gebhart/patrepeval huggingface dataset:
Anti-idiotypic mechanisms involved in suppression of a mouse B cell lymphoma, BCL1. (1987)

Immunization of BALB/c mice with idiotypic IgM rescued by hybridization from the syngeneic BCL1 lymphoma protects specifically against challenge with tumor cells, with 83% surviving greater than 100 days compared with controls (38 +/- 10 days). Spleens from long-term survivors (greater than 6 mo) with no macroscopically visible tumor, when examined with anti-idiotypic antibody, showed a range of apparently dormant tumor with BCL1 cells present at 2 to 50% of total. A spectrum of protection against tumor resulted from immunization, and tumor emerging in the period 53 to 173 days postpassage was investigated for expression of idiotype. It was found that cells from individual mice expressed variable amounts of idiotypic IgM at the cell surface, although it was always detectable in the intracellular compartment. Unlike typical BCL1 cells, tumor cells developing in immune spleens often secreted little idiotypic IgM either in vitro or in vivo. This modulation of expression and secretion of idiotype was detected even in the apparent absence of serum anti-idiotypic antibody. On passage of spleen cells from the long-term survivors into naive animals, BCL1 tumor developed and killed the recipients in a way indistinguishable from routine tumor passage. These tumor cells, however, both expressed and secreted IgM of the same idiotype as the original tumor. It appears therefore that tumor development in immunized mice is suppressed by a process that includes modulation but not selection of the tumor cell idiotypic determinants. Analysis of possible mechanisms of suppression revealed the presence of cytotoxic anti-idiotypic antibody at variable levels in sera of immunized mice, and splenic T cells that proliferated specifically in response to idiotypic IgM. Only low levels of cytotoxic T cells were found. Passive transfer studies demonstrated a major role for antibody in protection against tumor, with no significant enhancement by immune lymphocytes.
Peripheral nerve regeneration using acellular nerve grafts (2003)

Long gap peripheral nerve injuries usually require a graft to facilitate axonal regeneration into the distal nerve stump. The use of autografts is often limited because of graft availability and donor-site morbidity. We investigated whether acellular nerve allografts would provide an appropriate channel for the promotion and induction of sciatic nerve regeneration in rats. Axons sprouted from the proximal portion and reached the distal portion in the 1 cm-long grafts by 1 month. The number of axons in the regenerated nerves was similar to that of normal nerves at 1 month. Loading the grafts with betaNGF and VEGF increased the number and mean diameter of axons and neovascularization in the regenerated nerves at 1 month. The motor conduction velocity increased over time and reached 63 +/- 10% of that of normal nerves at 6 months. The nerve injuries treated with the acellular grafts had a significant improvement in motor, nociception, and proprioception function compared to untreated nerves. The results from this study suggest that acellular nerve allografts may be a useful biomaterial for functional peripheral nerve regeneration.
Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing (2013)

DNA methylation is crucial for a wide variety of biological processes, yet no technique suitable for the methylome analysis of DNA methylation at single-cell resolution is available. Here, we describe a methylome analysis technique that enables single-cell and single-base resolution DNA methylation analysis based on reduced representation bisulfite sequencing (scRRBS). The technique is highly sensitive and can detect the methylation status of up to 1.5 million CpG sites within the genome of an individual mouse embryonic stem cell (mESC). Moreover, we show that the technique can detect the methylation status of individual CpG sites in a haploid sperm cell in a digitized manner as either unmethylated or fully methylated. Furthermore, we show that the demethylation dynamics of maternal and paternal genomes after fertilization can be traced within the individual pronuclei of mouse zygotes. The demethylation process of the genic regions is faster than that of the intergenic regions in both male and female pronuclei. Our method paves the way for the exploration of the dynamic methylome landscapes of individual cells at single-base resolution during physiological processes such as embryonic development, or during pathological processes such as tumorigenesis.
Similarity mapping of software faults for self-healing applications (2010)

