gebhart/patrepeval huggingface dataset:
Exploiting shared scratch pad memory space in embedded multiprocessor systems (2002)

In this paper, we present a compiler strategy to optimize data accesses in regular array-intensive applications running on embedded multiprocessor environments. Specifically, we propose an optimization algorithm that targets the reduction of extra off-chip memory accesses caused by inter-processor communication. This is achieved by increasing the application-wide reuse of data that resides in the scratch-pad memories of processors. Our experimental results obtained on four array-intensive image processing applications indicate that exploiting inter-processor data sharing can reduce the energy-delay product by as much as 33.8% (and 24.3% on average) on a four-processor embedded system. The results also show that the proposed strategy is robust in the sense that it gives consistently good results over a wide range of several architectural parameters.
Site-selective spectroscopy in dysprosium-doped chalcogenide glasses for 13-m optical-fiber amplifiers (2001)

Dy3+-doped chalcogenide glasses are potential candidates for 1.3-µm optical-fiber amplifiers. We describe spectroscopic characterization of Dy3+-doped gallium lanthanum sulphide glasses with low and high oxide content. The spectroscopic investigations show that small amounts of oxide (∼1%) in low-oxide-content sulphide glass create a second group of sites with a local environment different than that of the main sulphide sites. Dy3+ ions in the oxide site, which can constitute up to approximately one third of the total number of Dy3+ ions, experience a high-phonon-energy environment and do not show any 1.3-µm emission and hence cannot provide gain for a potential 1.3-µm optical-fiber amplifier in this material.
Identification of a ZP3-binding protein on acrosome-intact mouse sperm by photoaffinity crosslinking. (1990)

During the process of fertilization in mammals, sperm bind in a relatively species-specific manner to the zona pellucida (ZP) of ovulated eggs. ZP3, a glycoprotein found in the mouse egg zona pellucida, serves as receptor for sperm during gamete adhesion. We report here that a Mr 56,000 protein found on mouse sperm has properties expected for a sperm component that recognizes and binds to ZP3. This sperm protein is radiolabeled preferentially by a photoactivatable heterobifunctional crosslinker ("Denny-Jaffee reagent") covalently linked to purified ZP3, binds very tightly to ZP3-affinity columns, and is localized to heads of acrosome-intact but not acrosome-reacted sperm. These and other findings suggest that this protein may be a "ZP3-binding protein" that, together with the sperm receptor, supports species-specific binding of mouse sperm to unfertilized eggs.
Efficient induction of specific cytotoxic T lymphocytes to tumor rejection peptide using functional matured 2 day-cultured dendritic cells derived from human monocytes (2006)

Dendritic cells (DCs) are powerful antigen-presenting cells (APCs), that have so far been applied for cancer specific immunotherapy. Recent results suggest that matured DCs derived from human monocytes have a significant impact on the outcome of vaccination. The conventional generation of mature DCs from human monocytes in vitro has been reported to require 5 days for differentiation with granulocyte macrophage colony-stimulating factor (GM-CSF), interleukin (IL)-4 and 2 days for stimulation. We herein report a new strategy for the functional maturation of monocyte-derived DCs within only 2 days of in vitro culture and the induction of specific cytotoxic T lymphocytes (CTLs) to tumor rejection peptide. The monocytes were incubated for 1 day with GM-CSF and IL-4, followed by activation with a bacterial product, OK-432 and prostaglandin E2 (PGE2) for another 1 day (rapid DC). Rapid DC expressed mature DC surface markers as well as chemokine receptor 7 and secreted Th1-type cytokines. The DCs generated in this study mobilized Ca2+ in response to CCL21/6Ckine and SDF-1, but only marginally did so to Mip-1alpha. Moreover, when rapid DC were compared with mature conventional 7-day DCs, they were equally potent in inducing specific CTLs in vitro. These results indicate that the rapid DC is as effective as the monocyte-derived conventional DCs. The rapid DC would be a potentially useful new cancer-specific immunotherapy.
Detection of preterm labor by ambulatory monitoring of uterine activity: a preliminary report. (1986)

