gebhart/patrepeval huggingface dataset:
Replica-molded high-Q polymer microresonators (2004)

Ultrahigh-Q microtoroids on a chip are applied as replication masters to demonstrate replica-molded high-Q microresonator arrays. Replica Q factors are nearly material loss limited, affirming the integrity of the replication process, and are as high as 5 x 10(6), or nearly a factor of 40 greater than previous polymer-based devices. Because the molding process is nondestructive, both the master and the molds can be reused. Additionally, by using a novel optical polymer (Vicast), we demonstrate storage of high-Q microresonators in the mold for weeks, providing a method to preserve the whispering-gallery Q factor.
State Space Implementation of the Algorithm of Mode Isolation (2003)

The Algorithm of Mode Isolation (AMI) extracts modal properties from complex frequency response data. Previous work used classic undamped modes as the analytical framework for the algorithm. The present work extends the algorithm to implement damped modal analysis, in which the eigenvalues and eigenvectors are complex. In order to assess how well this reformulation performs when natural frequencies are close and drive point mobilities are low, a prototypical system consisting of a cantilever beam with attached subsystems is introduced. One of these subsystems is selected to be a tuned vibration absorber for the isolated beam, so the system features a combination of modes whose natural frequencies are close and modes whose drive point mobility is low. The time domain response of this system is evaluated, contaminated with substantial white noise, and then FFT processed in order to obtain synthetic complex frequency response data. The performance of AMI is evaluated by comparing extracted values for natural frequency, modal damping ratio, and complex normal mode vectors to the analytical values. The results reveal that the pair of modes having proximite natural frequencies are accurately identified. Natural frequencies and damping ratios for those modes whose drive mobility is low are identified by processing the ensemble of frequency response functions, but identification of normal mode coefficients for such modes remains problematic.
Facet evolution in selective epitaxial growth of Si by cold-wall ultrahigh vacuum chemical vapor deposition (2004)

Si epitaxial layers were selectively grown on local-oxidation-of-silicon-patterned Si (100) substrates by cold-wall ultrahigh vacuum chemical vapor deposition. The Si windows were aligned along the [110] direction on Si (100) surface. As growth temperature increased from 550 to 650 °C, the development of (111) facets was dramatically suppressed, and the Si growth on sidewall facet planes was decreased. It is believed that surface diffusion of Si adatoms plays an important role in the morphological evolution of selective epitaxial growth (SEG). We propose a model to explain our experimental observations, and to clarify the effect of growth temperature on the facet morphology in terms of the surface mass transport and mass accumulation processes on facet surfaces. (211) facet formation between (311) and (111) facets in Si SEG is reported, and the stability of the (211) plane is also discussed. Finally, we investigated the changes in facet morphology with Si layer thickness, which supports our model for the facet evolution observed in Si SEG.
A geometric snake model for segmentation of medical imagery (1997)

In this note, we employ the new geometric active contour models formulated in [25] and [26] for edge detection and segmentation of magnetic resonance imaging (MRI), computed tomography (CT), and ultrasound medical imagery. Our method is based on defining feature-based metrics on a given image which in turn leads to a novel snake paradigm in which the feature of interest may be considered to lie at the bottom of a potential well. Thus, the snake is attracted very quickly and efficiently to the desired feature.
Retinal nerve fiber layer birefringence evaluated with polarization sensitive spectral domain OCT and scanning laser polarimetry: A comparison (2008)

A polarization-sensitive spectral domain optical coherence tomography (PS-SD-OCT) system is used to measure phase retardation and birefringence of the human retinal nerve fiber layer (RNFL) in vivo. The instrument records three parameters simultaneously: intensity, phase retardation and optic-axis orientation. 3D data sets are recorded in the optic nerve-head area of a healthy and a glaucomatous eye, and the results are presented in various ways: En-face phase-retardation maps of the RNFL are generated from the recorded 3D data and results are compared with scanning laser polarimetry (SLP). The depth information provided by OCT is used to segment the RNFL in the intensity image and measure the RNFL thickness. From the retardation and thickness data, 2D birefringence maps of the RNFL are derived. Circumpapillary plots of RNFL retardation and thickness obtained by PS-SD-OCT are quantitatively compared with those obtained by SLP.
Flexible Virtual Network Provisioning over Distance-Adaptive Flex-Grid Optical Networks (2014)