For self-healing software application, finding fix for a previously unseen fault is a grand challenge. Asking the user to provide fixes for every fault is bad for productivity, especially when the users are non-savvy in technical computing. If failure scenarios come into existence, the user wants the runtime environment to handle those situations autonomically. This paper proposes a new technique of matching unknown fault scenarios to already established fault models. By capturing runtime parameters and execution pathways, stable execution models are established and later are used to match with an unstable execution scenario. All these support is provided transparently and the added functionalities are incorporated into existing user application by using appropriate code transformation techniques. Initial results from experimentation show signs of promise and to be successful in providing transparent self-healing support to end user.
Verzweigte und kettenverlängerte Zucker, XXXI. Synthese des Sauerstoffanalogons der Desferriform von δ<sub>1</sub>‐Albomycin (1987)

Abstract Es wird das Sauerstoffanalogon der Desferriform des δ 1 ‐Albomycins synthetisiert. Zum Aufbau des Zuckerteils wird die xylo ‐Dialdopentofuranose 2 mit dem Anion des Lithiumsalzes 3 von N,N ‐Bis(trimethylsilyl)glycin‐trimethylsilylester umgesetzt. Die gewünschte 6‐Amino‐6‐desoxy‐ L ‐ glycero ‐ L ‐ ido ‐ heptofuranuronsäure wird mit guter Stereoselektivität gebildet und nach Derivatisierung als Verbindung 8 isoliert. Nach Überführung von 8 in das 1‐Acetat 23 ist mit Hilfe der modifizierten Hilbert‐Johnson‐Methode unter Verwendung des Uracil‐Derivates 24 das Nucleosid 26 darstellbar, das zu 28 N ‐methyliert werden kann. Nach dem Aktivesterverfahren ist nach Freisetzung der Aminogruppe zu 30 eine Anknüpfung des Serin‐Derivates 31 zum Peptid 32 möglich. Nach partieller Entblockierung zu 34 gelingt mit der Methode der gemischten Anhydride die Anknüpfung des Tripeptids 36 , welches aus drei Einheiten von N 5 ‐Acetyl‐ N 5 ‐hydroxy‐ L ‐ornithin besteht. Durch Hydrogenolyse ist aus 37 die freie Desferriform des Sauerstoffanalogons 38 erhältlich.
Gene sequences suggest inactivation of alpha-1,3-galactosyltransferase in catarrhines after the divergence of apes from monkeys. (1991)

The glycosylation enzyme alpha-1,3-galactosyltransferase (alpha 1,3GT; UDPgalactose:beta-D-galactosyl-1,4-N-acetyl-D-glucosaminide alpha-1,3-galactosyltransferase, EC 2.4.1.151) displays a unique pattern of distribution in mammals. It synthesizes an abundance of Gal(alpha 1-3)Gal(beta 1-4)GlcNAc-R (alpha-galactosyl) epitopes within the Golgi apparatus of cells of nonprimate mammals, prosimians, and New World monkeys (platyrrhines). The catarrhines, which include Old World monkeys, apes, and humans, lack this enzyme activity because of the inactivation of the alpha 1,3GT gene. In contrast, the catarrhines produce large amounts of antibodies, designated anti-Gal, against the alpha-galactosyl epitope. The inactivation of the alpha 1,3GT gene in ancestral catarrhines was probably the result of an intensive evolutionary pressure for alteration in the makeup of cell surface carbohydrates (i.e., suppression of alpha-galactosyl epitope expression) and for the production of the anti-Gal antibody. To determine the period in which the alpha 1,3GT gene was inactivated in ancestral catarrhines, comparative sequencing of a 370-base-pair region of this gene was performed by polymerase chain reactions with DNA of various primates. The data suggest that alpha 1,3GT inactivation occurred rather late in the course of catarrhine evolution (less than 28 million years ago), as separate events in apes and in Old World monkeys, after the two groups diverged from each other.
Efficient Spare Allocation in Reconfigurable Arrays (1986)

The issue of yield degradation due to physical failures in large memory and processor arrays is of significant importance to semiconductor manufacturers. One method of increasing the yield for iterated arrays of memory cells or processing elements is by incorporating spare rows and columns in the die or wafer which can be programmed into the array. This paper addresses the issue of computer-aided design approaches to optimal reconfiguration of such arrays. The paper presents the first formal analysis of the problem. The complexity of optimal reconfiguration is shown to be NP-complete for rectangular arrays utilizing spare rows and columns. In contrast to previously proposed exhaustive search and greedy algorithms, this paper develops a heuristic branch and bound approach based on the complexity analysis, which allows for flexible and highly efficient reconfiguration. Initial screening is performed by a bipartite graph matching algorithm.
Recent Advances in Peptide-Based Microarray Technologies (2004)

