gebhart/patrepeval huggingface dataset:
The development of the lung in mammals: An analysis of concepts and findings (1981)

Abstract To evaluate one model of mammalian‐lung development, i.e., division into periods, pre‐ and postnatal lung development in the CPB‐S mouse strain was divided into the currently distinguished periods: the pseudoglandular period, covering establishment of the air‐conducting portion; and the canalicular, terminal‐sac, and alveolar or postnatal periods, in which the respiratory portion develops. The last three periods would each cover the formation of a different component of the respiratory unit or pulmonary acinus (acinus pulmonaris) (nonalveolated respiratory bronchiole, nonalveolated duct and sac, and alveolar pouch). However, determination of the nature of the relevant structures on the basis of recent findings concerning the epithelia showed that these hypotheses are not tenable. Since the tubule with cuboidal epithelium (appearing in the pseudoglandular and following periods) is the basic structure in the genesis of the pulmonary acinus, the development of the respiratory portion must start in the pseudoglandular period. Likewise, since the definitive components of the acinus are derived from this acinar tubule, their establishment may not be restricted to one of the other periods. Because other postulated divisions of mammalian‐lung development were based on similar histological interpretations, they cannot reflect the course of mouse‐lung development either. Therefore, a developmental scheme based on the recent findings concerning the epithelia is given as well as a tentative scheme for the human lung. The respiratory portion proved to develop by budding of acinar tubules, the mode of budding being not restricted to any particular pattern.
Low-distortion baseline removal algorithm for electrocardiogram signals (2012)

A new ECG baseline removal method is presented in this paper. This method is based on the Savitzky-Golay polynomial smoothing filter. Since this filter is defined in the time domain, it has the advantage of following the trend of the baseline wander. The results from this method are compared to the cubic spline method and a heart rate adaptive high-pass filter. The comparison shows that the SG baseline filter has comparable performance to these two other established methods. This new method is simple, and does not require extra knowledge about the ECG, such as isoelectric points required by the cubic spline method or the heart rate required by the high-pass filter. Thus it is more suitable for implementation in ECG monitoring systems.
Deficiency of carbohydrate response element-binding protein (ChREBP) reduces lipogenesis as well as glycolysis (2004)

The liver provides for long-term energy needs of the body by converting excess carbohydrate into fat for storage. Insulin is one factor that promotes hepatic lipogenesis, but there is increasing evidence that glucose also contributes to the coordinated regulation of carbohydrate and fat metabolism in liver by mechanisms that are independent of insulin. In this study, we show that the transcription factor, carbohydrate response element-binding protein (ChREBP), is required both for basal and carbohydrate-induced expression of several liver enzymes essential for coordinated control of glucose metabolism, fatty acid, and the synthesis of fatty acids and triglycerides in vivo.
Automatic construction of optimizing parallelizing compilers from specification (1994)

Most people write their programs in high-level languages because they want to develop their algorithm and not concern themselves with the low-level details of the computer on which the program will be executed. However, execution speed of the program is still a concern. Translating a program written in a high-level language into efficient code targeting a particular parallel machine requires a powerful compiler to perform transformations appropriate for that particular machine. Developing such a compiler requires a great deal of effort, and much of this effort must be repeated for each new target machine. A number of tools to assist in the generation of lexical analyzers, parsers, optimizers, parallelizers, and code generators have been developed. Each of these tools generates a part of the compiler from a specification, but the compiler writer must combine and augment these components to synthesize a complete compiler. In contrast, this dissertation suggests that complete compilers can be mechanically derived by processing a set of specifications defining the source language; available analysis, optimization, and parallelization phases; and the relevant attributes of the target computer. Further, an integrated framework for this process is presented; this includes new methods for description and management of parallelism, selection and ordering of analysis and transformation phases, and computation and use of estimates of execution time. Most aspects of this approach have been prototyped in a proof-of-concept tool, the Parallel Instruction Generator Generator (PIGG), which is also described in this dissertation.
Atypical Rho GTPases Have Roles in Mitochondrial Homeostasis and Apoptosis (2003)

