gebhart/patrepeval huggingface dataset:
Sequence, expression in Escherichia coli, and analysis of the gene encoding a novel intracellular protease (PfpI) from the hyperthermophilic archaeon Pyrococcus furiosus (1996)

A previously identified intracellular proteolytic activity in the hyperthermophilic archaeon Pyrococcus furiosus (I. I. Blumentals, A. S. Robinson, and R. M. Kelly, Appl. Environ. Microbiol. 56:1992-1998, 1990) was found to be a homomultimer consisting of 18.8-kDa subunits. Dissociation of this native P. furiosus protease I (PfpI) into a single subunit was seen by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) but only after trichloroacetic acid precipitation; heating to 95 degrees C in the presence of 2% SDS and 80 mM dithiothreitol did not dissociate the protein. The gene (pfpI) coding for this protease was located in genomic digests by Southern blotting with probes derived from the N-terminal amino acid sequence. pfpI was cloned, sequenced, and expressed in active form in Escherichia coli as a fusion protein with a histidine tag. The recombinant protease from E. coli showed maximum proteolytic activity at 95 degrees C, and its half-life was 19 min at this temperature. This level of stability was significantly below that previously reported for the enzyme purified by electroelution of a 66-kDa band from SDS-PAGE after extended incubation of cell extracts at 98 degrees C in 1% SDS (>30 h). The pfpI gene codes for a polypeptide of 166 amino acid residues lacking any conserved protease motifs; no protease activity was detected for the 18.8-kDa PfpI subunit (native or recombinant) by substrate gel assay. Although an immunological relationship of this protease to the eukaryotic proteasome has been seen previously, searches of the available databases identified only two similar amino acid sequences: an open reading frame of unknown function from Staphylococcus aureus NCTC 8325 (171 amino acid residues, 18.6 kDa, 41% identity) and an open reading frame also of unknown function in E. coli (172 amino acid residues, 18.8 kDa, 47% identity). Primer extension experiments with P. furiosus total RNA defined the 5' end of the transcript. There are only 10 nucleotides upstream of the start of translation; therefore, it is unlikely that there are any pre- or pro-regions associated with PfpI which could have been used for targeting or assembly of this protease. Although PfpI activity appears to be the dominant proteolytic activity in P. furiosus cell extracts, the physiological function of PfpI is unclear.
Experimental broadband OFDM system: field results for OFDM and OFDM with frequency domain spreading (2003)

The paper presents link performance results of a series of field experiments conducted for OFDM and spread-OFDM/MC-CDMA in the context of a fourth-generation cellular system (4G) downlink. The experimental system is a 20 MHz 2/spl times/2 MIMO-OFDM system operating at a carrier frequency of 3.676 GHz. Measurements were conducted in a moderate density urban and suburban setting outside Chicago, Illinois, which exhibits varying degrees of delay spread and signal-to-noise ratio, with vehicle speeds ranging from 0 to 65 miles per hour. Coded performance (r=1/2 64-state convolutional coding) is compared for various link configurations: no receive diversity, 2-branch diversity, Alamouti transmit diversity, and 2/spl times/2 MIMO for QPSK, 16-QAM, and 64-QAM constellations. Results indicate that OFDM typically outperforms spread-OFDM, especially for higher order modulations. Moreover, the performance of dual-stream MIMO is sensitive to the channel condition number.
Combined Beamformers for Robust Broadband Regularized Superdirective Beamforming (2015)

