gebhart/patrepeval huggingface dataset:
Subspace Pursuit for Compressive Sensing Signal Reconstruction (2009)

We propose a new method for reconstruction of sparse signals with and without noisy perturbations, termed the subspace pursuit algorithm. The algorithm has two important characteristics: low computational complexity, comparable to that of orthogonal matching pursuit techniques when applied to very sparse signals, and reconstruction accuracy of the same order as that of linear programming (LP) optimization methods. The presented analysis shows that in the noiseless setting, the proposed algorithm can exactly reconstruct arbitrary sparse signals provided that the sensing matrix satisfies the restricted isometry property with a constant parameter. In the noisy setting and in the case that the signal is not exactly sparse, it can be shown that the mean-squared error of the reconstruction is upper-bounded by constant multiples of the measurement and signal perturbation energies.
An N-terminal fragment of bactericidal/permeability-increasing protein protects against hemodynamic and metabolic derangements in rat Gram-negative sepsis (1996)

Recombinant N-terminal fragments of bactericidal/permeability-increasing protein (BPI) are protective in acute models of endotoxemia or bacteremia. However, their usefulness in models utilizing slow infusion of bacteria has not been reported. Anesthetized rats were infused with Escherichia coli 07:K1 bacteria (5 x 109 cfu/h) for 2 h. Hemodynamics, glucose and lactate levels, tumor necrosis factor-α (TNFα) and endotoxin levels were measured for 210 min. The rats were treated with a 2 h infusion of RBPI 21 or thaumatin (10 mg/kg/h), a protein that does not bind endotoxin but is similar to rBPI 21 in molecular weight and isoelectric point. Control rats received only saline and vehicle. In animals treated with thaumatin, blood pressure, cardiac index and stroke volume declined rapidly (within 30 min). After 90 min glucose levels were significantly depressed whereas lactate was elevated. Endotoxemia (764 ± 353 ng/ml) was observed within 30 min. rBPI 21 significantly reduced the cardiovascular depression observed after 30 min and abolished all hemodynamic responses by the end of the experiment. rBPI 21 significantly reduced hypoglycemia, elevated lactate levels, and endotoxin levels after 90 min. These results indicate that reduction of endotoxin levels resulting from RBPI 21 therapy leads to significant protection in this model of acute Gram-negative bacterial sepsis.
A new algorithm for routing tree construction with buffer insertion and wire sizing under obstacle constraints (2001)

Buffer insertion and wire sizing are critical in deep submicron VLSI design. This paper studies the problem of constructing routing trees with simultaneous buffer insertion and wire sizing in the presence of routing and buffer obstacles. No previous algorithms consider all these factors simultaneously. Previous dynamic programming based algorithm is first extended to solve the problem. However, with the size of routing graph increasing and with wire sizing taken into account, the time and space requirement increases enormously. Then a new approach is proposed to formulate the problem as a series of graph problems. The routing tree solution is obtained by finding shortest paths in a series of graphs. In the new approach, wire sizing can be handled almost without any additional time and space requirement, Moreover, the time and space requirement is only polynomial in terms of the size of routing graph. Our algorithm differs from traditional dynamic programming, and is capable of addressing the problem of inverter insertion and sink polarity. Both theoretical and experimental results show that the graph-based algorithm outperforms the DP-based algorithm by a large margin. We also propose a hierarchical approach to construct routing tree for a large number of sinks.
Clinical use of C-reactive protein for the prognostic stratification of patients with ischemic heart disease. (2001)

C-reactive protein (CRP), the prototypic acute phase reactant and a sensitive marker of inflammation, consistently predicts new coronary events, including myocardial infarction and death, in patients with ischemic heart disease. The data are very consistent with regard to the long-term outcome, but in many studies are also significant for in-hospital events. The predictive value of CRP is, in the majority of the studies, independent of and additive to that of the troponins. Moreover recent data suggest that CRP may be a reliable marker of the risk of restenosis after percutaneous coronary interventions and that its levels can be modulated by statins. Taken together, all these data suggest that CRP, probably with different cut-offs, should be used as a marker of risk and as a guide to therapy in patients hospitalized for acute coronary syndromes and in outpatients suffering from ischemic heart disease.
Neurotensin is an autocrine trophic factor stimulated by androgen withdrawal in human prostate cancer. (1994)

