gebhart/patrepeval huggingface dataset:
Unitary Evolution Recurrent Neural Networks (2015)

Recurrent neural networks (RNNs) are notoriously difficult to train. When the eigenvalues of the hidden to hidden weight matrix deviate from absolute value 1, optimization becomes difficult due to the well studied issue of vanishing and exploding gradients, especially when trying to learn long-term dependencies. To circumvent this problem, we propose a new architecture that learns a unitary weight matrix, with eigenvalues of absolute value exactly 1. The challenge we address is that of parametrizing unitary matrices in a way that does not require expensive computations (such as eigendecomposition) after each weight update. We construct an expressive unitary weight matrix by composing several structured matrices that act as building blocks with parameters to be learned. Optimization with this parameterization becomes feasible only when considering hidden states in the complex domain. We demonstrate the potential of this architecture by achieving state of the art results in several hard tasks involving very long-term dependencies.
Human Granulocytic Ehrlichiosis in Wisconsin and Minnesota: A Frequent Infection with the Potential for Persistence (1996)

Human granulocytic ehrlichiosis (HGE) is a tickborne illness caused by an agent closely related to Ehrlichia equi and Ehrlichia phagocytophila. The clinical presentation is nonspecific, and diagnosis is made infrequently. Sixty-six sera were obtained from 54 patients in Minnesota and Wisconsin with undifferentiated fever during the summer and fall of 1993. Serologic reactivity with E. equi was observed in 6 (11%), including 4 seroconversions, 1 stable titer, and 1 seroreversion. Of the seropositive patients, HGE agent DNA was detected by polymerase chain reaction in the first serum from 4 of 5 patients and was present in the serum of 1 of 2 untreated patients after 21 days, even when E. equi antibodies also were present. HGE is a significant and potentially frequent cause of undifferentiated fever in Wisconsin and Minnesota during seasons with tick activity. The agent may persist in untreated patients for at least 1 months or may be cleared earlier, even if not treated with doxycycline or tetracycline.
New Methods for Competitive Coevolution (1997)

We consider "competitive coevolution," in which fitness is based on direct competition among individuals selected from two independently evolving populations of "hosts" and "parasites." Competitive coevolution can lead to an "arms race," in which the two populations reciprocally drive one another to increasing levels of performance and complexity. We use the games of Nim and 3-D Tic-Tac-Toe as test problems to explore three new techniques in competitive coevolution. "Competitive fitness sharing" changes the way fitness is measured; "shared sampling" provides a method for selecting a strong, diverse set of parasites; and the "hall of fame" encourages arms races by saving good individuals from prior generations. We provide several different motivations for these methods and mathematical insights into their use. Experimental comparisons are done, and a detailed analysis of these experiments is presented in terms of testing issues, diversity, extinction, arms race progress measurements, and drift.
MDS array codes with optimal rebuilding (2011)

MDS array codes are widely used in storage systems to protect data against erasures. We address the rebuilding ratio problem, namely, in the case of erasures, what is the the fraction of the remaining information that needs to be accessed in order to rebuild exactly the lost information? It is clear that when the number of erasures equals the maximum number of erasures that an MDS code can correct then the rebuilding ratio is 1 (access all the remaining information). However, the interesting (and more practical) case is when the number of erasures is smaller than the erasure correcting capability of the code. For example, consider an MDS code that can correct two erasures: What is the smallest amount of information that one needs to access in order to correct a single erasure? Previous work showed that the rebuilding ratio is bounded between 1/2 and 3/4, however, the exact value was left as an open problem. In this paper, we solve this open problem and prove that for the case of a single erasure with a 2-erasure correcting code, the rebuilding ratio is 1/2. In general, we construct a new family of r-erasure correcting MDS array codes that has optimal rebuilding ratio of 1/r in the case of a single erasure. Our array codes have efficient encoding and decoding algorithms (for the case r = 2 they use a finite field of size 3) and an optimal update property.
Ready‐to‐eat snack products: the role of extrusion technology in developing consumer acceptable and nutritious snacks (2013)