The human genomic sequencing effort has revealed the presence of a large number of Rho GTPases encoded by the human genome. Here we report the characterization of a new family of Rho GTPases with atypical features. These proteins, which were called Miro-1 and Miro-2 (for mitochondrial Rho), have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms from Saccharomyces cerevisiae, Caenorhabditis elegans, and Drosophila melanogaster to mammals, indicating that these genes evolved early during evolution. Immunolocalization experiments, in which transfected NIH3T3 and COS 7 cells were stained for ectopically expressed Miro as well as for the endogenous Miro-1 protein, showed that Miro was present in mitochondria. Interestingly, overexpression of a constitutively active mutant of Miro-1 (Miro-1/Val-13) induced an aggregation of the mitochondrial network and resulted in an increased apoptotic rate of the cells expressing activated Miro-1. These data indicate a novel role for Rho-like GTPases in mitochondrial homeostasis and apoptosis.
Hepatocellular carcinoma (2000)

Hepatocellular carcinoma (HCC) has ranked second in cancer mortality in China since the 1990s and is increasing in frequency among males in many countries. Hepatitis B and C viruses, aflatoxin and algal toxin in the contaminated drinking water remain major aetiological factors and hepatitis G virus and transfusion-transmitted virus can not be excluded. A prospective randomized control trial screening for HCC in a high-risk population using alpha fetoprotein (AFP) and ultrasonography has demonstrated a decrease in HCC mortality. Rapidly progressing medical imaging has continuously contributed to the improving treatment results. Surgical resection still plays a major role in influencing prognosis of HCC. Studies on recurrence and metastasis after curative resection have become a key issue for further improvement of the surgical outcome. Regional cancer therapies are progressing rapidly, based on the advances in early diagnosis. The advantages and disadvantages of these are noted. Multimodality combination and sequential treatment has been accepted as an important approach for unresectable HCC and cytoreduction and sequential resection have attracted attention. Conformal radiotherapy has shown important potential for HCC treatment. Intra-arterial chemotherapy has been repeatedly proved effective; however, systemic chemotherapy for HCC remains disappointing. The effects of tamoxifen are questionable, whereas alpha-interferon has been shown to have significant potential, particularly in prevention of recurrence. All of these treatments have resulted in continuing improvement of HCC prognosis in some centres.
Preemptive Scheduling Under Time and Resource Constraints (1987)

We consider the problem of scheduling a set of n preemptable tasks in a system having r resources. Each task has an arbitrary, but known, worst case processing time and a deadline, and may request simultaneous use of a number of resources. A resource can be used either in shared mode or exclusive mode. In this paper, we develop and evaluate algorithms for determining whether or not a set of preemptive tasks is schedulable in such a real-time system, and if so, determining a schedule for it. This scheduling problem is known to be computationally intensive. In many real-time application environments, tasks are scheduled dynamically, and hence the scheduling algorithms used must have low run-time costs. To keep run-time costs low, we propose the use of suboptimal but practical algorithms that employ computationally simple heuristics. The computational complexity of our algorithms for scheduling n tasks in a system having r resources is O(rn <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ), which is very much lower than that of known optimal algorithms. We report on the results of simulation studies performed on such heuristic preemptive scheduling algorithms and the sensitivity of the performance of the algorithms with respect to various scheduling parameters. These studies show that due to the complexity of the problem, straightforward heuristics do not perform satisfactorily. However, an algorithm that uses combinations of such heuristics in conjunction with limited backtracks works very well.
A Convenient and General Reduction of Amides to Amines with Low‐Valent Titanium (2013)

Abstract Low‐valent titanium readily prepared in situ from TiCl 4 and Mg powder in THF is found to be an active agent for the reduction of amides which were previously considered to be inert towards low‐valent titanium. The reaction proceeds under very mild conditions, and is applicable to all types of amides, primary, secondary and tertiary, to produce the corresponding amines in good to excellent yields. This new finding provides a practical, convenient and general method for the important transformation of amides to amines. A plausible reaction mechanism is proposed. magnified image
The synthesis of carbon‐14 labeled pravastatin (1993)