Superdirective fixed beamformers are known to attain high directivity factors, but are extremely sensitive to uncorrelated noise and slight errors in the array elements, which are modeled by the beamformer white noise gain measure. The delay-and-sum beamformer, on the other hand, manages to maximize the white noise gain, but suffers from a very low directivity factor. In this paper, we discuss the design of a broadband beamformer which controls both the directivity factor and the white noise gain. We combine a regularized version of the superdirective beamformer together with the delay-and-sum beamformer to create a robust regularized superdirective beamformer. We derive analytic closed-form expressions of the beamformer gain responses, and extend them to derive a beamformer with full control of the desired white noise gain or the directivity factor. The proposed approach offers a simple and robust broadband beamformer with controllable characteristics, shown here through persuasive simulation results.
Droplet Electrospray Mass Spectrometry (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDroplet Electrospray Mass SpectrometryDarcy B. Hager, Norman J. Dovichi, John. Klassen, and Paul. KebarleCite this: Anal. Chem. 1994, 66, 22, 3944–3949Publication Date (Print):November 15, 1994Publication History Published online1 May 2002Published inissue 15 November 1994https://pubs.acs.org/doi/10.1021/ac00094a015https://doi.org/10.1021/ac00094a015research-articleACS PublicationsRequest reuse permissionsArticle Views710Altmetric-Citations59LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Tartan (2006)

Spatial Computing (SC) has been shown to be an energy-efficient model for implementing program kernels. In this paper we explore the feasibility of using SC for more than small kernels. To this end, we evaluate the performance and energy efficiency of entire applications on Tartan, a general-purpose architecture which integrates a reconfigurable fabric (RF) with a superscalar core. Our compiler automatically partitions and compiles an application into an instruction stream for the core and a configuration for the RF. We use a detailed simulator to capture both timing and energy numbers for all parts of the system.Our results indicate that a hierarchical RF architecture, designed around a scalable interconnect, is instrumental in harnessing the benefits of spatial computation. The interconnect uses static configuration and routing at the lower levels and a packet-switched, dynamically-routed network at the top level. Tartan is most energyefficient when almost all of the application is mapped to the RF, indicating the need for the RF to support most general-purpose programming constructs. Our initial investigation reveals that such a system can provide, on average, an order of magnitude improvement in energy-delay compared to an aggressive superscalar core on single-threaded workloads.
Modeling micro-controller peripherals for high-level co-simulation and synthesis (1997)

Luciano Lavagno, Claudio Passerone, and Claudio SansoePolitecnico di TorinoMapping a behavior on an embedded system involves hardware-software partitioning and assignment of software and hardware tasks to different components. In particular, software tasks in embedded controllers are mostly assigned to a micro-controller. However, some micro-controller peripherals are implemented with partly programmable components that can be regarded as very simple co-processors with limited instruction sets and capabilities. Embedded system designers are used to mapping some simple software tasks onto these simple co-processors, obtaining overall performances that can be orders of magnitude superior to the ones obtained mapping all software tasks to the micro-controller itself. In this paper, we propose a methodology to specify, simulate, and partition tasks that can be implemented on programmable micro-controller peripherals such as Timing Processing Units (TPUs). Following our general philosophy, we let the designer propose a partition, and we provide an environment to: - efficiently simulate and evaluate a particular implementation choice, - automate downstream synthesis for software, hardware, as well as peripheral programming routines.
What is synergy? (1989)

Abstract Background This study aimed to examine the effect of pool walking on renal function in pregnant women. Methods Fifteen pregnant women (mean gestational age, 37.8 weeks) walked in a pool (depth 1.3 m) for 1 h. A few days later, they walked on a street for 1 h. Within each activity, the starting and ending levels of plasma renin activity (PRA) and serum aldosterone (SA) were compared using paired t-test. Total urine volume, creatinine clearance, and change in PRA levels between each activity were compared by t-test. Regression coefficients for total urine volume and creatinine clearance during pool walking were estimated by linear regression and additionally controlled for the change in PRA levels. Land walking served as the reference group. Results Within each activity, the renin-angiotensin-aldosterone levels were suppressed during pool walking: the mean starting and ending values of PRA and SA were 6.8 vs. 5.5 ng/mL/h (p=0.002) and 654 vs. 473 pg/mL (p=0.02), respectively. Compared to land walking, the decrease in PRA level was more evident in pool walking (−1.27 vs. 0.81 ng/mL/h, p=0.004), resulting in higher total urine volume and creatinine clearance in pool walking (both p Conclusions Pool walking may temporarily improve renal function in pregnant women, partly through the suppressed renin-angiotensin-aldosterone system. Clinical Trial Registration URL: https://upload.umin.ac.jp/cgi-bin/ctr/ctr_view_reg.cgi?recptno=10618 Unique Identifier: UMI09051
Anti-MUC1 Nanobody Can Redirect T-Body Cytotoxic Effector Function (2009)

