gebhart/patrepeval huggingface dataset:
Persistent Acylation Of High-Molecular-Weight Penicillin-Binding Proteins By Penicillin Induces The Postantibiotic Effect In Streptococcus Pyogmes (1994)

Penicillin at 10X MIC induced a postantibiotic effect (PAE) of 2.1 h in Streptococcus pyogenes. Progressive increases in the densities of penicillin-binding proteins (PBPs) 1-3 of the bacterium were detected at 30, 60, and 90 min during the postantibiotic phase. The increase in colony-forming units during this phase paralleled the kinetics of incorporation of lysine into proteins, suggesting that growth was triggered by de novo synthesis of PBPs. The question was raised as to whether the progressive increases in densities of PBPs were due to the restoration of preexisting PBPs or to synthesis of new PBPs. With 10X MIC of clindamycin to inhibit PBP synthesis during the postantibiotic phase, the temporal increase in densities of PBPs 1-3 were totally inhibited. These results suggest that the PAE of penicillin in S. pyogenes is caused by irreversible binding of penicillin to PBPs 1-3 and represents the time necessary for synthesis of new PBPs required for normal growth.
Tetramer guided, cell sorter assisted production of clinical grade autologous NY-ESO-1 specific CD8+ T cells (2014)

This study represents the first series using tetramer-guided cell sorting to generate T cells for adoptive therapy. This approach, when used to target more broadly expressed tumor antigens such as WT-1 and additional Cancer-Testis antigens will enhance the scope and feasibility of adoptive T cell therapy.
Nucleotide and primary sequence of a major rice prolamine (1988)

A recombinant cDNA clone encoding a major rice seed storage prolamine was isolated by antibody screening of a cDNA lambda gt 11 library. This clone contained a single open reading frame encoding a putative rice prolamine precursor (Mr 17,300). In contrast to other cereal prolamines, the primary sequence of the rice prolamine was devoid of any major tandem repetitive sequences, a feature prevalent in all cereal prolamines studied to date. No significant homology was detected between the rice prolamine and other cereal prolamines, indicating that the rice gene evolved from unique ancestral DNA segments.
Remote‐Control Photorelease of Caged Compounds Using Near‐Infrared Light and Upconverting Nanoparticles (2010)

Cage fighter: Lanthanide-doped upconverting nanoparticles convert near-infrared light into ultraviolet light, which drives the photoinduced release of a “caged” species on the nanoparticle surface. This approach overcomes the problem that low-energy light is necessary for penetrating deeper into tissue without damage but cannot be used to directly trigger important organic photochemical reactions.
TASA: traffic offloading by tag-assisted social-aware opportunistic sharing in mobile social networks (2015)

To solve the mobile traffic explosion problem, there have been many efforts to try to offload the mobile traffic from infrastructured cellular links to direct local short-range communications among users. In this paper, we propose a novel framework of traffic offloading by Tag-Assisted Social-Aware opportunistic sharing in mobile social networks, TASA, to offload traffic by device-to-device sharing. Based on the evaluation of the tags of users and contents, we select a subset of users who are likely to receive the same content as initial seeds depending on their spreading impacts in online SNSs and their mobility patterns in offline MSNs. Then users share the content via opportunistic local connectivity (e.g., Bluetooth, Wi-Fi Direct, LTE D2D) with each other. The observation from SNS activities reveals that individual users have distinct access patterns, which allows TASA to further exploit the user-dependent access delay between the content generation time and each users access time for traffic offloading purposes. We model and analyze the traffic offloading and content spreading among users by taking into account various options in linking SNS and MSN trace data. The trace-driven evaluation demonstrates that TASA can reduce up to 78.9% of the cellular traffic.
Evolution of ultrasound beamformers (2002)