Effective tocolytic therapy depends on the ability to make an early diagnosis of preterm labor. This study was designed to assess whether daily ambulatory home monitoring of uterine activity could facilitate early diagnosis of preterm labor. Of 76 patients at high risk for preterm labor who used daily ambulatory tocodynamometry, approximately half developed preterm labor. Evaluation when the diagnosis of preterm labor was first established has shown that in 8% of the patients the cervix was dilated more than 2 cm, shortened to less than 0.5 cm in 23%, and the fetal membranes were intact in all subjects. The same evaluation in 76 nonrandom contemporary controls matched for risk factors, maternal age, and parity has shown that more than 50% had a cervix dilated more than 2 cm, 38% had a cervix shorter than 0.5 cm, and 24% had rupture of the fetal membranes. Ultimately, 88% of the monitored patients and 59% of controls delivered at term. Comparisons between these groups indicate that intermittent home tocodynamometry may indeed be useful in making the early diagnosis of preterm labor.
Study of Dengue Virus Infection in SCID Mice Engrafted with Human K562 Cells (1998)

ABSTRACT Here we report that severe combined immunodeficient (SCID) mice engrafted with human K562 cells (K562-SCID mice) can be used as an animal model to study dengue virus (DEN) infection. After intratumor injection into K562 cell masses of PL046, a Taiwanese DEN-2 human isolate, the K562-SCID mice showed neurological signs of paralysis and died at approximately 2 weeks postinfection. In addition to being detected in the tumor masses, high virus titers were detected in the peripheral blood and the brain tissues, indicating that DEN had replicated in the infected K562-SCID mice. In contrast, the SCID mice were resistant to DEN infection and the mock-infected K562-SCID mice survived for over 3 months. These data illustrate that DEN infection contributed directly to the deaths of the infected K562-SCID mice. Other serotypes of DEN were also used to infect the K562-SCID mice, and the mortality rates of the infected mice varied with different challenge strains, suggesting the existence of diverse degrees of virulence among DENs. To determine whether a neutralizing antibody against DEN in vitro was also protective in vivo, the K562-SCID mice were challenged with DEN-2 and received antibody administration at the same time or 1 day earlier. Our results revealed that the antibody-treated mice exhibited a reduction in mortality and a delay of paralysis onset after DEN infection. In contrast to K562-SCID, the persistently DEN-infected K562 cells generated in vitro invariably failed to be implanted in the mice. It seems that in the early stage of implantation, a gamma interferon activated, nitric oxide-mediated anti-DEN effect might play a role in the innate immunity against DEN-infected cells. The system described herein offers an opportunity to explore DEN replication in vivo and to test various antiviral protocols in infected hosts.
Culture and Sustainable Development in China (2007)

Thank you for inviting me to participate in the discussion of how to achieve sustainable development in China in the age of globalization and the knowledge economy.This subject demands our full attention and is of the utmost urgency
Expression of Tie-2 by Human Monocytes and Their Responses to Angiopoietin-2 (2007)

Angiopoietins 1 and 2 bind to Tie-2 expressed on endothelial cells and regulate vessel stabilization and angiogenesis. Tie-2(+) monocytes have been shown to be recruited to experimental tumors where they promote tumor angiogenesis. In this study, we show that 20% of CD14(+) human blood monocytes express Tie-2, and that these cells coexpress CD16 (FcgammaRIII) and are predominantly CD34 negative. Ang-2 is up-regulated by endothelial cells in malignant tumors and inflamed tissues, so our finding that Ang-2 is a chemoattractant for human Tie-2(+) monocytes and macrophages, suggests that it may help to recruit and regulate their distribution in such tissues. Ang-2 was also found to markedly inhibit release of the important proinflammatory cytokine, TNF-alpha, by monocytes in vitro. Following extravasation of monocytes, and their differentiation into macrophages, many accumulate in the hypoxic areas of inflamed and malignant tissues. Ang-2 is known to be up-regulated by hypoxia and we show that monocytes and macrophages up-regulate Tie-2 when exposed to hypoxia. Furthermore, hypoxia augmented the inhibitory effect of Ang-2 on the release of the anti-angiogenic cytokine, IL-12 by monocytes. In sum, our data indicate that Ang-2 may recruit Tie-2(+) monocytes to tumors and sites of inflammation, modulate their release of important cytokines and stimulate them to express a proangiogenic phenotype.
Production of N 2 through Anaerobic Ammonium Oxidation Coupled to Nitrate Reduction in Marine Sediments (2002)