Abstract As asymmetric route to [ 14 C]β‐hydroxycompactin 1 bearing the ( S )‐2‐methyl‐[1‐ 14 C]butanoate side chain has been developed. Methylation of [N‐[1‐ 14 C]butyryl‐4‐( S )‐phenylmethyl‐2‐oxazolidinone 4 afforded a 95:5 mixture of diastereomeric [N‐( S,R )‐2‐methyl‐[1‐ 14 C]butyryl]‐4‐( S )‐phenylmethyl‐2‐oxazolidinones 5,6 which were separated by preparative HPLC. Oxidative cleavage of 5 afforded optically pure ( S )‐2‐methyl‐[1‐ 14 C]butanoic acid. Acylation of alcohol 9 with optically pure ( S )‐2‐methyl‐[1] 14 C]butyryl chloride afforded ester 10 . Removal of the silyl either produced diastereomerically pure compactin 11 . Hydroxylation was carried out by biotransformation with Mucor hiemelus to afford diastereomerically pure [[1‐ 14 C]butanoate]β‐hydroxycompactin, [ 14 C]Pravastatin 1 .
Public Opinion and Public Opinion Polling (1948)

T HIS paper presents some observations on and on polling as currently performed. It is hoped that these observations will provoke the discussion for which, I understand, this meeting has been arranged. The observations are not along the line of what seems to be the chief preoccupation of students of polling, to wit, the internal improvement of their technique. Instead, the -observations are designed to invite attention to whether polling actually deals with opinion. The first observations which I wish to make are in the nature of a prelude. They come from a mere logical scrutiny of polling as an alleged form of scientific investigation. What I note is the inability of polling to isolate public opinion as an abstract or generic concept which could thereby become the focal point for the formation of a system of propositions. It would seem needless to point out that in an avowed scientific enterprise seeking to study a class of empirical items and to develop a series of generalizations about that class it is necessary to identify the class. Such identification enables discrimination between the instances which fall within the class and those which do not. In this manner, the generic character of the object of study becomes delineated. When the generic object of study is distinguishable, it becomes possible to focus study on that object and thus to learn progressively more about that object. In this way the ground is prepared for cumulative generalizations or propositions relative to the generic object of investigation. As far as I can judge, the current study of by polling ignores the simple logical point which has just been made. This
Triangulation from Two Views Revisited: Hartley-Sturm vs. Optimal Correction (2008)

A higher order scheme is presented for the optimal correction method of Kanatani [5] for triangulation from two views and is compared with the method of Hartley and Sturm [3]. It is pointed out that the epipole is a singularity of the Hartley-Sturm method, while the proposed method has no singularity. Numerical simulation confirms that both compute identical solutions at other points. However, the proposed method is significantly faster.
Salient Region Detection via High-Dimensional Color Transform and Local Spatial Support (2015)

In this paper, we introduce a novel approach to automatically detect salient regions in an image. Our approach consists of global and local features, which complement each other to compute a saliency map. The first key idea of our work is to create a saliency map of an image by using a linear combination of colors in a high-dimensional color space. This is based on an observation that salient regions often have distinctive colors compared with backgrounds in human perception, however, human perception is complicated and highly nonlinear. By mapping the low-dimensional red, green, and blue color to a feature vector in a high-dimensional color space, we show that we can composite an accurate saliency map by finding the optimal linear combination of color coefficients in the high-dimensional color space. To further improve the performance of our saliency estimation, our second key idea is to utilize relative location and color contrast between superpixels as features and to resolve the saliency estimation from a trimap via a learning-based algorithm. The additional local features and learning-based algorithm complement the global estimation from the high-dimensional color transform-based algorithm. The experimental results on three benchmark datasets show that our approach is effective in comparison with the previous state-of-the-art saliency estimation methods.
Heterogeneous Gaussian Mechanism: Preserving Differential Privacy in Deep Learning with Provable Robustness (2019)