Real-time ultrasonic imaging systems have been available for more than thirty years. During this time much has occurred to the basic architecture and functions of these clinical systems and their beamformers, which are, in many ways, the most important components of these systems. This talk will review some of the changes that have occurred and will discuss current trends in beamformer design. Throughout most of the 30 years of real time imaging, analog beamformers have been the mainstay of all instruments. The common methods for the implementation of analog beamformers for annular, linear/curved arrays, and phased arrays will be reviewed and the distinguishing characteristics identified. At the present time the industry is undergoing a major shift toward digital beamformation with the introduction of several commercial systems. Given that the earliest digital systems were available roughly 15 years ago, it is fair to say that the introduction of digital beamformers has been relatively slow. Today this shift seems to be gaining momentum. Some of the factors causing these shifts will be reviewed along the the common types of designs and implementations. The ongoing search for improved imaging performance will continue to introduce new challenges for beamformer designers. Among already proposed imaging methods and techniques are elevation focusing (1.5D arrays), synthetic apertures, 2D and sparse arrays, phase aberration correction, and others. The most common complication introduced by these is a significant increase in channel count. Further, there will also be beamformer design issues related to signal processing. These include not only Doppler processing but also the processing of signals due to novel contrast agents. Finally, with advances in computer and microelectronics technologies, the way we view beamformation may have to undergo sizeable changes. These topics will be reviewed not only as technical challenges but also in light of the constraints introduced by today's marketplace.
Rail-to-rail multiple-input min/max circuit (1998)

The author presents a multiple-input min/max circuit technique that reduces the errors associated with previous analog implementations by combining a common-source voltage-mode configuration with a current-mode "winner takes all" circuit. The overall architecture exhibits linear complexity with the number of inputs. Both minimum and maximum two-input prototypes have been designed and built in a 2-/spl mu/m CMOS process. The active area for each circuit is 650/spl times/100 /spl mu/m/sup 2/, and the total power dissipation is 0.8 mW from a single 5-V supply. Experimental results confirm rail-to-rail operation and sharp transition regions.
Family Cluster of Middle East Respiratory Syndrome Coronavirus Infections (2013)

A human coronavirus, called the Middle East respiratory syndrome coronavirus (MERS-CoV), was first identified in September 2012 in samples obtained from a Saudi Arabian businessman who died from acute respiratory failure. Since then, 49 cases of infections caused by MERS-CoV (previously called a novel coronavirus) with 26 deaths have been reported to date. In this report, we describe a family case cluster of MERS-CoV infection, including the clinical presentation, treatment outcomes, and household relationships of three young men who became ill with MERS-CoV infection after the hospitalization of an elderly male relative, who died of the disease. Twenty-four other family members living in the same household and 124 attending staff members at the hospitals did not become ill. MERS-CoV infection may cause a spectrum of clinical illness. Although an animal reservoir is suspected, none has been discovered. Meanwhile, global concern rests on the ability of MERS-CoV to cause major illness in close contacts of patients.
A Retroviral Promoter and a Cellular Enhancer Define a Bipartite Element Which Controls <i>env</i> ERVWE1 Placental Expression (2004)

The HERV-W family contains hundreds of loci diversely expressed in several physiological and pathological contexts. A unique locus termed ERVWE1 encodes an envelope glycoprotein (syncytin) involved in hominoid placental physiology. Here we show that syncytin expression is regulated by a bipartite element consisting of a cyclic AMP (cAMP)-inducible long terminal repeat (LTR) retroviral promoter adjacent to a cellular enhancer conferring a high level of expression and placental tropism. Deletion mutant analysis showed that the ERVWE1 5' LTR contains binding sites essential for basal placental activity in the region from positions +1 to +125. The region from positions +125 to +310 represents a cAMP-responsive core HERV-W promoter active in all cell types. Site-directed mutagenesis analysis highlighted the complexity of U3 regulation. ERVWE1 placenta-specific positive (e.g., T240) and negative (e.g., G71) regulatory sites were identified, as were essential sites required for basic activity (e.g., A247). The flanking sequences of the ERVWE1 provirus contain several putative regulatory elements. The upstream HERV-H and HERV-P LTRs were found to be inactive. Conversely, the 436-bp region located between the HERV-P LTR and ERVWE1 was shown to be an upstream regulatory element (URE) which is significantly active in placenta cells. This URE acts as a tissue-specific enhancer. Genetic and functional analyses of hominoid UREs revealed large differences between UREs of members of the Hominidae and the Hylobatidae. These data allowed the identification of a positive regulatory region from positions -436 to -128, a mammalian apparent LTR retrotransposon negative regulatory region from positions -128 to -67, and a trophoblast-specific enhancer (TSE) from positions -67 to -35. Putative AP-2, Sp-1, and GCMa binding sites are essential constituents of the 33-bp TSE.
Spatial filters for focusing ultrasound images (2002)