We present a flexible virtual optical network provisioning procedure for distance-adaptive flex-grid optical networks. Simulations show ~3 times increase in effective network capacity by leveraging the combined effect of flexible node mapping and distance-adaptive modulation.
Dihydrofolate Reductase from Pyrimethamine-resistant Plasmodium berghei (1970)

Abstract An investigation of the H2-folate reductases from pyrimethamine-sensitive (Pb/WLTM) and -resistant (Pb/WLTM/50–63) strains of Plasmodium berghei has revealed that the specific activity of the enzyme from the resistant strain is 10-fold higher than that of the sensitive strain. Since turnover numbers (based on amethopterin binding) are equivalent, the increase in specific activity must be due to an increased number of catalytic sites. Marked differences were found between the two enzymes in several of the properties studied. The Km value for H2-folate is 12.4-fold higher for the enzyme from the resistant strain. The Pb/WLTM/50–63 H2-folate reductase is only slightly stimulated by KCl, in contrast to the 3-fold stimulation observed with the enzyme from the sensitive strain. The Ki values for pyrimethamine and two other antifolates are higher for the enzyme from the resistant strain. In addition, the inhibition is competitive with H2-folate for the enzyme from Pb/WLTM and noncompetitive for the enzyme from Pb/WLTM/50–63. It is proposed that Pb/WLTM/50–63 is resistant in vivo to the action of pyrimethamine because of the combined effects of the increase in enzyme content and the decrease in inhibitor binding. It is suggested that these alterations in enzymatic properties and enzyme levels reflect mutations in the gene or genes responsible for the coding of this enzyme.
Tumor suppression and normal aging in mice with constitutively high p53 activity (2006)

The p53 inhibitor murine double-minute gene 2 (Mdm2) is a target for potential cancer therapies, however increased p53 function can be lethal. To directly address whether reduced Mdm2 function can inhibit tumorigenesis without causing detrimental side effects, we exploited a hypomorphic murine allele of mdm2 to compare the effects of decreased levels of Mdm2 and hence increased p53 activity on tumorigenesis and life span in mice. Here we report that mice with decreased levels of Mdm2 are resistant to tumor formation yet do not age prematurely, supporting the notion that Mdm2 is a promising target for cancer therapeutics.
A statistical model-based voice activity detection (1999)

In this letter, we develop a robust voice activity detector (VAD) for the application to variable-rate speech coding. The developed VAD employs the decision-directed parameter estimation method for the likelihood ratio test. In addition, we propose an effective hang-over scheme which considers the previous observations by a first-order Markov process modeling of speech occurrences. According to our simulation results, the proposed VAD shows significantly better performances than the G.729B VAD in low signal-to-noise ratio (SNR) and vehicular noise environments.
The tyrosyl‐tRNA synthetase from <i>Escherichia coli</i> (1982)

The structural component of the tyrS gene of Escherichia coli, comprising 1269 base pairs, has been fully sequenced by the combined M13/dideoxychain termination approach. The gene has a codon usage pattern which is typical of highly expressed proteins and similar to other Escherichia coli aminoacyl-tRNA synthetase genes. Peptide purification and sequencing has been used to locate the N-terminus and to provide confirmation of 95% of the translated protein sequence. This latter yields on Mr of 47,403 for the Escherichia coli tyrosyl-tRNA synthetase, and reveals considerable homology with the primary structure of the analogous enzyme isolated from Bacillus staerothermophilus.
Cloned Cattle Derived from a Novel Zona-Free Embryo Reconstruction System (2003)