Chimeric antigen T cell receptors provide a good approach for adoptive immunotherapy of cancer, especially in the context of cancerous cells that fail to express major histocompatibility complex antigen and co-stimulatory molecules. Clinical applications of these receptors are limited, mostly due to the xenogenic origin of the antibodies, which cause immunogenic reactions. Nanobodies are the smallest fragments of antibodies that have great homology to human VH and low immunogenic potential. MUC1 is a highly attractive immunotherapeutic target owing to increased expression, altered glycosylation, and loss of polarity in more than 80% of human malignancies. We used anti-MUC1 nanobody as an antigen binding domain, CD28 and CD3zeta as signaling domains, and IgG3 as a spacer in a chimeric receptor construct. This construct was transfected to Jurkat cells. The transfected Jurkat cells were exposed to MUC1-positive MCF7 cells. Then we analyzed the secretion of IL2, proliferation of Jurkat cells, and death of MCF7 cells. These data revealed that the nanobody chimeric receptor can target tumor-associated antigen-positive cells. Regarding the efficient and specific function of nanobody chimeric receptor and non-immunogenic nature of nanobodies, these chimeric receptors might be used as promising candidates for clinical applications.
DNA methyltransferase and demethylase in human prostate cancer (2002)

Recent studies have shown that cytosine-5 methylation at CpG islands in the regulatory sequence of a gene is one of the key mechanisms of inactivation. The enzymes responsible for CpG methylation are DNA methyltransferase (DNMT) 1, DNMT3a, and DNMT3b, and the enzyme responsible for demethylation is DNA demethylase (MBD2). Studies on methylation-demethylation enzymes are lacking in human prostate cancer. We hypothesize that MBD2 enzyme activity is repressed and that DNMT1 enzyme activity is elevated in human prostate cancer. To test this hypothesis, we analyzed enzyme activities, mRNA, and protein levels of MBD2 and DNMT1, DNMT3a, and DNMT3b in human prostate cancer cell lines and tissues. The enzyme activities of DNMTs and MBD2 were analyzed by biochemical assay. The mRNA expression was analyzed by reverse transcriptase-polymerase chain reaction and by Northern blotting. The protein expression was measured by immunohistochemistry with specific antibodies. The results of these experiments demonstrated that (1) the activity of DNMTs was twofold to threefold higher in cancer cell lines and cancer tissues, as compared with a benign prostate epithelium cell line (BPH-1) and benign prostatic hyperplasia (BPH) tissues; (2) MBD2 activity was lacking in prostate cancer cell lines but present in BPH-1 cells; (3) immunohistochemical analyses exhibited higher expression of DNMT1 in all prostate cancer cell lines and cancer tissues, as compared with BPH-1 cell lines and BPH tissues; (4) MBD2 protein expression was significantly higher in BPH-1 cells and lacking in prostate cancer cell lines and, in BPH tissues, MBD2 protein expression was poorly observed, as compared with no expression in prostate cancer tissues; and (5) mRNA expression for DNMT1 was upregulated in prostate cancer, as compared with BPH-1, and mRNA expression for MBD2 was found to be significantly expressed in all cases. The results of these studies clearly demonstrate that DNMT1 activity is upregulated, whereas MBD2 is repressed at the level of translation in human prostate cancer. These results may demonstrate molecular mechanisms of CpG hypermethylation of various genes in prostate cancer.
Small Fish Models for Identifying and Assessing the Effects of Endocrine-disrupting Chemicals (2004)