In the global nitrogen cycle, bacterial denitrification is recognized as the only quantitatively important process that converts fixed nitrogen to atmospheric nitrogen gas, N(2), thereby influencing many aspects of ecosystem function and global biogeochemistry. However, we have found that a process novel to the marine nitrogen cycle, anaerobic oxidation of ammonium coupled to nitrate reduction, contributes substantially to N(2) production in marine sediments. Incubations with (15)N-labeled nitrate or ammonium demonstrated that during this process, N(2) is formed through one-to-one pairing of nitrogen from nitrate and ammonium, which clearly separates the process from denitrification. Nitrite, which accumulated transiently, was likely the oxidant for ammonium, and the process is thus similar to the anammox process known from wastewater bioreactors. Anaerobic ammonium oxidation accounted for 24 and 67% of the total N(2) production at two typical continental shelf sites, whereas it was detectable but insignificant relative to denitrification in a eutrophic coastal bay. However, rates of anaerobic ammonium oxidation were higher in the coastal sediment than at the deepest site and the variability in the relative contribution to N(2) production between sites was related to large differences in rates of denitrification. Thus, the relative importance of anaerobic ammonium oxidation and denitrification in N(2) production appears to be regulated by the availability of their reduced substrates. By shunting nitrogen directly from ammonium to N(2), anaerobic ammonium oxidation promotes the removal of fixed nitrogen in the oceans. The process can explain ammonium deficiencies in anoxic waters and sediments, and it may contribute significantly to oceanic nitrogen budgets.
Tumor endothelial marker 1 ( Tem1 ) functions in the growth and progression of abdominal tumors (2006)

Tumor endothelial marker 1 (Tem1; endosialin) is the prototypical member of a family of genes expressed in the stroma of tumors. To assess the functional role of Tem1, we disrupted the Tem1 gene in mice by targeted homologous recombination. Tem1(-/-) mice were healthy, their wound healing was normal, and tumors grew normally when implanted in s.c. sites. However, there was a striking reduction in tumor growth, invasiveness, and metastasis after transplantation of tumors to abdominal sites in mice without functional Tem1 genes. These data indicate that the stroma can control tumor aggressiveness and that this control varies with anatomic site. Therefore, they have significant implications for the mechanisms underlying tumor invasiveness and for models that evaluate this process.
GFP-labelled Rubisco and aspartate aminotransferase are present in plastid stromules and traffic between plastids (2004)

Plastid stromules are membrane-bound protrusions of the plastid envelope that contain soluble stroma. Stromules are often found connecting plastids within a cell and fluorescence recovery after photobleaching (FRAP) experiments have demonstrated that green fluorescent protein (GFP) can move between plastids via these connections. In this report, the ability of endogenous plastid proteins to travel through stromules was investigated. The motility of GFP-labelled plastid aspartate aminotransferase and the Rubisco small subunit was studied in stromules by FRAP. Both fusion proteins assemble into protein complexes that appear to behave similarly to their endogenous counterparts. In addition, both enzymes are capable of trafficking between plastids via stromules.
Computer-assisted Total Knee Arthroplasty Using Patient-specific Templating (2006)