As the demand for cloned embryos and offspring increases, the need arises for the development of nuclear transfer procedures that are improved in both efficiency and ease of operation. Here, we describe a novel zona-free cloning method that doubles the throughput in cloned bovine embryo production over current procedures and generates viable offspring with the same efficiency. Elements of the procedure include zona-free enucleation without a holding pipette, automated fusion of 5-10 oocyte-donor cell pairs and microdrop in vitro culture. Using this system, zona-free embryos were reconstructed from five independent primary cell lines and cultured either singularly (single-IVC) or as aggregates of three (triple-IVC). Blastocysts of transferable quality were obtained at similar rates from zona-free single-IVC, triple-IVC, and control zona-intact embryos (33%, 25%, and 29%, respectively). In a direct comparison, there was no significant difference in development to live calves at term between single-IVC, triple-IVC, and zona-intact embryos derived from the same adult fibroblast line (10%, 13%, and 15%, respectively). This zona-free cloning method could be straightforward for users of conventional cloning procedures to adopt and may prove a simple, fast, and efficient alternative for nuclear cloning of other species as well.
Expression of human tumor-associated antigen RCAS1 in Reed-Sternberg cells in association with Epstein-Barr virus infection: A potential mechanism of immune evasion (2001)

RCAS1 (receptor-binding cancer antigen expressed on SiSo cells) is present in neoplastic cells, induces apoptosis of natural killer (NK)/T cells and plays a role in immune evasion. Fas ligand (FasL) is considered to have similar roles. The Epstein-Barr virus (EBV)-encoded latent membrane protein is expressed by malignant Hodgkin and Reed-Sternberg (H&RS) cells of EBV-associated Hodgkin's disease (HD) and considered to be a target of cytotoxic T lymphocytes (CTLs). However, CTL response is inadequate in HD. To determine whether RCAS1 and FasL are expressed in EBV-associated HD and participate in immune evasion, tissues of 20 EBV(-) and 15 EBV(+) HD cases were immunohistochemically stained for RCAS1, FasL and HLA classes I and II, whose deficiencies could explain CTL escape. Lymphocytes surrounding H&RS cells tended to be CD4(+) cells and rarely CD8(+), TIA-1(+) (cytotoxic marker) or NK cells. HLA class I and/or II were expressed in all EBV(+) HD cases, and RCAS1-expressing H&RS cells were found in 14/15 (93%) EBV(+) HD cases but only 8/20 (40%) EBV(-) HD cases (p < 0.05). FasL was detected in 9/15 (60%) and 7/20 (35%) EBV(+) and EBV(-) HD cases, respectively. ssDNA-positive (apoptotic) lymphocytes, surrounding H&RS cells, were rarely seen but were present in RCAS1(+) cases (20/22 cases, 91%) rather than negative cases (0/13 cases, 0%) (p < 0.005). Our findings suggest that EBV(+) H&RS cells might evade the host immune response by expressing RCAS1 rather than FasL.
Natural Defenses against Candida Colonization Breakdown in the Oral Cavities of the Elderly (1999)

Candida colonization of the oral cavity increases in the elderly. A major predisposing condition is denture use, which also increases in the elderly. To test whether the increase in colonization is age-related in a fashion independent of denture use, we analyzed the frequency (incidence) of carriage, the intensity of carriage, the multiplicity of species, and the genetic relatedness of strains in the oral cavities of 93 test subjects separated into the three age groups: 60 to 69 yr, 70 to 79 yr, and > or = 80 yr. Each age group was further subdivided into subjects with and without dentures, and into males and females. The results demonstrate that the frequency of carriage, the intensity of carriage, and multispecies carriage all increase as a function of age and differ according to gender, in both cases independent of denture use, suggesting that the natural suppression of yeast carriage in the oral cavity breaks down in the elderly. In addition, it is demonstrated that Candida glabrata colonizes the oral cavities of elderly individuals without dentures only after 80 yr of age, suggesting that there are age-related compromising conditions other than denture use in this most elderly age group.
Hierarchical analyzer for VLSI power supply networks based on a new reduction method (2002)

The author presents an algorithm for hierarchical analysis of VLSI power supply networks. The algorithms utilizes the design hierarchy and is independent of network topology. Networks in each block are recursively reduced to equivalent and small circuits in a bottom-up manner, and node voltages in the network are calculated in a top-down manner. This makes it possible to decrease the size of the matrix to be solved and to reduce the execution time. Using the prototype program XPOWER, the power lines of excess current density and voltage drop are fed back quickly to the chip floor plan designer. XPOWER reduces the matrix size to be solved from 1/10 to 1/40 and its execution is about six times faster than with the flat method for the tested examples.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The Concepts of Stress and Stress System Disorders (1992)