Endocrine-disrupting chemicals (EDCs), particularly those that affect the hypothalamic-pituitary-gonadal (HPG) axis of vertebrates, have become a focus of regulatory screening and testing throughout the world. Small fish species, principally the fathead minnow (Pimephales promelas), Japanese medaka (Oryzias latipes), and zebrafish (Danio rerio), are used as model organisms for several of these testing programs. Fish are appropriate models for testing EDCs, not only from the perspective of existing ecological impacts, but also in terms of species extrapolation. Specifically, there is a significant degree of conservation of basic aspects of the HPG axis across vertebrates, which provides a technically robust basis for using results from fish tests to predict likely modes/mechanisms of action of potential EDCs in other vertebrates. Different experimental designs/endpoints for partial- and full-life cycle tests with fish that enable a consideration of a broad range of EDCs are described. Examples of results with specific chemicals in tests with the fathead minnow, medaka, and zebrafish are presented and discussed in terms of sensitivity and specificity for different classes of EDCs.
The Extracellular Membrane-Proximal Domain of Human Membrane IgE Controls Apoptotic Signaling of the B Cell Receptor in the Mature B Cell Line A20 (2006)

Ag engagement of BCR in mature B cells can deliver specific signals, which decide cell survival or cell death. Circulating membrane IgE+ (mIgE+) cells are found in extremely low numbers. We hypothesized that engagement of an epsilonBCR in a mature isotype-switched B cell could induce apoptosis. We studied the role of the extracellular membrane-proximal domain (EMPD) of human mIgE upon BCR engagement with anti-Id Abs. Using mutants lacking the EMPD, we show that this domain is involved in controlling Ca2+ mobilization in immunoreceptors of both gamma and epsilon isotypes, as well as apoptosis in signaling originated only from the epsilonBCR. We mapped to the epsilonCH4 ectodomain the region responsible for apoptosis in EMPD-deleted receptors. Ca2+ mobilization was not related to apoptotic signaling. This apoptotic pathway was caspase independent, involved ERK1/2 phosphorylation and was partially rescued by CD40 costimulation. We therefore conclude that the EMPD of human mIgE is a key control element of apoptotic signaling delivered through engagement of epsilonBCR within the context of a mature B cell.
Applying polymer process studies using molecular modeling (2002)

Although process studies are usually done experimentally within the microelectronics board and packaging industry, at Honeywell we have been concerned about facilitating such studies though use of molecular-scale simulation support. For instance, we have used bleed modeling for several years now to understand and target bleed modification additives and to help us predict the effect of both organic and inorganic components on underfill flow. In a similar strategy we have used an adhesion modeling extension to understand stress cycling reliability, and to predict the relative ability of our formulations to withstand thermal cycling. Most recently we have used thermal cycling to help us understand process differences in several resin coated copper foils used in circuit board manufacture. All of these studies have demonstrated usefulness in understanding specific interfacial mechanisms that could not be understood from larger scale simulations or experimental evidence alone. As these studies encompass aspects of both the pre-cure and post-cure state of the adhesive, they require different assumption bases as well as different methodologies to address the performance issues. In this paper we will discuss the strategies applied, their results in in-house formulation and the impacts of using the molecular perspective to increase adhesive understanding in a development scenario.
High intensity focused ultrasound—potential for cancer treatment (1995)

The prospect of being able to use "minimally invasive" surgical techniques is of great interest today, particularly for reasons of health economics, patient acceptability and reduced morbidity. High intensity focused ultrasound (HIFU) has long been known to offer the potential of very precise "trackless lesioning" but has only recently, with the advent of high quality methods of medical imaging, become a practicable possibility. High intensity beams can readily be achieved using either bowel or lens focusing procedures and, by choice of a suitable acoustic frequency, regions of tissue destruction--"lesions"--can be induced at depths of up to at least 10 cm with exposure times of the order of 1 s. Theoretical and experimental evidence indicates that the primary mechanism of damage is thermal, i.e. "cooking" of the tissues. Both conventional cavitation and boiling of tissue water may complicate the situation. Furthermore, substantial non-linear behaviour is involved. On histological appearance the lesions have a spatially sharp demarcation between regions of normal and dead cells. When attempts are made to ablate a block of tissue, by creating an array of adjacent elementary lesions, a phenomenon is observed of inhibition of formation of a lesion whose placing is too close to that of a neighbour. Provided that this problem is dealt with, complete ablation of an extended block of tissue can be achieved. For animal tumours in particular, this observation is reinforced by evidence both of in vitro cell survival and of tumour growth delay experiments. Clinically, the sites accessible for HIFU treatment will be limited by the need for a suitably wide acoustic window that either is available naturally or can be provided by a relatively minor surgical procedure. Tumour sites which thus offer a realistic prospect for local control (and some of which are already the subject of phase 1 trials) include liver, bladder, kidney, prostate, breast and brain. There is also considerable interest in non-cancer applications in these and other sites.
Development of Fine Pitch Solder Microbumps for 3D Chip Stacking (2008)