Peptide array is a rapidly growing tool that provides both large-scale and high-throughput capabilities for protein detection and activity studies. Materials presented in this review will examine the recent advances in the field of peptide microarray with special emphasis on the generation and applications of high-density arrays of peptides on glass slides.
Epitaxial growth of γ-(Al<i><sub>x</sub></i>Ga<sub>1−</sub><i><sub>x</sub></i>)O<sub>3</sub>alloy films for band-gap engineering (2017)

Defective-spinel-structured γ-(AlxGa1−x)2O3 alloy films were successfully stabilized on MgAl2O4 substrates for the entire composition range using molecular beam epitaxy, though both end members are metastable. The crystallinity of the alloy films (x ≥ 0.22) was considerably better than that of the γ-Ga2O3 film, indicating that the Al2O3 lattice is more flexible and sensitive to the epitaxial force exerted by the substrate than Ga2O3 lattice. The direct and indirect band gaps obtained using deep-UV spectroscopy were in the ranges of 4.96–6.97 and 4.80–6.86 eV, for which the bowing parameters were 0.183 and 0.43 eV, respectively. Our results will be beneficial for further development of γ-(AlxGa1−x)2O3 systems.
Purification of Molecularly Bridged Metal Nanoparticle Arrays by Centrifugation and Size Exclusion Chromatography (2001)

Size exclusion chromatography and centrifugation separation protocols were developed and compared for isolating enriched fractions of phenylethynyl-bridged metal nanoparticle dimers and trimers from the monomeric particle starting material. Both methods enabled the isolation of enriched fractions of a desired array without causing significant sample aggregation or replacement of the phenylethynyl bridge. Solutions containing ca. 70% bridged gold dimers were obtained using either method. The further development of methods for separating discrete arrays of covalently bridged nanoparticle homo and hetero structures is expected to help advance our understanding of collective metal particle electronic structure-function relationships.
Colchicine for pericarditis: hype or hope? (2009)

Colchicine has been effectively used in the treatment of several inflammatory conditions, such as gouty attacks, serositis related to familial Mediterranean fever, Behçet syndrome, and more recently also in acute and recurrent pericarditis. Growing evidence has shown that the drug may be useful to treat an acute attack and may be a way to cope with the prevention of pericarditis in acute and recurrent cases and after cardiac surgery. Nevertheless, clinicians are often sceptical about the efficacy of the drug, and concerns have risen on possible side effects and tolerability. In this review, we analyse current evidence to support the use of the drug, as well as possible harms and risks related to drug interactions, reaching the conclusion that colchicine is safe and useful in recurrent pericarditis, if specific precautions are followed, although less evidence supports its use for the treatment of acute pericarditis, where colchicine remains optional and there is a need for further multicentre confirmatory studies. This paper also reviews specific dosing and precautions for the clinical use.
The origin recognition complex interacts with a bipartite DNA binding site within yeast replicators. (1995)

Replicators are genetically defined elements within chromosomes that determine the location of origins of DNA replication. In the yeast Saccharomyces cerevisiae, the ARS1 replicator contains multiple functional DNA elements: an essential A element and three important B elements--B1, B2, and B3. Functionally similar A, B1, and B2 elements are also present in the ARS307 replicator. The B3 element binds a replication and transcription enhancer protein Abf1p, whereas the A element is required for binding the origin recognition complex (ORC). The function of the B1 and B2 elements remains to be defined. We have used a gel-based DNA binding assay to study the interaction between replicators and the putative initiator protein ORC. In addition to the established requirements for ATP and the A element for ORC-DNA interaction, the new data demonstrate that sequences in the B1 element are also important for ORC-DNA association. This conclusion is supported by DNase I footprint analyses and demonstrates that ORC binds to a bipartitite recognition element within the DNA. Furthermore, mutation of nucleotides in the B1 element suggests that this element has other functions in the initiation of DNA replication besides participating in the ORC-DNA interaction.
Targeting immune checkpoints in lymphoma (2015)

