gebhart/patrepeval huggingface dataset:
Electronically steered antenna system for the australian mobilesat (1996)

The paper describes an L-band land-vehicle mobile satellite-communications system which is designed for the Australian continent. A 14-element cylindrical antenna array for use at the vehicle end of the link is presented. The array uses electronic steering in the azimuth to maintain a communications channel to the satellite. It incorporates novel, low-cost antenna elements which feature increased impedance and ellipticity bandwidth. Also included is a novel configuration of a switched radial divider/combiner which allows for the use of low-cost switching diodes. The indoor and outdoor test results for the subsystems and the entire antenna system are presented in the paper.
The Reversible Masking of Amino Groups in Ribonuclease and Its Possible Usefulness in the Synthesis of the Protein (1962)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Reversible Masking of Amino Groups in Ribonuclease and Its Possible Usefulness in the Synthesis of the ProteinRobert F. Goldberger and Christian B. AnfinsenCite this: Biochemistry 1962, 1, 3, 401–405Publication Date (Print):May 25, 1962Publication History Published online1 May 2002Published inissue 25 May 1962https://pubs.acs.org/doi/10.1021/bi00909a005https://doi.org/10.1021/bi00909a005research-articleACS PublicationsRequest reuse permissionsArticle Views270Altmetric-Citations136LEARN 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
Prevalent Role of TCR α-Chain in the Selection of the Preimmune Repertoire Specific for a Human Tumor-Associated Self-Antigen (2003)

The specificity of recognition of pMHC complexes by T lymphocytes is determined by the V regions of the TCR alpha- and beta-chains. Recent experimental evidence has suggested that Ag-specific TCR repertoires may exhibit a more V alpha- than V beta-restricted usage. Whether V alpha usage is narrowed during immune responses to Ag or if, on the contrary, restricted V alpha usage is already defined at the early stages of TCR repertoire selection, however, has remained unexplored. Here, we analyzed V and CDR3 TCR regions of single circulating naive T cells specifically detected ex vivo and isolated with HLA-A2/melan-A peptide multimers. Similarly to what was previously observed for melan-A-specific Ag-experienced T cells, we found a relatively wide V beta usage, but a preferential V alpha 2.1 usage. Restricted V alpha 2.1 usage was also found among single CD8(+) A2/melan-A multimer(+) thymocytes, indicating that V alpha-restricted selection takes place in the thymus. V alpha 2.1 usage, however, was independent from functional avidity of Ag recognition. Thus, interaction of the pMHC complex with selected V alpha-chains contributes to set the broad Ag specificity, as underlined by preferential binding of A2/melan-A multimers to V alpha 2.1-bearing TCRs, whereas functional outcomes result from the sum of these with other interactions between pMHC complex and TCR.
The major outer membrane protein, CD, extracted from Moraxella (Branhamella) catarrhalis is a potential vaccine antigen that induces bactericidal antibodies (1997)

The major outer membrane protein of Moraxella (Branhamella) catarrhalis, CD, was detergent-extracted from the bacterial cell wall and purified to homogeneity in high yields by a simple process. The purified protein appeared to exhibit immunogenic properties similar to those of native CD exposed on the surface of the bacterium. Antibodies to CD raised in mice specifically bound to intact B. catarrhalis, as determined by flow cytometry analysis. The IgG subclass distributions of anti-CD antibodies in sera from mice immunized with purified CD or with B. catarrhalis were also similar. CD was found to be antigenically conserved among a panel of B. catarrhalis isolates, as demonstrated by the consistent reactivities of mouse anti-CD antisera with a common 60 kDa protein on immunoblots. Furthermore, convalescent sera collected from patients with otitis media due to B. catarrhalis infection were found to be reactive with the CD protein by immunoblotting. Finally, the purified protein induced antibodies in guinea pigs and mice that exhibited in vitro bactericidal activity against the pathogen. Therefore, the native CD outer membrane protein represents a potentially useful antigen for inclusion in a vaccine against B. catarrhalis.
Inhibition of translocation of viable Escherichia coli from the gastrointestinal tract of mice by bacterial antagonism (1979)