Developments of ultra fine pitch and high density solder microbumps for advanced 3D stacking technologies are discussed in this paper. CuSn solder microbumps with 25 ¿m in pitch are fabricated at wafer level by electroplating method and the total thicknesses of the platted Cu and Sn are 10 ¿m. After plating, the micro bumps on the Si chip are reflowed at 265°C and the variation of bump height measured within a die is less than 5%. The under bump metallurgy (UBM) layer on the Si carrier used is electroless plated nickel and immersion gold (ENIG) with total thickness less than 5 ¿m. Assembly of the Si chip and the Si carrier is conducted with the FC150 flip chip bonder at different temperatures, times, and pressures and the optimized bonding conditions are obtained. After assembly, underfill process is carried out to fill the gap and a void free underfilling is achieved using an underfill material with fine filler size.
Identification of the Xenopus DNA2 protein as a major nuclease for the 5'->3' strand-specific processing of DNA ends (2008)

The first step of homology-dependent DNA double-strand break (DSB) repair is the 5' strand-specific processing of DNA ends to generate 3' single-strand tails. Despite extensive effort, the nuclease(s) that is directly responsible for the resection of 5' strands in eukaryotic cells remains elusive. Using nucleoplasmic extracts (NPE) derived from the eggs of Xenopus laevis as the model system, we have found that DNA processing consists of at least two steps: an ATP-dependent unwinding of ends and an ATP-independent 5'-->3' degradation of single-strand tails. The unwinding step is catalyzed by DNA helicases, the major one of which is the Xenopus Werner syndrome protein (xWRN), a member of the RecQ helicase family. In this study, we report the purification and identification of the Xenopus DNA2 (xDNA2) as one of the nucleases responsible for the 5'-->3' degradation of single-strand tails. Immunodepletion of xDNA2 resulted in a significant reduction in end processing and homology-dependent DSB repair. These results provide strong evidence that xDNA2 is a major nuclease for the resection of DNA ends for homology-dependent DSB repair in eukaryotes.
FTY720 suppresses CD4+CD44highCD62L− effector memory T cell-mediated colitis (2006)

FTY720, a sphingosine-derived immunomodulator, causes immunosuppression via enhancement of lymphocyte sequestration into secondary lymphoid organs, thereby preventing their antigen-activated T cell egress to sites of inflammation. FTY720 is highly effective in inhibiting autoimmunity in various animal models. However, there is little known about how FTY720 controls the migration property of memory T cells. Here, we demonstrated that FTY720 prevents the development of colitis induced by the adoptive transfer of lamina propria (LP) colitogenic effector memory CD4+ T cells (TEM cells; CD45RB(low)CD44(high)CD62L-) into severe combined immunodeficiency (SCID) mice and suppresses interferon-gamma, interleukin-2, and tumor necrosis factor-alpha production by LP CD4+ T cells. The numbers of spleen, peripheral blood, mesenteric lymph node, and LP CD4+ T cells in FTY720-treated mice were significantly reduced compared with those in control mice. Notably, LP CD4+ TEM cells as well as splenic CD4+CD45RBhigh T cells expressed several spingosine-1-phosphate receptors that are targets for FTY720. Furthermore, FTY720 also prevented the development of colitis induced by the adoptive transfer of splenic CD4+CD45RBhigh T cells into SCID mice. Collectively, the present data indicate that FTY720 treatment may offer the potential not only to prevent the onset of disease but also to treat memory T cell-mediated autoimmune diseases including inflammatory bowel diseases.