The use of immune checkpoint inhibitors, including nivolumab and pembrolizumab, in relapsed and refractory patients with lymphoma is proving highly successful. Patients with Hodgkin lymphoma, in particular, have a very high response rate to PD-1 blockade and responses in these patients appear durable.
Interactions between mercury and phytoplankton: Speciation, bioavailability, and internal handling (2013)

The present review describes and discusses key interactions between mercury (Hg) and phytoplankton to highlight the role of phytoplankton in the biogeochemical cycle of Hg and to understand direct or indirect Hg effects on phytoplankton. Phytoplankton are exposed to various Hg species in surface waters. Through Hg uptake, phytoplankton affect the concentration, speciation, and fate of Hg in aquatic systems. The mechanisms by which phytoplankton take up Hg are still not well known, but several studies have suggested that both facilitated transport and passive diffusion could be involved. Once internalized, Hg will impact several physiological processes, including photosynthesis. To counteract these negative effects, phytoplankton have developed several detoxification strategies, such as the reduction of Hg to elemental Hg or its sequestration by intracellular ligands. Based on the toxicological studies performed so far in the laboratory, Hg is unlikely to be toxic to phytoplankton when they are exposed to environmentally relevant Hg concentrations. However, this statement should be taken with caution because questions remain as to which Hg species control Hg bioavailability and about Hg uptake mechanisms. Finally, phytoplankton are primary producers, and accumulated Hg will be transferred to higher consumers. Phytoplankton are a key component in aquatic systems, and their interactions with Hg need to be further studied to fully comprehend the biogeochemical cycle of Hg and the impact of this ubiquitous metal on ecosystems.
12.5 Gbps Indoor Optical Wireless Communication System with Single Channel Imaging Receiver (2011)

In this paper we propose a novel single channel imaging receiver for high-speed indoor optical wireless communication system. Up to 12.5Gbps communication has been experimentally demonstrated and error-free beam footprint can be improved by &gt;20%.
Battery Energy Storage Station (BESS)-Based Smoothing Control of Photovoltaic (PV) and Wind Power Generation Fluctuations (2013)

The battery energy storage station (BESS) is the current and typical means of smoothing wind- or solar-power generation fluctuations. Such BESS-based hybrid power systems require a suitable control strategy that can effectively regulate power output levels and battery state of charge (SOC). This paper presents the results of a wind/photovoltaic (PV)/BESS hybrid power system simulation analysis undertaken to improve the smoothing performance of wind/PV/BESS hybrid power generation and the effectiveness of battery SOC control. A smoothing control method for reducing wind/PV hybrid output power fluctuations and regulating battery SOC under the typical conditions is proposed. A novel real-time BESS-based power allocation method also is proposed. The effectiveness of these methods was verified using MATLAB/SIMULINK software.
The present state of seismic data acquisition; one view (1985)

Abstract Seismic data acquisition in the mid-1980s is briefly reviewed. In terms of hardware, the trend has been toward an increased number of data channels in both land and marine applications. This has led to the development of digital telemetry systems. Positioning systems, particularly for marine work, have made use of artificial satellites. The perceived need for S-wave information has led to development of S-wave sources such as the horizontal vibrator. S-waves in a few cases have been used to validate hydrocarbon indicators on seismic records. There has been a distinct trend toward three-dimensional (3-D) seismic recording, both on land and at sea, and for both exploration and production applications.
Structure and Physiology of the RET Receptor Tyrosine Kinase (2013)

The identification of the ret oncogene by Masahide Takahashi and Geoffrey Cooper in 1985 was both serendipitous and paradigmatic ( Takahashi et al. 1985). By transfecting total DNA from a human lymphoma into mouse NIH3T3 cells, they obtained one clone, which in secondary transformants yielded more than 100-fold improvement in transformation efficiency. Subsequent investigations revealed that the ret oncogene was not present as such in the primary lymphoma, but was derived by DNA rearrangement during transfection from normal human sequences of the ret locus. At the time, activation by DNA rearrangement had not been previously described for a transforming gene with the NIH3T3 transfection assay. The discovery of ret opened a field of study that has had a profound impact in cancer research, developmental biology, and neuroscience, and that continues to yield surprises and important insights to this day.
Characterization of Intracellular Reverse Transcription Complexes of Human Immunodeficiency Virus Type 1 (2001)