The incidence of translocation of viable Escherichia coli C25 from the gastrointestinal tract to the mesenteric lymph nodes was compared in gnotobiotic mice colonized with only E. coli C25 and in gnotobiotic mice colonized with E. coli C25 plus the whole cecal flora from specific pathogen-free mice. The population levels of E. coli C25 in the ilea and ceca of these mice also were compared. E. coli C25 maintained high population levels in the gastrointestinal tracts of the monoassociated gnotobiotes, and the incidence of translocation to the mesenteric lymph nodes was 100%. The gastrointestinal population levels of E. coli C25 were reduced drastically in the gnotobiotes associated with both E. coli C25 and a cecal flora with concomitant reduction in the incidence of translocation of E. coli C25 from 100 to 0%. A decrease in the numbers of viable E. coli C25 per mesenteric lymph node also accompanied the decrease in C. coli C25 population levels in the gastrointestinal tracts of these mice. Thus, high population levels of E. coli C25 in the gastrointestinal tracts of monoassociated gnotobiotic mice appear to promote translocation of viable E. coli C25 to the mesenteric lymph nodes. Bacterial antagonism of E. coli population levels in conventional mice, therefore, could be one mechanism whereby viable E. coli are confined to the gastrointestinal tract.
A PAM50-Based Chemoendocrine Score for Hormone Receptor–Positive Breast Cancer with an Intermediate Risk of Relapse (2016)

<b>Purpose:</b> Hormone receptor-positive (HR<sup>+</sup>) breast cancer is clinically and biologically heterogeneous, and subgroups with different prognostic and treatment sensitivities need to be identified.<b>Experimental Design:</b> Research-based PAM50 subtyping and expression of additional genes was performed on 63 patients with HR<sup>+</sup>/HER2<sup>-</sup> disease randomly assigned to neoadjuvant multiagent chemotherapy versus endocrine therapy in a phase II trial. The biology associated with treatment response was used to derive a PAM50-based chemoendocrine score (CES). CES's predictive ability was evaluated in 4 independent neoadjuvant data sets (<i>n</i> = 675) and 4 adjuvant data sets (<i>n</i> = 1,505). The association of CES, intrinsic biology, and PAM50 risk of relapse (ROR) was explored across 6,007 tumors.<b>Results:</b> Most genes associated with endocrine sensitivity were also found associated with chemotherapy resistance. In the chemotherapy test/validation data sets, CES was independently associated with pathologic complete response (pCR), even after adjusting for intrinsic subtype. pCR rates of the CES endocrine-sensitive (CES-E), uncertain (CES-U), and chemotherapy-sensitive (CES-C) groups in both data sets combined were 25%, 11%, and 2%, respectively. In the endocrine test/validation data sets, CES was independently associated with response. Compared with ROR, >90% of ROR-low and ROR-high tumors were identified as CES-E and CES-C, respectively; however, each CES group represented >25% of ROR-intermediate disease. In terms of survival outcome, CES-C was associated with poor relapse-free survival in patients with ROR-intermediate disease treated with either adjuvant endocrine therapy only or no adjuvant systemic therapy, but not in patients treated with (neo)adjuvant chemotherapy.<b>Conclusions:</b> CES is a genomic signature capable of estimating chemoendocrine sensitivity in HR<sup>+</sup> breast cancer beyond intrinsic subtype and risk of relapse. <i>Clin Cancer Res; 23(12); 3035-44. ©2016 AACR</i>.
B4 and after (2018)

Private WANs are increasingly important to the operation of enterprises, telecoms, and cloud providers. For example, B4, Google's private software-defined WAN, is larger and growing faster than our connectivity to the public Internet. In this paper, we present the five-year evolution of B4. We describe the techniques we employed to incrementally move from offering best-effort content-copy services to carrier-grade availability, while concurrently scaling B4 to accommodate 100x more traffic. Our key challenge is balancing the tension introduced by hierarchy required for scalability, the partitioning required for availability, and the capacity asymmetry inherent to the construction and operation of any large-scale network. We discuss our approach to managing this tension: i) we design a custom hierarchical network topology for both horizontal and vertical software scaling, ii) we manage inherent capacity asymmetry in hierarchical topologies using a novel traffic engineering algorithm without packet encapsulation, and iii) we re-architect switch forwarding rules via two-stage matching/hashing to deal with asymmetric network failures at scale.
Invasion by cultured human follicular thyroid cancer correlates with increasedβ1 integrins and production of proteases (1992)