After therapeutic hormone deprivation, prostate cancer cells often develop androgen-insensitive growth through mechanisms thus far undefined. Neuropeptides have been previously implicated as growth factors in some prostate cancers. Here, we demonstrate that androgen-sensitive LNCaP human prostate cancer cells produce and secrete neurotensin following androgen withdrawal. We show that while LNCaP cells express the neurotensin receptor, only androgen-deprived cells exhibit a growth response to exogenous neurotensin. We further demonstrate that androgen-stimulated cells may be refractory to exogenous neurotensin due to androgen induction of a metalloprotease active toward neurotensin. Thus, prostate cancer cells deprived of androgen develop an alternative autocrine growth mechanism involving neurotensin.
Three-terminal devices of high- Tc superconductors: A status report and future challenges (1992)

A study has been conducted on the recent progress of the three-terminal devices with transistor-like characteristics fabricated from the high-{Tc} superconducting materials. This study explored the operating principles and characteristics of these devices in relation to the relevant materials and techniques. A comparison of a variety of techniques for superconducting thin film deposition will be given. This study indirates that the feasibility of fabricating hybrid devices composed of semiconductors and superconductors appear to be the key issue to push forward the applications of high-{Tc} superconductors in microelectronics. The junction field-effect transistors with a semiconductor base controlled by the proximity effect are likely to be more manufacturable. The factors that influence the operating reliability of devices and the problems arising from integrating and packaging the devices will also be discussed.
Challenges in information retrieval and language modeling (2003)

Information retrieval (IR) research has reached a point where it is appropriate to assess progress and to define a research agenda for the next five to ten years. This report summarizes a discussion of IR research challenges that took place at a recent workshop.\nThe attendees of the workshop considered information retrieval research in a range of areas chosen to give broad coverage of topic areas that engage information retrieval researchers. Those areas are retrieval models, cross-lingual retrieval, Web search, user modeling, filtering, topic detection and tracking, classification, summarization, question answering, metasearch, distributed retrieval, multimedia retrieval, information extraction, as well as testbed requirements for future work. The potential use of language modeling techniques in these areas was also discussed.\nThe workshop identified major challenges within each of those areas. The following are recurring themes that ran throughout:\nâ¢ User and context sensitive retrieval\nâ¢ Multi-lingual and multi-media issues\nâ¢ Better target tasks\nâ¢ Improved objective evaluations\nâ¢ Substantially more labeled data\nâ¢ Greater variety of data sources\nâ¢ Improved formal models\nContextual retrieval and global information access were identified as particularly important long-term challenges.
Molecular cloning and expression of a δ‐opioid recetpor from rat brain (1994)

We have isolated and characterized a rat delta-opioid receptor. The deduced amino acid sequence (372 aa) closely resembles the murine delta-opioid receptor, DOR-1. In fact, 97% of the amino acid residues are conserved between the two species, while 93% of the nucleic acid residues are identical. A 6 kb mRNA was detected in rat cortex using rat DOR-1 as a probe. When expressed in COS cells, the clone shows high-affinity opioid binding with selectivity for delta-opioids. The rat delta-opioid receptor cDNA clone will be a useful tool for studying the function of delta-opioid receptor in rats.
Effect of Wheat Fiber and Vitamins C and E on Rectal Polyps in Patients With Familial Adenomatous Polyposis (1989)

Over a 4-year period in a chemoprevention trial on large bowel neoplasia, 58 patients with familial adenomatous polyposis were treated with 4 g of ascorbic acid (vitamin C)/day plus 400 mg of alpha-tocopherol (vitamin E)/day alone or with a grain fiber supplement (22.5 g/day). In this randomized, double-blind, placebo-controlled study, we determined the effects of these supplements on rectal polyps in these patients. Analysis by intent to treat suggested that the high-fiber supplement had a limited effect. Analysis adjusted for patient compliance showed a stronger benefit from the high-fiber supplement during the middle 2 years of the trial. The results provide evidence for inhibition of benign large bowel neoplasia by grain fiber supplements in excess of 11 g/day in this study population. The findings are consistent with the hypothesis that dietary grain fiber and total dietary fat act as competing variables in the genesis of large bowel neoplasia.
Increasing Walking and Bright Light Exposure to Improve Sleep in Community‐Dwelling Persons with Alzheimer's Disease: Results of a Randomized, Controlled Trial (2011)