Current techniques used for total knee arthroplasty rely on conventional instrumentation that violates the intramedullary canals. Accuracy of the instrumentation is questionable, and assembly and disposal of the numerous pieces is time consuming. Navigation techniques are more accurate, but their broad application is limited by cost and complexity. We aimed to prove a new concept of computer-assisted preoperative planning to provide patient-specific templates that can replace conventional instruments. Computed tomography-based planning was used to design two virtual templates. Using rapid prototyping technology, virtual templates were transferred into physical templates (cutting blocks) with surfaces that matched the distal femur and proximal tibia. We performed 45 total knee arthroplasties on 16 cadaveric and 29 plastic knees, including a comparative trial against conventional instrumentations. All operations were performed using patient-specific templates with no conventional instrumentations, intramedullary perforation, tracking, or registration. The mean time for bone cutting was 9 minutes with a surgical assistant and 11 minutes without an assistant. Computer-assisted analyses of six random computed tomography scans showed mean errors for alignment and bone resection within 1.7 degrees and 0.8 mm (maximum, 2.3 degrees and 1.2 mm, respectively). Patient-specific templates are a practical alternative to conventional instrumentations, but additional clinical validation is required before clinical use.
Sequence logos: a new way to display consensus sequences (1990)

A graphical method is presented for displaying the patterns in a set of aligned sequences. The characters representing the sequence are stacked on top of each other for each position in the aligned sequences. The height of each letter is made proportional to its frequency, and the letters are sorted so the most common one is on top. The height of the entire stack is then adjusted to signify the information content of the sequences at that position. From these 'sequence logos', one can determine not only the consensus sequence but also the relative frequency of bases and the information content (measured in bits) at every position in a site or sequence. The logo displays both significant residues and subtle sequence patterns.
Fault Secure Encoder and Decoder for Memory Applications (2007)

We introduce a reliable memory system that can tolerate multiple transient errors in the memory words as well as transient errors in the encoder and decoder (corrector) circuitry. The key novel development is the fault-secure detector (FSD) error-correcting code (ECC) definition and associated circuitry that can detect errors in the received encoded vector despite experiencing multiple transient faults in its circuitry. The structure of the detector is general enough that it can be used for any ECC that follows our FSD-ECC definition. We prove that two known classes of Low-Density Parity-Check Codes have the FSD-ECC property: Euclidean Geometry and Projective Geometry codes. We identify a specific FSD-LDPC code that can tolerate up to 33 errors in each memory word or supporting logic that requires only 30% area overhead for memory blocks of 10 Kbits or larger. Larger codes can achieve even higher reliability and lower area overhead. We quantify the importance of protecting encoder and decoder (corrector) circuitry and illustrate a scenario where the system failure rate (FIT) is dominated by the failure rate of the encoder and decoder.
Receiver Operating Characteristic (ROC) Curve Analysis for Medical Diagnostic Test Evaluation. (2013)

This review provides the basic principle and rational for ROC analysis of rating and continuous diagnostic test results versus a gold standard. Derived indexes of accuracy, in particular area under the curve (AUC) has a meaningful interpretation for disease classification from healthy subjects. The methods of estimate of AUC and its testing in single diagnostic test and also comparative studies, the advantage of ROC curve to determine the optimal cut off values and the issues of bias and confounding have been discussed.
O-Sulfonation of Serine and Threonine (2004)

Protein sulfonation on serine and threonine residues is described for the first time. This post-translational modification is shown to occur in proteins isolated from organisms representing a broad span of eukaryote evolution, including the invertebrate mollusk Lymnaea stagnalis, the unicellular malaria parasite Plasmodium falciparum, and humans. Detection and structural characterization of this novel post-translational modification was carried out using liquid chromatography coupled to electrospray tandem mass spectrometry on proteins including a neuronal intermediate filament and a myosin light chain from the snail, a cathepsin-C-like enzyme from the parasite, and the cytoplasmic domain of the human orphan receptor tyrosine kinase Ror-2. These findings suggest that sulfonation of serine and threonine may be involved in multiple functions including protein assembly and signal transduction.
Heterogeneously Integrated Silicon Photonics for the Mid-Infrared and Spectroscopic Sensing (2014)

