-linear Eyring plots are discussed.
Body weight support systems: considerations for clinicians (2006)

The Body Weight Support (BWS) system used in conjunction with a treadmill has become increasingly popular in the clinical arena for the treatment of a variety of patient populations. Currently, commercially available BWS systems are designed with different types of suspension mechanisms and a variety of additional features. The purposes of this article are to: (i) provide an overview of the three main types of BWS suspension systems; (ii) review the uses, advantages, and disadvantages of each type; and (iii) highlight and discuss the many additional features that are available. Rehabilitation research conducted with neurological and non-neurological patient populations using a BWS system as a therapeutic modality is highlighted to assist the clinician to select the most suitable BWS system and features for a particular clinical purpose or patient group. Additionally, research findings for the biomechanical effects of varied BWS suspension devices on gait are discussed.