Traditionally focusing is done by taking out one sample in the received signal from each transducer element and then sum these signals. This method does not take into account the temporal or spatial spread of the received signal from a point scatterer and does not make an optimal focus of the data. A new method for making spatial matched filter focusing of RF ultrasound data is proposed based on the spatial impulse response description of the imaging. The response from a scatterer at any given point in space relative to the transducer can be calculated, and this gives the spatial matched filter for beamforming the received RF signals from the individual transducer elements. The matched filter is applied on RF signals from individual transducer elements, thus properly taking into account the spatial spread of the received signal. The method can be applied to any transducer and can also be used for synthetic aperture imaging for single element transducers. It is evaluated using the Field II program. Data from a single 3 MHz transducer focused at a distance of 80 mm is processed. Far from the transducer focal region, the processing greatly improves the image resolution: the lateral slice of the autocovariance function of the image shows a -6 dB width reduction by a factor of 3.3 at 20 mm and by a factor of 1.8 at 30 mm. Other simulations use a 64 elements, 3 MHz, linear array. Different receiving conditions are compared and this shows that the effect of the filter is progressively lower, but the approach always yields point spread functions better or equal to a traditional dynamically focused image. Finally, the process was applied to in-vivo clinical images of the liver and right kidney from a 28 years old male. The data was obtained with a single element transducer focused at 100 mm. The improvement in resolution was in this case less evident and further optimization is needed.
Pumping Of Low-Temperature Deep Sea Water For Cooling Of Facilities On Land (1983)

The low-temperature deep-sea water is pumped up to coast through pipes. We cool refrigerants of refrigerating machines in the pumped low-temperature sea water. This reduces the electric power of refrigerating machines. The electric power saved exceeds the power for pumping, so that we can operate the refrigerating system with less electric power. We also use the pumped low-temperature sea water for cooling of nuclear power plants on coast. The pumped low-temperature sea water is heated by the plants only up to the temperature of surface sea water, so that enviromental changes caused by the increase of the temperature of surface sea water can be avoided.
Trade-off bounds for the Pareto surface approximation in multi-criteria IMRT planning (2009)

One approach to multi-criteria IMRT planning is to automatically calculate a data set of Pareto-optimal plans for a given planning problem in a first phase, and then interactively explore the solution space and decide on the clinically best treatment plan in a second phase. The challenge of computing the plan data set is to ensure that all clinically meaningful plans are covered and that as many clinically irrelevant plans as possible are excluded to keep computation times within reasonable limits. In this work, we focus on the approximation of the clinically relevant part of the Pareto surface, the process that constitutes the first phase. It is possible that two plans on the Pareto surface have a small, clinically insignificant difference in one criterion and a significant difference in another criterion. For such cases, only the plan that is clinically clearly superior should be included into the data set. To achieve this during the Pareto surface approximation, we propose to introduce bounds that restrict the relative quality between plans, the so-called trade-off bounds. We show how to integrate these trade-off bounds into the approximation scheme and study their effects. The proposed scheme is applied to two artificial cases and one clinical case of a paraspinal tumor. For all cases, the quality of the Pareto surface approximation is measured with respect to the number of computed plans, and the range of values occurring in the approximation for different criteria is compared. Through enforcing trade-off bounds, the scheme disregards clinically irrelevant plans during the approximation. Thereby, the number of plans necessary to achieve a good approximation quality can be significantly reduced. Thus, trade-off bounds are an effective tool to focus the planning and to reduce computation time.
FAB (2004)