Walking, light exposure, and their combination are potentially effective treatments for improving sleep in community-dwelling persons with AD, but consistent adherence to treatment recommendations is required.
IL-22 is increased in active Crohn’s disease and promotes proinflammatory gene expression and intestinal epithelial cell migration (2006)

IL-22 is produced by activated T cells and signals through a receptor complex consisting of IL-22R1 and IL-10R2. The aim of this study was to analyze IL-22 receptor expression, signal transduction, and specific biological functions of this cytokine system in intestinal epithelial cells (IEC). Expression studies were performed by RT-PCR. Signal transduction was analyzed by Western blot experiments, cell proliferation by 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium assay and Fas-induced apoptosis by flow cytometry. IEC migration was studied in wounding assays. The IEC lines Caco-2, DLD-1, SW480, HCT116, and HT-29 express both IL-22 receptor subunits IL-22R1 and IL-10R2. Stimulation with TNF-α, IL-1β, and LPS significantly upregulated IL-22R1 without affecting IL-10R2 mRNA expression. IL-22 binding to its receptor complex activates STAT1/3, Akt, ERK1/2, and SAPK/JNK MAP kinases. IL-22 significantly increased cell proliferation ( P = 0.002) and phosphatidylinsitol 3-kinase-dependent IEC cell migration ( P &lt; 0.00001) as well as mRNA expression of TNF-α, IL-8, and human β-defensin-2. IL-22 had no effect on Fas-induced apoptosis. IL-22 mRNA expression was increased in inflamed colonic lesions of patients with Crohn’s disease and correlated highly with the IL-8 expression in these lesions ( r = 0.840). Moreover, IL-22 expression was increased in murine dextran sulfate sodium-induced colitis. IEC express functional receptors for IL-22, which increases the expression of proinflammatory cytokines and promotes the innate immune response by increased defensin expression. Moreover, our data indicate intestinal barrier functions for this cytokine-promoting IEC migration, which suggests an important function in intestinal inflammation and wound healing. IL-22 is increased in active Crohn’s disease and promotes proinflammatory gene expression and IEC migration.
Using semantic content as cues for better scanpath prediction (2008)

Under natural viewing conditions, human observers use shifts in gaze to allocate processing resources to subsets of the visual input. There are many computational models that try to predict these shifts in eye movement and attention. Although the important role of high level stimulus properties (e.g., semantic information) stands undisputed, most models are based solely on low-level image properties. We here demonstrate that a combined model of high-level object detection and low-level saliency significantly outperforms a low-level saliency model in predicting locations humans fixate on. The data is based on eye-movement recordings of humans observing photographs of natural scenes, which contained one of the following high-level stimuli: faces, text, scrambled text or cell phones. We show that observers - even when not instructed to look for anything particular, fixate on a face with a probability of over 80% within their first two fixations, on text and scrambled text with a probability of over 65.1% and 57.9% respectively, and on cell phones with probability of 8.3%. This suggests that content with meaningful semantic information is significantly more likely to be seen earlier. Adding regions of interest (ROI), which depict the locations of the high-level meaningful features, significantly improves the prediction of a saliency model for stimuli with high semantic importance, while it has little effect for an object with no semantic meaning.
Comparison of oocyte activation and Ca2+ oscillation-inducing abilities of round/elongated spermatids of mouse, hamster, rat, rabbit and human assessed by mouse oocyte activation assay (2000)