To examine the early events of the life cycle of human immunodeficiency virus type 1 (HIV-1), we analyzed the intracellular complexes mediating reverse transcription isolated from acutely infected cells. Partial purification of the reverse transcription complexes (RTCs) by equilibrium density fractionation and velocity sedimentation indicated that two species of RTCs are formed but only one species is able to synthesize DNA. Most of the capsid, matrix, and reverse transcriptase (RT) proteins dissociate from the complex soon after cell infection, but Vpr remains associated with the RTC. The RTCs isolated 1, 4, and 7 h after infection are competent for reverse transcription in vitro, indicating that a small proportion of RT remains associated with them. HIV RTCs isolated early after infection have a sedimentation velocity of approximately 560S. Later, different species with a sedimentation velocity ranging from 350S to 100S appear. Nuclear-associated RTCs have a sedimentation velocity of 80S. Shortly after initiation of reverse transcription, the viral strong-stop DNA within the RTC is sensitive to nuclease digestion and becomes protected when reverse transcription is almost completed.
S-Nitrosothiols: a class of nitric oxide-donor drugs (2000)

Nitric oxide (NO) was originally described as the principal endothelium-derived relaxing factor, but it is now known to subserve a variety of functions throughout the body, both physiological and pathophysiological. NO-donor drugs decompose in the body, by a variety of mechanisms, to generate NO. Such drugs have been used for many years in cardiovascular therapeutics, in particular the organic nitrates for the prevention and treatment of angina pectoris and sodium nitroprusside for the treatment of hypertensive emergencies. However, patients taking long-term nitrates often develop tolerance, and prolonged nitroprusside administration can give rise to cyanide accumulation in the body. Newer NO-donor drugs, in particular the S-nitrosothiols, offer advantages over the existing drugs, since they do not share these drawbacks, and initial small clinical studies suggest that they may be of benefit in a variety of cardiovascular disorders. Here we briefly review the chemistry and physiology of NO, and discuss the chemistry and clinical possibilities of the S-nitrosothiols.
The rate-distortion function for the quadratic Gaussian CEO problem (1998)

A new multiterminal source coding problem called the CEO problem was presented and investigated by Berger, Zhang, and Viswanathan. Recently, Viswanathan and Berger have investigated an extension of the CEO problem to Gaussian sources and call it the quadratic Gaussian CEO problem. They considered this problem from a statistical viewpoint, deriving some interesting results. In this paper, we consider the quadratic Gaussian CEO problem from a standpoint of multiterminal rate-distortion theory. We regard the CEO problem as a certain multiterminal remote source coding problem with infinitely many separate encoders whose observations are conditionally independent if the remote source is given. This viewpoint leads us to a complete solution to the problem. We determine the tradeoff between the total amount of rate and squared distortion, deriving an explicit formula of the rate-distortion function. The derived function has the form of a sum of two nonnegative functions. One is a classical rate-distortion function for single Gaussian source and the other is a new rate-distortion function which dominates the performance of the system for a relatively small distortion. It follows immediately from our result that the conjecture of Viswanathan and Berger on the asymptotic behavior of minimum squared distortion for large rates is true.
Introduction to Block Copolymers (2004)

This chapter contains sections titled: Introduction Synthesis Block Copolymer Melts Block Copolymer Films Block Copolymers in Solution Crystallization in Block Copolymers Blends Containing Block Copolymers References
Operational Efficiency Analysis using DEA Approach for the Major Airports in Asia (2004)

There have been various research in analyzing airport productivity such as measuring total factor productivity using the models of translog cost function. DEA(Data Envelopment Analysis) model is very useful in measuring productivity with linear programming when the output is not clearly identified and measured quantitatively in such complex facilities as airport. This study is to measure airport productivity using DEA approach for Northeast Asia. Seven international airports were analyzed including Incheon International Airport in Korea, Cheklapkok Airport in Hongkong, Narita Airport in Japan, and Changi Airport in Singapore. With the productivity measured, we can identify one of the important aspects of comparative advantage in hub competition in Asia.