In this paper, we propose a novel Heterogeneous Gaussian Mechanism (HGM) to preserve differential privacy in deep neural networks, with provable robustness against adversarial examples. We first relax the constraint of the privacy budget in the traditional Gaussian Mechanism from (0, 1] to (0, infty), with a new bound of the noise scale to preserve differential privacy. The noise in our mechanism can be arbitrarily redistributed, offering a distinctive ability to address the trade-off between model utility and privacy loss. To derive provable robustness, our HGM is applied to inject Gaussian noise into the first hidden layer. Then, a tighter robustness bound is proposed. Theoretical analysis and thorough evaluations show that our mechanism notably improves the robustness of differentially private deep neural networks, compared with baseline approaches, under a variety of model attacks.
Estrogen Induces Early and Timed Activation of Cyclin-Dependent Kinases 4, 5, and 6 and Increases Cyclin Messenger Ribonucleic Acid Expression in Rat Uterus<sup>1</sup> (1997)

Cyclin-dependent kinases (cdks) are serine-threonine protein kinases that play a key role in the regulation of the mitotic cycle, in transcription initiation, and in the control of specific metabolic pathways in eukaryotic cells. cdk activity is controlled via phosphode-phosphorylation of the catalytic subunits of these enzymes and their physical association with cyclins and cdk inhibitors. In adult rats, estrogen stimulation results in massive proliferation of endometrial epithelial cells, accompanied by functional and structural modifications in all other tissue components of the uterus. We report here that administration of 17 beta-estradiol (E2) to adult ovariectomized rats induces within the first 25 h significant activation of cdk 4, 5, and 6, but not cdk 2, in the uterus, accompanied by increased expression of D-type (D1-3), A and E cyclin messenger RNAs (mRNAs). Furthermore, expression of the cdk inhibitor p27Kip1, a key regulator of uterine functions, is induced by E2 in this organ. Analysis of RNA extracted from E2-stimulated rat endometria shows early accumulation of D1 and D3, but not D2, cyclin mRNA, preceded by transient accumulation of c-fos mRNA. These results indicate an involvement of cdks and cyclins in estrogen actions in adult rat uterus and suggest that cyclins D1 and D3 are part of the molecular pathway that allows hormonal regulation of G1 progression in endometrial cells.
Development and testing of new biologically-based polymers as advanced biocompatible contact lenses (2000)

Nature has evolved complex and elegant materials well suited to fulfill a myriad of functions. Lubricants, structural scaffolds and protective sheaths can all be found in nature, and these provide a rich source of inspiration for the rational design of materials for biomedical applications. Many biological materials are based in some fashion on hydrogels, the crosslinked polymers that absorb and hold water. Biological hydrogels contribute to processes as diverse as mineral nucleation during bone growth and protection and hydration of the cell surface. The carbohydrate layer that coats all living cells, often referred to as the glycocalyx, has hydrogel-like properties that keep cell surfaces well hydrated, segregated from neighboring cells, and resistant to non-specific protein deposition. With the molecular details of cell surface carbohydrates now in hand, adaptation of these structural motifs to synthetic materials is an appealing strategy for improving biocompatibility. The goal of this collaborative project between Prof. Bertozzi's research group, the Centerfor Advanced Materials at Lawrence Berkeley National Laboratory and Sunsoft Corporation was the design, synthesis and characterization of novel hydrogel polymers for improved soft contact lens materials. Our efforts were motivated by the urgent need for improved materials that allow extended wear, and essential feature for those whose occupation requires the use of contact lenses rather than traditional spectacles. Our strategy was to transplant the chemical features of cell surface molecules into contact lens materials so that they more closely resemble the tissue in which they reside. Specifically, we integrated carbohydrate molecules similar to those found on cell surfaces, and sulfoxide materials inspired by the properties of the carbohydrates, into hydrogels composed of biocompatible and manufacturable substrates. The new materials were characterized with respect to surface and bulk hydrophilicity, and non-specific protein adsorption, properties which are thought to correlate with comfort in the eye. The outcome of these studies was the discovery of a new material that is superior to present commercial materials. Contact lenses composed of a sulfoxide acrylate and 2-(hydroxyethyl)methacrylate are presently undergoing clinical evaluation at Sunsoft and, if successful, these novel lenses should be commercially available within the next two years.
<title>"Comparative Thermal Modeling Of Er:YAG, Ho:YAG And CO<formula><inf><roman>2</roman></inf></formula> Laser Pulses For Tissue Vaporization"</title> (1987)