Summary Consumer appeal for ready‐to‐eat (RTE) products is forecast to grow rapidly over the next 5 years as consumers demand convenient snacks with exciting sensory and textural properties. Extrusion technology has been used extensively in the production of cereal RTE snacks due to its ease of operation and ability to produce a variety of textures and shapes which appeal to consumers. Many of the existing RTE products are relatively high in sugar and salt, thus being regarded as energy dense but nutritionally poor foods. However, there exists a potential to manipulate the nutritional status of extruded RTEs by altering the digestion potentials of starch and protein, and by the incorporation of bioactive components such as dietary fibre. The review article explores some of the recent research in this field and illustrates opportunities by which the global food industry could react to consumers' requirements for healthful RTE snack products in the coming years.
Near-eye light field displays (2013)

We propose a light-field-based approach to near-eye display that allows for thin, lightweight head-mounted displays capable of depicting accurate accommodation, convergence, and binocular disparity depth cues. Our near-eye light field displays depict sharp images from out-of-focus display elements by synthesizing light fields corresponding to virtual scenes located within the viewer's natural accommodation range. While sharing similarities with existing integral imaging displays and microlens-based light field cameras, we optimize performance in the context of near-eye viewing. Near-eye light field displays support continuous accommodation of the eye throughout a finite depth of field; as a result, binocular configurations provide a means to address the accommodation-convergence conflict occurring with existing stereoscopic displays. We construct a binocular prototype and a GPU-accelerated stereoscopic light field renderer.
Flow Injection Proton Nuclear Magnetic Resonance Spectroscopy Combined With Pattern Recognition Methods: Implications for Rapid Structural Studies and High Throughput Biochemical Screening (1997)

The applicability of novel NMR flow probe technology has been tested by the measurement of 300 MHz 1H NMR spectra of a series of rat urine samples. Compared with conventional automatic operation, the method resulted in a significantly increased rate of sample throughput, required minimal spectrometer optimisation before each measurement and avoided the need for expensive and fragile NMR sample tubes. The NMR approach has been coupled with computer methods for spectral data reduction and classification using, in this case, principal components analysis. The flow probe NMR approach offers distinct advantages in situations where large numbers of samples require NMR analysis in a short period of time. These could include routine samples from high throughput chemical synthesis, biofluid samples for drug toxicity monitoring as shown here, samples for clinical diagnosis or real-time analysis in chemical production facilities.
Mean body weight, height, and body mass index, United States 1960-2002. (2004)

This report presents trends in national estimates of mean weight, height, and body mass index (BMI) from the National Health Examination and the National Health and Nutrition Examination Surveys between 1960 and 2002. The tables included in this report present data for adults by sex, race/ethnicity, and age group and for children by sex and year of age. Mean weight and BMI have increased for both sexes, all race/ethnic groups, and all ages. Among adults, mean weight increased more than 24 pounds. Although not as dramatically, mean height has also increased for most ages and for both males and females.
Designing specific protein–protein interactions using computation, experimental library screening, or integrated methods (2012)

Given the importance of protein-protein interactions for nearly all biological processes, the design of protein affinity reagents for use in research, diagnosis or therapy is an important endeavor. Engineered proteins would ideally have high specificities for their intended targets, but achieving interaction specificity by design can be challenging. There are two major approaches to protein design or redesign. Most commonly, proteins and peptides are engineered using experimental library screening and/or in vitro evolution. An alternative approach involves using protein structure and computational modeling to rationally choose sequences predicted to have desirable properties. Computational design has successfully produced novel proteins with enhanced stability, desired interactions and enzymatic function. Here we review the strengths and limitations of experimental library screening and computational structure-based design, giving examples where these methods have been applied to designing protein interaction specificity. We highlight recent studies that demonstrate strategies for combining computational modeling with library screening. The computational methods provide focused libraries predicted to be enriched in sequences with the properties of interest. Such integrated approaches represent a promising way to increase the efficiency of protein design and to engineer complex functionality such as interaction specificity.
MOSFET drain breakdown voltage (1986)