Oocyte activation and Ca2+ oscillation-inducing abilities of round spermatid (ROS) and elongated spermatid (ELS) of some rodents and human were assessed by their injection into mouse (B6D2F1) oocytes (mouse test). With mice (B6D2F1, ICR) and rat, ROS displayed no oocyte activation or Ca2+ oscillation-inducing abilities. Although ELS could induce activation at 87, 86 and 31% of injected oocytes respectively, most of the intracellular calcium concentration ([Ca2+]i) responses of ELS-injected oocytes did not show oscillation patterns; only several transient [Ca2+]i rises (transient pattern) were seen. Similarly, with hamster, rabbit and human, while ROS could induce oocyte activation efficiently (70, 71 and 52% respectively), most of the [Ca2+]i patterns of injected oocytes were transient patterns, and not oscillation patterns. When ROS nuclei only from these latter species were injected into mouse oocytes, most of the oocytes could not be activated. [Ca2+]i patterns of oocytes injected with immature sperm cells changed from transient pattern to oscillation pattern while the cells were maturing into spermatozoa. With hamster ROS, oocyte-activating factor was found to be distributed mainly in the cytoplasm. It was interesting that there is a dissociation between the timings of appearance of oocyte activation and that of Ca2+ oscillation of oocytes injected with developing immature sperm cells.
Solid-liquid filtration and separation technology (1996)

SLS technology filtration fundamentals sedimentation fundamentals filter media pretreatment techniques clarifying filtration sedimentation and thickening cetrifugal separation post-treatment processes membrance technology filtration process equipment particle size distributions rheology computer spreadsheet files.
Essence: A Resource Discovery System Based on Semantic File Indexing (1993)

Discovering different types of file resources (such as documentation, programs, and images) in the vast amount of data contained within network file systems is useful for both users and system administrators. In this paper we discuss the Essence resource discovery system, which exploits file semantics to index both textual and binary files. By exploiting semantics, Essence extracts keywords that summarize a file, and generates a compact yet representative index. Essence understands nested file structures (such as uuencoded, compressed, &amp;quot;tar&amp;quot; files), and recursively unravels such files to generate summaries for them. These features allow Essence to be used in a number of useful settings, such as anonymous FTP archives. We present measurements of our prototype and compare them to related projects, such as the Wide Area Information Servers (WAIS) system and the MIT Semantic File System (SFS). We demonstrate that Essence can index more data types, generate smaller indexes, and in some cases index data faster than these systems. Our prototype generates WAIS-compatible indexes, allowing WAIS users to take advantage of the Essence indexing methods.
20 Reverse Transcription and Evolution (1993)

Originally discovered as part of the retrovirus life cycle, reverse transcription is now known to play a number of roles in biology: in the replication of several groups of viruses, in the mobilization of retrovirus-like and other transposable elements, in the generation of chromosomal ends, and in other contexts yet to be understood. The previous chapters described the specific biological and biochemical systems within which reverse transcriptase is found and the possible relationships among these systems and their origins. Here, I focus on the role of reverse transcription in the evolution of the elements that rely on it for replication as well as the role of these elements in the evolution of their hosts. Like much of evolutionary biology, this discussion will include speculation and reliance on untested assumptions. In at least one respect, we are fortunate. The high error rates of retroviral reverse transcriptases, combined with the relatively short generation times of the genomes they replicate, provide observable evolutionary changes in experimentally tractable time frames. Lessons learned from this sort of change can illuminate the larger evolutionary picture. Thus, in experimental time, we can observe the acquisition and loss of viral genes, the evolution of populations by accumulation of mutation and recombination events, and the effects on the host cell and organism of the insertion of reverse transcripts into the genome. For these reasons, this discussion concentrates on retroviruses, with reference to some less easily studied systems — LINEs and pseudogenes —which are products of reverse transcription and constitute a...
Large-Scale Fabrication of Aligned Single-Walled Carbon Nanotube Array and Hierarchical Single-Walled Carbon Nanotube Assembly (2004)

Aligned single-walled carbon nanotubes (SWNTs) and hierarchical SWNT assembly were fabricated by electrospinning. The high fiber elongation and high DC electric field applied during the electrospinning process result in the orientation of the SWNTs along the axial direction of the fiber. The alignment of the electropsun composite fiber transfers this local SWNT orientation to macroscopically aligned SWNTs. After removing the polymer component from the aligned composite fiber, we produced large area aligned SWNTs. The results show that the directional control of SWNT alignment and debundling of SWNTs into individual tubes can be simultaneously realized.
Novel genes identified in a high-density genome wide association study for nicotine dependence (2006)