This paper describes the design, implementation, and evaluation of a Federated Array of Bricks (FAB), a distributed disk array that provides the reliability of traditional enterprise arrays with lower cost and better scalability. FAB is built from a collection of bricks , small storage appliances containing commodity disks, CPU, NVRAM, and network interface cards. FAB deploys a new majority-voting-based algorithm to replicate or erasure-code logical blocks across bricks and a reconfiguration algorithm to move data in the background when bricks are added or decommissioned. We argue that voting is practical and necessary for reliable, high-throughput storage systems such as FAB. We have implemented a FAB prototype on a 22-node Linux cluster. This prototype sustains 85MB/second of throughput for a database workload, and 270MB/second for a bulk-read workload. In addition, it can outperform traditional master-slave replication through performance decoupling and can handle brick failures and recoveries smoothly without disturbing client requests.
Mapping ATP-binding cassette transporter gene expression profiles in melanocytes and melanoma cells (2007)

ATP-binding cassette (ABC) transporters regulate the transport of a variety of physiologic substrates. Moreover, several human ABC proteins are responsible for drug exclusion in compound-treated tumor cells, providing cellular mechanisms for the development of multidrug resistance and, therefore, playing an important role in malignant transformation. As only limited information exists on the role of ABC transporters in melanoma, the aim of the study was to generate a complete expression profile of ABC transporters in this tumor entity. Using a TaqMan low-density array for 47 human ABC transporters, mRNA expression analysis was performed from normal human epidermal melanocytes (NHEM P2 and NHEM P3), nine different cell lines originating from primary melanoma (Mel Ei, Mel Juso, Mel Ho and Mel Wei), and metastases of malignant melanoma (Mel Im, Mel Ju, SK Mel 28, HTZ 19 and HMB2). Cell line-specific expression levels were compared with gene expression in pooled RNA from a variety of other human tissues. High expression levels were detected in pooled tissue RNA as well as in cells of melanocytic origin for ABCA5, ABCB2, ABCB6, ABCD3, ABCD4, ABCF1, ABCF2 and ABCF3, whereas ABCB5 revealed a melanocyte-specific high transcript level. In relation to normal melanocytes, ABCB3, ABCB6, ABCC2, ABCC4, ABCE1 and ABCF2 were significantly increased in melanoma cell lines, whereas ABCA7, ABCA12, ABCB2, ABCB4, ABCB5 and ABCD1 showed lower expression levels. In summary, we present here for the first time an ABC-transporter mRNA expression profile in melanoma in comparison to normal melanocytes. The differentially regulated ABC transporters detected by our approach may be candidate genes involved in melanoma tumorigenesis, progression and therapy resistance and could therefore be of great importance to identify novel options for melanoma therapy.
Wild‐type superoxide dismutase acquires binding and toxic properties of ALS‐linked mutant forms through oxidation (2007)

Recent studies suggest that superoxide dismutase (SOD1) may represent a major target of oxidative damage in neurodegenerative diseases. To test the possibility that oxidized species of wild-type (WT) SOD1 might be involved in pathogenic processes, we analyzed the properties of the WT human SOD1 protein after its oxidation in vivo or in vitro by hydrogen peroxide (H2O2) treatment. Using transfected Neuro2a cells expressing WT or amyotrophic lateral sclerosis-linked SOD1 species, we show that exposure to H2O2 modifies the properties of WT SOD1. Western blot analysis of immunoprecipitates from cell lysates revealed that, like mutant SOD1, oxidized WT SOD1 can be conjugated with poly-ubiquitin and can interact with Hsp70. Chromogranin B, a neurosecretory protein that interacts with mutant SOD1 but not with WT SOD1, was co-immunoprecipitated with oxidized WT SOD1 from lysates of Neuro2a cells treated with H2O2. Treatment of microglial cells (line BV2) with either oxidized WT SOD1 or mutant SOD1 recombinant proteins induced tumor necrosis factor-alpha and inducible nitric oxide synthase. Furthermore, exposure of cultured motor neurons to oxidized WT SOD1 caused dose-dependent cell death like mutant SOD1 proteins. These results suggest that WT SOD1 may acquire binding and toxic properties of mutant forms of SOD1 through oxidative damage.
Bayesian Hierarchical Changepoint Methods in Modeling the Tumor Growth Profiles in Xenograft Experiments (2010)

Compared with the tumor doubling time approach, the BHC model utilizes all data, providing more descriptive features that address mechanisms underlying tumor growth inhibition and maximize the biological information obtained from tumor xenografts studies.
Caval Interruption for Prevention of Pulmonary Embolism (1969)