We will present a thermal model for laser pulses with pulse widths small compared to the material's thermal time constant. This model will then be used to generate computer plots of the zones of vaporized tissue as well as the predicted tissue temperature rise. Using published values of absorption coefficients, we will predict the vaporization energy thresholds for Er:YAG (2.94μm), Ho:YAG (2.1μm) and CO<sub>2</sub> (10.6μm) laser pulses. We will also examine the extent of the thermally denatured zone surrounding the zone of vaporization. Using typical energies available from these lasers we will then predict material removed per pulse, and per second.
2 Taxonomy of Retroviruses (1982)

I. INTRODUCTION Although the bulk of this text is concerned with the biology and molecular biology of the RNA tumor viruses, we consider here and, to some extent, in Chapters 6 and 8 the entire Retroviridae virus family. The family encompasses all viruses containing an RNA genome and an RNA-dependent DNA polymerase (reverse transcriptase) enzymic activity (Fenner 1975). The family is divided into three subfamilies: (1) Oncovirinae, including all the oncogenic members and many closely related nononcogenic viruses; (2) Lentivirinae, the “slow” viruses, such as visna virus; and (3) Spumavirinae, the “foamy” viruses that induce persistent infections without any clinical disease. The latter two subfamilies are generally given summary treatment in discussions on retroviruses and, therefore, we propose to present at least some of their salient features. The spumaviruses provide an excellent model system for chronic viral disease, whereas the lentiviruses are in the mystical realm of slow neurological diseases. To some extent, a taxonomical description is, of necessity, a tedious job and relatively unimaginative, since the essence of the matter is covered in the chapters to follow. What we propose to do here is to cover the viruses isolated (or particles seen but without infectious transmission) in the different invertebrate and vertebrate genera. Obviously, much of the focus in later chapters is devoted to the viruses from the best-characterized systems: chickens, mice, cats, cattle, and monkeys. Therefore, the coverage here of the more familiar isolates may seem disproportionately small with respect to the plethora of available data; needless to...
Lung Physiology and Aerosol Deposition Imaged with Positron Emission Tomography (2012)

Physiological conditions and pathophysiological changes in the lungs may affect many applications in aerosol medicine and pulmonary drug delivery. In the diseased lung, spatial heterogeneity in function and structure may cause substantial changes in aerosol transport and local deposition among different lung regions. Non-uniform aerosol deposition affects airway or tissue pharmacological dosing, which could reduce the therapeutic effectiveness of inhalation therapy. This review article presents examples of pulmonary imaging using PET and PET-CT in lung physiology with an emphasis on their implications for aerosol medicine. Measurements of regional ventilation, perfusion, and ventilation/perfusion ratio, by imaging local kinetics of intravenously injected Nitrogen-13 in saline solution, and of pulmonary inflammation, by assessing the regional uptake of the radiotracer (18)F-FDG, are presented. These examples demonstrate that it is possible to access both preexisting conditions, such as heterogeneity of ventilation, perfusion, and/or inflammatory stimuli, which may affect inhalation therapy, and the functional effects of inhaled medications or inflammatory agents on lung regional function. The imaging techniques described could be efficient tools to evaluate quantitatively and noninvasively these processes in vivo. Furthermore, it can be expected that imaging of respiratory structure and function will yield sensitive biomarkers of disease, which will help and speed drug discovery, and the evaluation of novel inhalation therapies.