<h3>Objective.</h3> —This article defines stress and related concepts and reviews their historical development. The notion of a stress system as the effector of the stress syndrome is suggested, and its physiologic and pathophysiologic manifestations are described. A new perspective on human disease states associated with dysregulation of the stress system is provided. <h3>Data Sources.</h3> —Published original articles from human and animal studies and selected reviews. Literature was surveyed utilizing MEDLINE and the<i>Index Medicus</i>. <h3>Study Selection.</h3> —Original articles from the basic science and human literature consisted entirely of controlled studies based on verified methodologies and, with the exception of the most recent studies, replicated by more than one laboratory. Many of the basic science and clinical studies had been conducted in our own laboratories and clinical research units. Reviews cited were written by acknowledged leaders in the fields of neurobiology, endocrinology, and behavior. <h3>Data Extraction.</h3> —Independent extraction and cross-referencing by the authors. <h3>Data Synthesis.</h3> —Stress and related concepts can be traced as far back as written science and medicine. The stress system coordinates the generalized stress response, which takes place when a stressor of any kind exceeds a threshold. The main components of the stress system are the corticotropin-releasing hormone and locus ceruleus-norepinephrine/autonomic systems and their peripheral effectors, the pituitary-adrenal axis, and the limbs of the autonomic system. Activation of the stress system leads to behavioral and peripheral changes that improve the ability of the organism to adjust homeostasis and increase its chances for survival. There has been an exponential increase in knowledge regarding the interactions among the components of the stress system and between the stress system and other brain elements involved in the regulation of emotion, cognitive function, and behavior, as well as with the axes responsible for reproduction, growth, and immunity. This new knowledge has allowed association of stress system dysfunction, characterized by sustained hyperactivity and/or hypoactivity, to various pathophysiologic states that cut across the traditional boundaries of medical disciplines. These include a range of psychiatric, endocrine, and inflammatory disorders and/or susceptibility to such disorders. <h3>Conclusions.</h3> —We hope that knowledge from apparently disparate fields of science and medicine integrated into a working theoretical framework will allow generation and testing of new hypotheses on the pathophysiology and diagnosis of, and therapy for, a variety of human illnesses reflecting systematic alterations in the principal effectors of the generalized stress response. We predict that pharmacologic agents capable of altering the central apparatus that governs the stress response will be useful in the treatment of many of these illnesses. (<i>JAMA</i>. 1992;267:1244-1252)
An Efficient Mode Decision Algorithm for H.264/AVC Encoding Optimization (2007)

The H.264 video coding standard significantly outperforms previous standards in terms of coding efficiency. However, this comes as a cost of extremely high computational complexity due to mode decision where variable block size motion estimation (ME) is employed. In this paper, we propose an efficient algorithm to jointly optimize mode decision and ME. A theoretical analysis is performed to study the sufficient condition to detect all-zero blocks in H.264, and thus adaptive thresholds are derived to early terminate mode decision and ME. Besides the aforementioned early termination technique, the proposed algorithm also introduces temporal-spatial checking, thresholds based prediction and monotonic error surface based prediction methods to skip checking unnecessary modes. Experimental results demonstrate that the proposed algorithm can significantly reduce the computational complexity of H.264 encoding while maintaining almost the same rate distortion (RD) performance as the original encoder
Immunostimulatory Oligodeoxynucleotide Containing TTTCGTTT Motif from <i>Lactobacillus rhamnosus</i> GG DNA Potentially Suppresses OVA‐specific IgE Production in Mice (2008)