Patients with nonfatal pulmonary emboli may be managed by administration of anticoagulants, by inferior vena caval ligation, or by one of a number of operations to partition the inferior vena cava (IVC),<sup>1-6</sup>all of which methods have certain disadvantages. Anticoagulants carries the risk of further embolism and ligation or partition of IVC, even though blocking emboli arising from veins of the legs or pelvis of necessity requires general anesthesia and a fairly extensive operation. This report describes the long-term results of a new simplified method of IVC interruption by an intracaval prosthesis which is implanted intravenously under local anesthesia. Experimental studies and initial clinical experience was reported earlier.<sup>7,8</sup>This procedure avoids a major surgical operation and can be performed with minimal risk even in critically ill patients with acute pulmonary embolism. <h3>Materials and Methods</h3> The intracaval prosthesis (Fig 1) is of an umbrella design and consists of six
Correlation between near-infrared spectroscopy and magnetic resonance imaging of rat brain oxygenation modulation (2003)

We measure the tissue oxygen and haemoglobin concentrations in the rat brain during modulation of inhaled oxygen concentration (FiO2), using non-invasive frequency domain near-infrared oximetry. The rise in oxygenated haemoglobin concentration and the decline in deoxygenated haemoglobin concentration are demonstrated in correspondence with the modulation of FiO2, which is changed from 20% to 100% in increments of 20%. Furthermore, the tissue oxygenation saturation also shows the corresponding trend and changes ranging from approximately 70% to 90%. The relative changes in deoxygenated haemoglobin concentration are compared to the blood-oxygenation-level-dependent (BOLD) MRI signal recorded during a similar FiO2 protocol. A linear relationship with high correlation coefficient between the relative changes in the BOLD MRI signal and the NIRS signal is observed.
The relationship between exposed galactose and N-acetylglucosamine residues on IgG in rheumatoid arthritis (RA), juvenile chronic arthritis (JCA) and Sjögren's syndrome (SS) (1996)

The relationship between exposed galactose and N-acetylglucosamine on IgG in RA, JCA and SS was investigated. This was achieved using IgG isolated from serum where the levels of galactose and N-acetylglucosamine (GlcNAc) were detected using biotinylated lectins. Galactose and GlcNAc on IgG from patients with RA and JCA are inversely related, but in contrast, in SS, galactose expression on IgG decreased while GlcNAc expression remained similar to normal levels. Alterations in IgG glycosylation are closely associated with the development of adult and juvenile chronic arthritis and SS, but the changes involved are different in RA compared with SS, suggesting that the precise pattern of exposed sugars is associated with different rheumatological diseases.
A Retrospective Analysis of Outcomes Using Three Common Methods for Immediate Breast Reconstruction (2008)

High satisfaction rates were seen across all three reconstructive groups, with the highest satisfaction levels seen in the expander/implant group, despite higher reoperation rates and lower aesthetic scores for this group.
Just-for-us (2005)

Mobile computer technologies are increasingly being appropriated and used to facilitate people's social life outside the work domain. Addressing this emerging domain of use, we present the design of a context-aware mobile information system prototype facilitating sociality in public places: Just-for-Us. The design of the prototype system was informed by two empirical studies: an architectural analysis of a recently built public space in Melbourne, Australia and a field study of small groups socialising there. We describe these two studies and illustrate how findings informed our prototype design. Finally, we outline an ongoing field study of the use of the Just-for-Us prototype.
Vectors for RNA interference. (2004)

Introduction of double-stranded RNA into cells causes gene silencing in a sequence-specific manner, involving the coordinated activity of enzymes such as Dicer and RNA-induced silencing complex. Several groups have recently demonstrated that this phenomenon of RNA interference (RNAi) occurs in mammalian cells when small interfering (si)RNAs are used, and have developed vector-based siRNA expression systems that can induce RNAi in living cells. These vector systems use polymerase III promoters, such as U6 or H1, and are classified into two groups based on the form of expressed RNA, tandem or hairpin. This review describes the basis for, and methodology of siRNA expression vectors for mammalian cells.