A recognized model of tumor invasion requires cells to adhere to epithelial basement membrane and extracellular matrix components triggering release of proteases thus allowing cancer cells to invade the substrate. This adhesion is mediated by beta 1 integrins, a family of receptors to substrates such as collagen, laminin, and fibronectin. In order to study tumor invasion in follicular thyroid cancer (FTC), we used cell lines derived from a single patient's FTC primary tumor (FTC-133), neck lymph node metastases (FTC-236), and lung metastases (FTC-238). In vitro invasion as determined by the ability of the tumor cells to penetrate Matrigel was assessed by scanning electron microscopy. FTC-133 did not invade, FTC-236 was moderately invasive, and FTC-238 was highly invasive. Immunoprecipation with a monoclonal antibody to beta 1 integrin subunits and SDS-PAGE showed increased synthesis and flow cytometry showed increased expression of this subunit in FTC-236 and FTC-238 compared to FTC-133. Proteolytic activity was assessed by gelatin zymography. FTC-238 cell extract and conditioned media exhibited a more complex array of proteases consistent with activated type I collagenase and stromelysin compared to the less invasive clones, however 72 and 92 kd gelatinases consistent with type IV collagenases were present in the conditioned media from all three lines. In conclusion, in vitro invasion parallels in vivo metastasis by the source cells in the FTC-133/236/238 cell-lines. The ability to invade basement membrane preparation correlates with increased synthesis and expression of beta 1 integrins and activation of tumor proteases.
Machine learning optimization of peptides for presentation by class II MHCs (2021)

Supplementary data are available at Bioinformatics online.
Real-Time Monitoring of the Interactions of Two-Stranded de Novo Designed Coiled-Coils:  Effect of Chain Length on the Kinetic and Thermodynamic Constants of Binding (2003)

We have de novo designed a heterodimeric coiled-coil formed by two peptides as a capture/delivery system that can be used in applications such as affinity tag purification, immobilization in biosensors, etc. The two strands are designated as K coil (KVSALKE heptad sequence) and E coil (EVSALEK heptad sequence), where positively charged or negatively charged residues occupy positions e and g of the heptad repeat. In this study, for each E coil or K coil, three peptides were synthesized with lengths varying from three to five heptads. The effect of the chain length of each partner upon the kinetic and thermodynamic constants of interaction were determined using a surface plasmon resonance-based biosensor. Global fitting of the interactions revealed that the E5 coil interacted with the K5 coil according to a simple binding model. All the other interactions involving shorter coils were better described by a more complex kinetic model involving a rate-limiting reorganization of the coiled-coil structure. The affinities of these de novo designed coiled-coil interactions were found to range from 60 pM (E5/K5) to 30 microM (E3/K3). From these K(d) values, we were able to determine the free energy contribution of each heptad, depending on its relative position within the coiled-coils. We found that the free energy contribution of a heptad occupying a central position was 3-fold higher than that of a heptad at either end of the coiled-coil. The wide range of stabilities and affinities for the E/K coil system provides considerable flexibility for protein engineering and biotechnological applications.
Fabricating RNA Microarrays with RNA−DNA Surface Ligation Chemistry (2005)

