gebhart/patrepeval huggingface dataset:
Realization of Microwave Quantum Circuits Using Hybrid Superconducting-Semiconducting Nanowire Josephson Elements (2015)

We report the realization of quantum microwave circuits using hybrid superconductor-semiconductor Josephson elements comprised of InAs nanowires contacted by NbTiN. Capacitively shunted single elements behave as transmon circuits with electrically tunable transition frequencies. Two-element circuits also exhibit transmonlike behavior near zero applied flux but behave as flux qubits at half the flux quantum, where nonsinusoidal current-phase relations in the elements produce a double-well Josephson potential. These hybrid Josephson elements are promising for applications requiring microwave superconducting circuits operating in a magnetic field.
Satellite applications of spread spectrum frequency hopping techniques (2003)

Some features of frequency-hopping (FH) code-division multiple-access (CDMA) techniques are discussed in connection with the mitigation of the effects of interferences in multiple-user satellite systems. The authors show how some specific satellite applications-data relay satellites, space station, mobile satellite systems, VSATs (very small aperture terminals)-may take advantage of CDMA features offered by spread-spectrum modulations. FH is briefly reviewed as a valid alternative to direct-sequence spread-spectrum methods, and FH techniques are analyzed in a specific scenario concerning space station communications. The design of spreading and forward error correction codes for FH systems is addressed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Effectiveness Indices for Statistical Process Control Chart Performance (2010)

The current standard practice in manufacturing industries and SPC textbooks only specify how to set up control limits and how to choose different run rules (such as the WECO rules) for control charts for process quality characteristic under monitoring. The cost modeling has also been developed in literature to determine the control chart settings for economic design; however, it has very limited applications in semiconductor manufacturing because the complexity of many process steps and multiple process equipments at each step made it nearly impossible to do cost modeling. For process characteristics with wide conformance specification, control limits width wider than 3σ has been widely in practical applications and a simple WECO rule of one point beyond control limits is popularly used. However, no index is designed to evaluate the effectiveness of control chart settings (the width of control limits). We define alarm types and the corresponding rates to distinguish alarms without root causes found during diagnostics from statistical false alarms. A new alarm type of non-OOC excursions is also defined and introduced. We use them to form indices and inequalities to evaluate whether the control limits are set too wide. When inexperienced engineers are unable to perform effective troubleshooting and root cause diagnostics, some true alarms are treated as false ones. These new indices and inequalities have made it possible to evaluate whether engineers need to improve their engineering troubleshooting skills. An overall index is also designed to judge the relative performance with different control limit settings.
Purification and Biochemical Characterization of the Promoter-Specific Transcription Factor, Sp1 (1986)

The biochemical analysis of cellular trans-activators involved in promoter recognition provides an important step toward understanding the mechanisms of gene expression in animal cells. The promoter selective transcription factor, Sp1, has been purified from human cells to more than 95 percent homogeneity by sequence-specific DNA affinity chromatography. Isolation and renaturation of proteins purified from sodium dodecyl sulfate polyacrylamide gels allowed the identification of two polypeptides (105 and 95 kilodaltons) as those responsible for recognizing and interacting specifically with the GC-box promoter elements characteristic of Sp1 binding sites.
ADSM: a multi-platform, scalable, backup and archive mass storage system (2002)

The ADSTAR Distributed Storage Manager (ADSM) is a client-server system whose goal is to provide the illusion of infinite storage for a range of applications. The first deployed application is backup and archive services. ADSM is a configurable system targeted to serve any client at user installations with heterogeneous architectures that offers the same level of data management for LANs, midrange and mainframe systems. ADSM moves the responsibilities of backup and archive media management to the server while maintaining the benefits of local workstation systems. In ADSM, incremental backups are all that a user needs to do to restore its data with maximum performance. The ADSM server has been deployed in five IBM and two non-IBM platforms, while the ADSM clients operate in more than twelve IBM and non-IBM platforms.
Challenges in Antibody Development against Tn and Sialyl-Tn Antigens (2015)

The carbohydrate antigens Tn and sialyl-Tn (STn) are expressed in most carcinomas and usually absent in healthy tissues. These antigens have been correlated with cancer progression and poor prognosis, and associated with immunosuppressive microenvironment. Presently they are used in clinical trials as therapeutic vaccination, but with limited success due to their low immunogenicity. Alternatively, anti-Tn and/or STn antibodies may be used to harness the immune system against tumor cells. Whilst the development of antibodies against these antigens had a boost two decades ago for diagnostic use, so far no such antibody entered into clinical trials. Possible limitations are the low specificity and efficiency of existing antibodies and that novel antibodies are still necessary. The vast array of methodologies available today will allow rapid antibody development and novel formats. Following the advent of hybridoma technology, the immortalization of human B cells became a methodology to obtain human monoclonal antibodies with better specificity. Advances in molecular biology including phage display technology for high throughput screening, transgenic mice and more recently molecularly engineered antibodies enhanced the field of antibody production. The development of novel antibodies against Tn and STn taking advantage of innovative technologies and engineering techniques may result in innovative therapeutic antibodies for cancer treatment.
Metabolism and disposition of the HIV-1 protease inhibitor ritonavir (ABT-538) in rats, dogs, and humans. (1997)