The grounded-gate or gate-assisted drain breakdown voltage of n-channel MOSFET's has been characterized for wide ranges of oxide thickness and substrate doping concentration. Two distinct regimes, one being channel-doping limited and the other being oxide-thickness limited, have been identified. We propose that these two regimes reflect two possible locations of breakdown-at the n+-p junction and in the deep-depletion layer in the n+ drain. They can be separated by their different breakdown voltage dependences on V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</inf> and require different approaches to process improvement.
Skin reactions to hexylene glycol (1989)

Hexylene glycol (HG), which has been used for years in industrial chemicals and cosmetics, has recently been introduced in topical corticosteroids. We studied the irritant and sensitizing properties of HG in eczema patients. HG at 50% or 30% and propylene glycol (PG) at 30% in water were patch tested in 823 eczema patients subjected to routine patch testing. Oedema and erythema reactions from HG occurred in 2.8% of the patients. The corresponding result for PG was 3.8%. 50% HG equalled 30% PG in producing a visible reaction. In patch tests with dilution series, 2 patients reacted to 1% HG, but in both cases ROAT with HG remained negative. One other patient with a 3+ patch test reaction to both 30% PG and 50% HG had a positive ROAT result to 30% HG in water and to 5% PG in a cream base. PG, but not HG, increased transepidermal water loss both in atopic normal-looking skin and among healthy controls. The present results suggest that HG is less irritating that PG under occlusion, but that delayed contact allergic reactions may occur.
Interleukin-1 and interleukin-1 antagonism (1991)

The polypeptide cytokine interleukin-1 (IL-1) affects nearly every tissue and organ system. IL-1 is the prototype of the pro-inflammatory cytokines in that it induces the expression of a variety of genes and the synthesis of several proteins that, in turn, induce acute and chronic inflammatory changes. IL-1 is also the prototypic "alarm" cytokine in that it brings about increases in a variety of defense mechanisms, particularly immunologic and hematologic responses. Most studies on the biology of IL-1 have been performed in animals, but human subjects have recently been injected with recombinant IL-1 and the results confirm the two fundamental properties of IL-1 as being both a mediator of disease as well as of host defense. However, in either situation, over or continued production of IL-1 leads to debilitation of normal host functions; therefore, reduction of IL-1 synthesis or its effects becomes a target of therapy in many diseases. In this review, the structure, gene expression, synthesis, and secretion of IL-1 are described. In addition, the two IL-1 surface receptors, possible signal transduction mechanisms, various biologic activities, and production of IL-1 during disease states are discussed. Similarities and differences between IL-1, tumor necrosis factor, and IL-6 are presented. Although various agents for reducing the synthesis and/or for antagonizing the effects of IL-1 have been proposed, the recent cloning of a naturally occurring IL-1 receptor antagonist (IL-1ra) has opened new experimental and clinical approaches. The ability of this IL-1ra to block the triggering of IL-1 receptors in animals without agonist effects has reduced the severity of diseases such as hemodynamic shock, lethal sepsis, inflammatory bowel disease, experimental arthritis, and the spontaneous proliferation of human leukemic cells.
Effects of Tamoxifen Therapy on Lipid and Lipoprotein Levels in Postmenopausal Patients With Node-Negative Breast Cancer (1990)