A novel surface attachment strategy that utilizes RNA-DNA surface ligation chemistry to create renewable RNA microarrays from single-stranded DNA (ssDNA) microarrays on gold surfaces is demonstrated. The enzyme T4 DNA ligase was used to catalyze the formation of a phosphodiester bond between 5'-phosphate-modified ssDNA attached to the surface and the 3'-hydroxyl group of unlabeled RNA molecules from solution in the presence of a complementary template DNA strand. Surface plasmon resonance imaging (SPRI) measurements were performed to characterize the ligation process as well as to verify the bioactivity of the ssRNA microarray in terms of (i) the hybridization adsorption of complementary DNA onto the RNA array to form a surface RNA-DNA heteroduplex and (ii) the hydrolysis of the RNA microarrays with either ribonuclease S or ribonuclease H (RNase H). The hydrolysis of the surface-bound RNA with RNase H required the presence of a surface heteroduplex and, upon completion, regenerated the original 5'-phosphate-terminated ssDNA array elements. These ssDNA array elements could be ligated again to create a new RNA microarray. These RNA microarrays can be used in the study of RNA-protein/RNA/aptamer bioaffinity interactions and for the enzymatically amplified SPRI detection of DNA in the presence of RNase H.
Recurrence of Hyperparathyroidism from Autografted Parathyroid Fragments in Uremic Patients in Spite of Administration of 25(OH)D3 and 1a(OH)D3 (1979)

Recurrence of Hyperparathyroidism from Autografted Parathyroid Fragments in Uremic Patients in Spite of Administration of 25(OH)D3 and 1a(OH)D3 was published in Vitamin D. Basic Research and its Clinical Application on page 791.
Aerosol-induced Immunoglobulin (Ig)-E Unresponsiveness to Ovalbumin Does Not Require CD8+ or T Cell Receptor (TCR)-γ/δ+ T Cells or Interferon (IFN)-γ in a Murine Model of Allergen Sensitization (1998)

Mice exposed for 20 min daily to aerosolized ovalbumin (OVA) for 10 d at concentrations from 1 to 0.01% OVA made greatly reduced immunoglobulin (Ig)-E responses to subsequent immunogenic OVA challenges, given either intraperitoneally or by aerosol. This IgE-specific unresponsiveness lasted for at least four months. However, these aerosol-treated mice were primed for larger OVA-specific IgG1 and IgG2a responses. The specific reduction in IgE responses was not due to preferential induction of a T helper (Th)-1 response as aerosol OVA- primed mice made greatly reduced Th2 and no detectable Th1 response after rechallenge in vitro. Consistent with this, the increase in circulating eosinophils observed in control Th2-primed mice was absent in aerosol OVA-treated animals. Interferon (IFN)-gamma was not required for this unresponsiveness, as IFN-gamma knockout mice and anti-IFN-gamma antibody-treated wild-type mice had greatly reduced levels of IgE similar to wild-type controls. CD8+ T cells played a relatively small role as IgE responses were reduced to about the same extent in beta2 microglobulin-deficient, or in anti-CD8-treated wild-type mice as in normal mice after aerosol OVA treatment. Similarly, T cell receptor (TCR)-gamma/delta T cells were not required for maximal inhibition of the IgE response. These results demonstrate that exposure to inhaled protein antigens can induce a state of unresponsiveness of CD4+ T cells that results in a prolonged loss of IgE and eosinophil responses to subsequent challenges. This T cell unresponsiveness was shown not to require CD8+ or TCR-gamma/delta+ T cells or IFN-gamma.
Loss of Brain-enriched miR-124 MicroRNA Enhances Stem-like Traits and Invasiveness of Glioma Cells (2012)

miR-124 is a brain-enriched microRNA that plays a crucial role in neural development and has been shown to be down-regulated in glioma and medulloblastoma, suggesting its possible involvement in brain tumor progression. Here, we show that miR-124 is down-regulated in a panel of different grades of glioma tissues and in all of the human glioma cell lines we examined. By integrated bioinformatics analysis and experimental confirmation, we identified SNAI2, which is often up-regulated in glioma, as a direct functional target of miR-124. Because SNAI2 has been shown to regulate stem cell functions, we examined the roles of miR-124 and SNAI2 in glioma cell stem-like traits. The results showed that overexpression of miR-124 and knockdown of SNAI2 reduced neurosphere formation, CD133(+) cell subpopulation, and stem cell marker (BMI1, Nanog, and Nestin) expression, and these effects could be rescued by re-expression of SNAI2. Furthermore, enhanced miR-124 expression significantly inhibited glioma cell invasion in vitro. Finally, stable overexpression of miR-124 and knockdown of SNAI2 inhibited the tumorigenicity and invasion of glioma cells in vivo. These findings reveal, for the first time, that the tumor suppressor activity of miR-124 could be partly due to its inhibitory effects on glioma stem-like traits and invasiveness through SNAI2.
Deregulated expression of the Myc cellular oncogene drives development of mouse “Burkitt-like” lymphomas from naive B cells (2004)