Besides being the foundational material for microelectronics, crystalline silicon has long been used for the production of infrared lenses and mirrors. More recently, silicon has become the key material to achieve large-scale integration of photonic devices for on-chip optical interconnect and signal processing. For optics, silicon has significant advantages: it offers a very high refractive index and is highly transparent in the spectral range from 1.2 to 8 μm. To fully exploit silicon’s superior performance in a remarkably broad range and to enable new optoelectronic functionalities, here we describe a general method to integrate silicon photonic devices on arbitrary foreign substrates. In particular, we apply the technique to integrate silicon microring resonators on mid-infrared compatible substrates for operation in the mid-infrared. These high-performance mid-infrared optical resonators are utilized to demonstrate, for the first time, on-chip cavity-enhanced mid-infrared spectroscopic analysis of organic chemicals with a limit of detection of less than 0.1 ng.
Complex demodulation of heart rate changes during orthostatic testing (2002)

Heart rate changes induced by the standing up of young healthy subjects are processed by a complex demodulation algorithm yielding time-local estimates of the amplitude of the heart-rate variability function. Complex demodulate of the high-frequency band (0.15 to 0.45 Hz) shows an abrupt decrease of amplitude immediately after standing up, presumably due into vagal withdrawal. Complex demodulation of a part of the low frequency band (0 to 0.055 Hz) shows a typical form of a bell-shaped curve. It is concluded that while the complex demodulation of the high-frequency band probably reflects parasympathetic activity, the complex demodulation of the low-frequency band does not seem to indicate the level of the sympathetic activity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Comparison of Data-Driven Bandwidth Selectors (1990)

Abstract This article compares several promising data-driven methods for selecting the bandwidth of a kernel density estimator. The methods compared are least squares cross-validation, biased cross-validation, and a plug-in rule. The comparison is done by asymptotic rate of convergence to the optimum and a simulation study. It is seen that the plug-in bandwidth is usually most efficient when the underlying density is sufficiently smooth, but is less robust when there is not enough smoothness present. We believe the plug-in rule is the best of those currently available, but there is still room for improvement.
A yellow-emitting Ce3+ phosphor, La1−xCexSr2AlO5, for white light-emitting diodes (2008)

A yellow-emitting phosphor, La1−xCex3+Sr2AlO5, is reported that displays a peak in the excitation at 450nm and a peak in the emission at 556nm. When this phosphor is pumped by a blue InGaN light-emitting diode (λmax=450nm) we obtain white light with color rendering index (Ra) between 81 and 85 and color temperatures between 4200 and 5500K, suggesting that this material is competitive as a blue-pumped yellow phosphors.
Acremonium phylogenetic overview and revision of Gliomastix, Sarocladium, and Trichothecium (2011)

Over 200 new sequences are generated for members of the genus Acremonium and related taxa including ribosomal small subunit sequences (SSU) for phylogenetic analysis and large subunit (LSU) sequences for phylogeny and DNA-based identification. Phylogenetic analysis reveals that within the Hypocreales, there are two major clusters containing multiple Acremonium species. One clade contains Acremonium sclerotigenum, the genus Emericellopsis, and the genus Geosmithia as prominent elements. The second clade contains the genera Gliomastixsensu stricto and Bionectria. In addition, there are numerous smaller clades plus two multi-species clades, one containing Acremonium strictum and the type species of the genus Sarocladium, and, as seen in the combined SSU/LSU analysis, one associated subclade containing Acremonium breve and related species plus Acremonium curvulum and related species. This sequence information allows the revision of three genera. Gliomastix is revived for five species, G. murorum, G. polychroma, G. tumulicola, G. roseogrisea, and G. masseei. Sarocladium is extended to include all members of the phylogenetically distinct A. strictum clade including the medically important A. kiliense and the protective maize endophyte A. zeae. Also included in Sarocladium are members of the phylogenetically delimited Acremonium bacillisporum clade, closely linked to the A. strictum clade. The genus Trichothecium is revised following the principles of unitary nomenclature based on the oldest valid anamorph or teleomorph name, and new combinations are made in Trichothecium for the tightly interrelated Acremonium crotocinigenum, Spicellum roseum, and teleomorph Leucosphaerinaindica. Outside the Hypocreales, numerous Acremonium-like species fall into the Plectosphaerellaceae, and A. atrogriseum falls into the Cephalothecaceae.