We conducted a 2-year, randomized, double-blind, placebo-controlled toxicity trial of therapy with tamoxifen (10 mg twice a day) in 140 postmenopausal women with a history of breast cancer and histologically negative axillary lymph nodes. These women had been treated with surgery with or without radiotherapy. At a 3-month evaluation, tamoxifen-treated women showed a significant decrease in fasting plasma levels of total cholesterol and low-density lipoprotein (LDL) cholesterol, which persisted at 6- and 12-month evaluations. During the first 12 months, plasma triglyceride levels increased; small but significant decreases in high-density lipoprotein cholesterol (HDL) were observed in tamoxifen-treated women, but ratios of total cholesterol to HDL cholesterol and of LDL to HDL cholesterol changed favorably. While data relating lipid/lipoprotein profiles and cardiovascular disease are limited in women, current evidence suggests that total cholesterol and possibly low-density lipoprotein cholesterol are risk factors. We conclude that during the first 12 months of treatment, tamoxifen exerts a favorable effect on the lipid profile in postmenopausal women with early stage breast cancer.
Isolation of peptides from phage-displayed random peptide libraries that interact with the talin-binding domain of vinculin (1997)

Peptides isolated from combinatorial libraries typically interact with, and thus help to characterize, biologically relevant binding domains of target proteins. To characterize the binding domains of the focal adhesion protein vinculin, vinculin-binding peptides were isolated from two phage-displayed random peptide libraries. Altogether, five non-similar vinculin-binding peptides were identified. Despite the lack of obvious sequence similarity between the peptides, binding and competition studies indicated that all five interact with the talin-binding domain of vinculin and do not disrupt the binding of alpha-actinin or paxillin to vinculin. The identified peptides and talin bind to vinculin in a comparable manner; both bind to immobilized vinculin, but neither binds to soluble vinculin unless the C-terminus of vinculin has been deleted. An analysis of amino acid variants of one of the peptides has revealed three non-contiguous motifs that also occur in the region of talin previously demonstrated to bind vinculin. Amino acid substitutions within a 127-residue segment of talin capable of binding vinculin confirmed the importance of two of the motifs and suggest that residues critical for binding are within a 16-residue region. This study demonstrates that the vinculin-binding peptides interact with vinculin in a biologically relevant manner and represent an excellent tool for further study of the biochemistry of vinculin.
Dynamic imaging of the upper airway during respiration in normal subjects (1993)

The present study was conducted to determine the effects of quiet respiration on upper airway caliber in 15 normal subjects by using cine computed tomography. The cine computed tomography (Imatron) scanner was programmed to obtain 8-mm-thick axial slices every 0.4 s during inspiration and expiration at four anatomic levels, from the nasopharynx to the retroglossal region. Airflow (pneumotachograph) was measured, and tidal volume was obtained by integration. Upper airway area, determined by an objective edge detection algorithm, was plotted as a function of tidal volume to generate a loop describing upper airway area changes at each level during a respiratory cycle. The results demonstrate a 17% change in airway size across all anatomic levels during respiration. The maximum upper airway cross-sectional area at all four anatomic levels was significantly greater during expiration than during inspiration. Other major findings include 1) upper airway cross-sectional area decreases slightly during early inspiration, enlarges toward end inspiration, and is larger at end inspiration than at the beginning of inspiration; 2) upper airway cross-sectional area enlarges from end inspiration to the first point in expiration; the airway enlarges further, reaching its maximum early in expiration, and then narrows toward end expiration; and 3) the changes in upper airway dimensions during resting tidal breathing are greater in the lateral than in the anteroposterior direction. The data suggest that during inspiration, the action of negative intraluminal pressure may be largely balanced by the action of the upper airway dilator muscles, whereas during expiration, positive intraluminal pressure produces expansion of the upper airway.
Phase I Dose-Escalation Study and Biomarker Analysis of E7080 in Patients with Advanced Solid Tumors (2011)

E7080 has manageable toxicity up to 13 mg bid when administered in a 2-week-on/1-week-off cycle and shows preliminary activity for durable disease control. Biomarker analysis suggested antiangiogenic activity correlated with antitumor activity in patients with a wide range of solid tumors.
Exploiting Topological Constraints To Reveal Buried Sequence Motifs in the Membrane-Bound N-Linked Oligosaccharyl Transferases (2011)