Chromosomal translocations juxtaposing immunoglobulin (Ig) and MYC genes are the hallmarks of human Burkitt lymphoma (BL), with deregulated MYC expression being a critical factor in pathogenesis. By inserting an intact mouse Myc gene into the mouse genome, proximal to the Ig enhancer Emu, the effect of a precise mimic of the major t(8;14) translocation of human endemic BL (eBL) could be investigated. Knock-in mice developed IgM-positive B-cell tumors, with most being typical of eBL by histology and immunophenotype, including expression of the germinal center (GC)-associated protein, BCL6. Unlike eBL, however, analysis of Ig V(H) sequences revealed no significant level of somatic mutation. Thus, constitutive expression of Myc in the knock-in mice is apparently able to induce "Burkitt-like" lymphomas before antigen stimulation and formation of a GC. In contrast, human eBL development occurs in a GC or post-GC site with a likely contribution to pathogenesis from Epstein-Barr virus (EBV) and other epigenetic factors.
Diagnosis of Acute Appendicitis With Sliding Slab Ray-Sum Interpretation of Low-Dose Unenhanced CT and Standard-Dose IV Contrast-Enhanced CT Scans (2009)

Low-dose unenhanced CT is potentially useful in the diagnosis of appendicitis.
Regulation of the heat shock transcriptional response: cross talk between a family of heat shock factors, molecular chaperones, and negative regulators (1998)

Our cells and tissues are challenged constantly by exposure to extreme conditions that cause acute and chronic stress. Consequently, survival has necessitated the evolution of stress response networks to detect, monitor, and respond to environmental changes (Morimoto et al. 1990, 1994a; Baeuerle 1995; Baeuerle and Baltimore 1996; Feige et al. 1996; Morimoto and Santoro 1998). Prolonged exposure to stress interferes with efficient operations of the cell, with negative consequences on the biochemical properties of proteins that, under ideal conditions, exist in thermodynamically stable states. In stressed environments, proteins can unfold, misfold, or aggregate. Therefore, the changing demands on the quality control of protein biogenesis, challenges protein homeostasis, for which the heat shock response, through the elevated synthesis of molecular chaperones and proteases, repairs protein damage and assists in the recovery of the cell. The inducible transcription of heat shock genes is the response to a plethora of stress signals (Lis and Wu 1993; Morimoto 1993; Wu 1995) (Fig. 1), including (1) environmental stresses, (2) nonstress conditions, and (3) pathophysiology and disease states. Although changes in heat shock protein (HSP) expression are associated with certain diseases (Morimoto et al. 1990), these observations leave open the question of whether this is an adaptation to the particular pathophysiological state, a reflection of the suboptimal cellular environment associated with the disease, or serves to warn other cells and tissues of imminent danger. The protective role of HSPs is a measure of their capacity to assist in the repair of protein damage. Whether in prokaryotes, plants, or animals, overexpression of one or more HSPs is often sufficient to protect cells and tissues against otherwise lethal exposures to diverse environmental stresses including hydrogen peroxide and other oxidants, toxic chemicals, extreme temperatures, and ethanol-induced toxicity (Parsell and Lindquist 1994). In vertebrate tissue culture cells and animal models, elevating HSPs level, either by modulation of the heat shock response or by constitutive overexpression of specific heat shock proteins, restricts or substantially reduces the level of pathology and cell death (Mizzen and Welch 1988; Huot et al. 1991; Jaattela et al. 1992; Parsell and Lindquist 1994; Mestril et al. 1994; Plumier et al. 1995; Marber et al. 1995; Mehlen et al. 1995; Mosser et al. 1997). This has led to the recognition that HSPs, via their chaperoning effects on proteins, protect cells from many forms of stress-induced cell damage and could influence the course of disease.