Tobacco use is a leading contributor to disability and death worldwide, and genetic factors contribute in part to the development of nicotine dependence. To identify novel genes for which natural variation contributes to the development of nicotine dependence, we performed a comprehensive genome wide association study using nicotine dependent smokers as cases and non-dependent smokers as controls. To allow the efficient, rapid, and cost effective screen of the genome, the study was carried out using a two-stage design. In the first stage, genotyping of over 2.4 million single nucleotide polymorphisms (SNPs) was completed in case and control pools. In the second stage, we selected SNPs for individual genotyping based on the most significant allele frequency differences between cases and controls from the pooled results. Individual genotyping was performed in 1050 cases and 879 controls using 31 960 selected SNPs. The primary analysis, a logistic regression model with covariates of age, gender, genotype and gender by genotype interaction, identified 35 SNPs with P-values less than 10(-4) (minimum P-value 1.53 x 10(-6)). Although none of the individual findings is statistically significant after correcting for multiple tests, additional statistical analyses support the existence of true findings in this group. Our study nominates several novel genes, such as Neurexin 1 (NRXN1), in the development of nicotine dependence while also identifying a known candidate gene, the beta3 nicotinic cholinergic receptor. This work anticipates the future directions of large-scale genome wide association studies with state-of-the-art methodological approaches and sharing of data with the scientific community.
The Ca2+ Ion as a Cofactor for a Novel RNA‐Cleaving Deoxyribozyme (1996)

In vitro selection experiments yield unexpected results. An RNA‐cleaving DNA enzyme that was selected in the presence of Mg 2+ ions is much more efficient with Ca 2+ as the cofactor. The result is even more surprising because of the lower hydrolytic efficiency of Ca 2+ itself.
Expression and regulation of vascular endothelial growth factor in osteoblasts. (1995)

Bone formation is linked closely to angiogenesis. Because prostaglandin E2 (PGE2) is a potent stimulator of bone formation, its effects were evaluated on vascular endothelial growth factor, a secreted endothelial cell-specific mitogen, and a potent angiogenic protein. Prostaglandin E2 increased vascular endothelial growth factor protein in conditioned media of osteoblastic RCT-3 cells within 3 hours. Prostaglandin E2 also increased the steady-state levels of vascular endothelial growth factor mRNA in a dose-dependent manner. The increased expression of vascular endothelial growth factor mRNA produced by PGE2 was rapid (maximal at 1 hour) and was enhanced by the protein synthesis inhibitor cycloheximide (5 micrograms/ml). The increase in vascular endothelial growth factor mRNA by PGE2 was inhibited strongly by pretreatment for 3 hours with dexamethasone (10(-7) M). Stimulation of vascular endothelial growth factor by PGE2 and its suppression by dexamethasone implicate the involvement of vascular endothelial growth factor in bone metabolism.
Characteristics of solid-state nanometre pores fabricated using a transmission electron microscope (2007)

Solid-state nanopores can be used to detect nucleic acid structures at the single molecule level. An e-beam has been used to fabricate nanopores in silicon nitride and silicon dioxide membranes, but the pore formation kinetics, and hence its final structure, remain poorly understood. With the aid of high-resolution TEM imaging as well as TEM tomography we examine the effect of Si3N4 material properties on the nanopore structure. In particular, we study the dependence of membrane thickness on the nanopore contraction rate for different initial pore sizes. We explain nanopore formation kinetics as a balance of two opposite processes: (a) material sputtering and (b) surface-tension-induced shrinking.
Studies on Transmissibility of a Tissue-Culture-Modified Laryngotracheitis Virus (1992)

The spreading characteristic of a tissue-culture-modified laryngotracheitis virus (LTV) was demonstrated in chickens under both laboratory and field conditions. An enzyme-linked immunosorbent assay was used to measure serum antibodies to LTV in experimental chickens. Contact controls developed immunity comparable to that of vaccinates and were able to resist challenge with a virulent LTV inoculated into the infraorbital sinus.