The central enzyme in N-linked glycosylation is the oligosaccharyl transferase (OTase), which catalyzes glycan transfer from a polyprenyldiphosphate-linked carrier to select asparagines within acceptor proteins. PglB from Campylobacter jejuni is a single-subunit OTase with homology to the Stt3 subunit of the complex multimeric yeast OTase. Sequence identity between PglB and Stt3 is low (17.9%); however, both have a similar predicted architecture and contain the conserved WWDxG motif. To investigate the relationship between PglB and other Stt3 proteins, sequence analysis was performed using 28 homologues from evolutionarily distant organisms. Since detection of small conserved motifs within large membrane-associated proteins is complicated by divergent sequences surrounding the motifs, we developed a program to parse sequences according to predicted topology and then analyze topologically related regions. This approach identified three conserved motifs that served as the basis for subsequent mutagenesis and functional studies. This work reveals that several inter-transmembrane loop regions of PglB/Stt3 contain strictly conserved motifs that are essential for PglB function. The recent publication of a 3.4 Å resolution structure of full-length C. lari OTase provides clear structural evidence that these loops play a fundamental role in catalysis [ Lizak , C. ; ( 2011 ) Nature 474 , 350 - 355 ]. The current study provides biochemical support for the role of the inter-transmembrane domain loops in OTase catalysis and demonstrates the utility of combining topology prediction and sequence analysis for exposing buried pockets of homology in large membrane proteins. The described approach allowed detection of the catalytic motifs prior to availability of structural data and reveals additional catalytically relevant residues that are not predicted by structural data alone.
<title>Optical routing with liquid crystal arrays</title> (2001)

This paper outlines two ways in which liquid crystal devices can be used as optical switches in telecommunications networks. This has become a very important area of research as electronic switches are becoming bottleneck in both circuit switched and packet switched networks. These two applications have been highlighted as they require radically different switching techniques, yet liquid crystals can be used in both as the reconfigurable element. The first application is in circuit switching, where optical loss, crosstalk and polarization dependence are all critical parameters, whereas reconfigurration time is not. For this application a reconfigurable hologram written in phase with liquid crystal modulators is used to diffract optical beams in an optically transparent switch fabric. This technique does not suit packet switching as a much faster reconfigurration rate is required and loss and crosstalk are not critical. Hence a shutter based crossbar is used as a packet switch using a liquid crystal which can be reconfigured in 1 msec. A hybrid electronic/optical approach is also taken as this allows a much more scalable packet switch to be built.
Engineering macrophages to eat cancer: from “marker of self” CD47 and phagocytosis to differentiation (2017)

The ability of a macrophage to engulf and break down invading cells and other targets provides a first line of immune defense in nearly all tissues. This defining ability to "phagos" or devour can subsequently activate the entire immune system against foreign and diseased cells, and progress is now being made on a decades-old idea of directing macrophages to phagocytose specific targets, such as cancer cells. Engineered T cells provide precedence with recent clinical successes against liquid tumors, but solid tumors remain a challenge, and a handful of clinical trials seek to exploit the abundance of tumor-associated macrophages instead. Although macrophage differentiation into such phenotypes with deficiencies in phagocytic ability can raise challenges, newly recognized features of cancer cells that might be manipulated to increase the phagocytosis of those cells include ≥1 membrane protein, CD47, which broadly inhibits phagocytosis and is abundantly expressed on all healthy cells. Physical properties of the target also influence phagocytosis and again relate-via cytoskeleton forces-to differentiation pathways in solid tumors. Such pathways extend to mechanosensing by the nuclear lamina, which is known to influence signaling by soluble retinoids that can regulate the macrophage SIRPα, the receptor for CD47. Here, we highlight some of those past, present, and rapidly emerging efforts to understand and control macrophages for cancer therapy.