In a previous study of the immunoregulatory properties of commensal bacterial DNA, we identified the strong immunostimulatory oligodeoxynucleotide (ISS-ODN) ID35 in the genomic DNA of Lactobacillus rhamnosus GG (LGG). The observed effects of ID35 are because of the unique TTTCGTTT motif located at the 5' end of the ODN, which is different from the previously identified ISS motifs in humans and mice. In the present study, we used an ovalbumin (OVA)-sensitized mouse model to show that ID35 is a potent suppressor of antigen-specific immunoglobulin E (IgE) production in vivo. This effect was toll-like receptor 9-dependent, as GpC negID35 failed to suppress antigen-specific IgE production. ID35 activated the specific subset of CD11c+CD8a+ dendritic cells, which are associated with T-helper 1 (Th1)-type systemic responses, and effectively induced interferon-gamma (IFN-gamma) production by CD4+ T cells in OVA-challenged mice. These immunoregulatory effects of ID35 were comparable with those induced by the murine prototype ODN 1826. Thus, ID35 is the first ISS-ODN with such a strong immunostimulatory and IgE suppressor activity to be found in immunobiotic bacterial DNA.
Cello (1998)

In this paper, we present the Cello disk scheduling framework for meeting the diverse service requirements of applications. Cello employs a two-level disk scheduling architecture, consisting of a class-independent scheduler and a set of class-specific schedulers. The two levels of the framework allocate disk bandwidth at two time-scales: the class-independent scheduler governs the coarse-grain allocation of bandwidth to application classes, while the class-specific schedulers control the fine-grain interleaving of requests. The two levels of the architecture separate application-independent mechanisms from application-specific scheduling policies, and thereby facilitate the co-existence of multiple class-specific schedulers. We demonstrate that Cello is suitable for next generation operating systems since: (i) it aligns the service provided with the application requirements, (ii) it protects application classes from one another, (iii) it is work-conserving and can adapt to changes in work-load, (iv) it minimizes the seek time and rotational latency overhead incurred during access, and (v) it is computationally efficient.
Apoptosis Signal-regulating Kinase 1 (ASK1) Induces Neuronal Differentiation and Survival of PC12 Cells (2000)

Apoptosis signal-regulating kinase 1 (ASK1) is a ubiquitously expressed mitogen-activated protein kinase kinase kinase that activates the c-Jun N-terminal kinase (JNK) and p38 mitogen-activated protein kinase signaling cascades. We report here that expression of constitutively active ASK1 (ASK1DeltaN) induces neurite outgrowth in the rat pheochromocytoma cell line PC12. We found that p38 and to a lesser extent JNK, but not ERK, were activated by the expression of ASK1DeltaN in PC12 cells. ASK1DeltaN-induced neurite outgrowth was strongly inhibited by treatment with the p38 inhibitor SB203580 but not with the MEK inhibitors, suggesting that activation of p38, rather than of ERK, is required for the neurite-inducing activity of ASK1 in PC12 cells. We also observed that ASK1DeltaN induced expression of several neuron-specific proteins and phosphorylation of neurofilament proteins, confirming that PC12 cells differentiated into mature neuronal cells by ASK1. Moreover, ASK1DeltaN-expressing PC12 cells survived in serum-starved condition. ASK1 thus appears to mediate signals leading to both differentiation and survival of PC12 cells. Together with previous reports indicating that ASK1 functions as a pro-apoptotic signaling intermediate, these results suggest that ASK1 has a broad range of biological activities depending on cell types and/or cellular context.
Stress State Variables for Unsaturated Soils (1977)

Practicing engineers are well aware that many of the problems they encounter involve unsaturated soils. The construction of earthfill dams, highways, and airport runways all use compacted soils that are unsaturated. Also, large portions of the earth's land surface are subjected to desiccating influences that leave the upper portion of the profile cracked and unsaturated.
Developmental Regulation of Human Globin Genes in Transgenic Mice (1985)

The globin gene family represents a particularly interesting system for the study of developmental gene regulation. Not only are the globin genes expressed specifically in erythroid cells, but different members of the gene family are utilized at sequential stages of development, a phenomenon known as “hemoglobin switching.” Of the genes encoding β-like chains in the human, the first to be expressed is the ϵ-globin gene, which is active primarily in the primitive erythroid cells that develop in the blood islands of the yolk sac. Between the 5th and 10th weeks of gestation, there is a shift to “definitive” fetal liver erythropoiesis, and during this time the ϵ gene is switched off and the two γ-globin genes begin to be expressed. The γ-globin genes are maximally active through most of fetal life and are switched off around the time of birth. In contrast, the “adult” genes, δ and β, are active...