The metabolism and disposition of [14C]ritonavir (ABT-538, NOR-VIR), a potent, orally active HIV-1 protease inhibitor, were investigated in male and female Sprague-Dawley rats, beagle dogs, and HIV-negative male human volunteers. Rats and dogs received a 5 mg/kg iv, 20 mg/kg oral or 20 mg/kg intraduodenal dose, whereas humans received a single 600-mg liquid oral dose. Ritonavir was cleared primarily via hepatobiliary elimination in all three species. After iv or oral dosing in either rats or dogs, > 92% of the dose was recovered in rat and dog feces and < or = 4% was recovered in the urine. Humans excreted 86.3% of the oral dose in feces and 11.3% in urine over 6 days. Bile-exteriorized rats and dogs excreted 85.5% and 39.8%, respectively, of the iv dose in bile, with < 3% recovered in urine. Radio-HPLC analysis of bile, feces, and urine from all three species indicated extensive metabolism of ritonavir to a number of oxidative metabolites, some being species-specific, and all involving metabolism at the terminal functional groups of the molecule. Glucuronide metabolites were observed in dog only. Plasma radioactivity consisted predominantly of unchanged parent drug in all three species. M-2, the product of hydroxylation at the methine carbon of the terminal isopropyl moiety of ritonavir, was the only metabolite present in human plasma and made up 30.4% of the total dose recovered in human excreta over 6 days. Tissue distribution of ritonavir in rat was widespread, with good distribution into lymphatic tissue but low CNS penetration. Plasma protein binding of ritonavir was high (96-99.5%) in all species and was nonsaturable in humans at concentrations up to 30 micrograms/ml. Partitioning into the formed elements of whole blood was minimal.
Gene Cloning, Expression, and Characterization of the Sac7 Proteins from the Hyperthermophile Sulfolobus acidocaldarius (1995)

The genes for two Sac7 DNA-binding proteins, Sac7d and Sac7e, from the extremely thermophilic archaeon Sulfolobus acidocaldarius have been cloned into Escherichia coli and sequenced. The sac7d and sac7e open reading frames encode 66 amino acid (7608 Da) and 65 amino acid (7469 Da) proteins, respectively. Southern blots indicate that these are the only two Sac7 protein genes in S. acidocaldarius, each present as a single copy. Sac7a, b, and c proteins appear to be carboxy-terminal modified Sac7d species. The transcription initiation and termination regions of the sac7d and sac7e genes have been identified along with the promoter elements. Potential ribosome binding sites have been identified downstream of the initiator codons. The sac7d gene has been expressed in E. coli, and various physical properties of the recombinant protein have been compared with those of native Sac7. The UV absorbance spectra and extinction coefficients, the fluorescence excitation and emission spectra, the circular dichroism, and the two-dimensional double-quantum filtered 1H NMR spectra of the native and recombinant species are essentially identical, indicating essentially identical local and global folds. The recombinant and native proteins bind and stabilize double-stranded DNA with a site size of 3.5 base pairs and an intrinsic binding constant of 2 x 10(7) M-1 for poly[dGdC].poly[dGdC] in 0.01 M KH2PO4 at pH 7.0. The availability of the recombinant protein permits a direct comparison of the thermal stabilities of the methylated and unmethylated forms of the protein. Differential scanning calorimetry demonstrates that the native protein is extremely thermostable and unfolds reversibly at pH 6.0 with a Tm of approximately 100 degrees C, while the recombinant protein unfolds at 92.7 degrees C.
Structural Requirements for Function of the Crkl Adapter Protein in Fibroblasts and Hematopoietic Cells (1998)

Crkl is an adapter protein and phosphotyrosine-containing substrate implicated in transformation by the bcr-abl oncogene and in signaling by cytokines. When phosphorylated, Crkl binds through its Src homology 2 (SH2) domain to other tyrosine phosphoproteins such as paxillin and Cbl. Overexpression of Crkl in fibroblasts induces transformation. Here we examine the role of Crkl in hematopoietic cells and find that overexpression of Crkl confers a signal leading to increased adhesion to fibronectin. In both fibroblasts and hematopoietic cells, individual mutations or deletions of each SH2 and SH3 domain abrogated transformation and adhesion, respectively, indicating that interactions with other proteins such as Cbl and paxillin (SH2 domain) and Abl, Sos, and C3G (N-terminal SH3 domain) are essential for biological activity. In vivo and in vitro tryptic phosphopeptide mapping studies show that Crkl is phosphorylated on multiple tyrosine residues when overexpressed or when activated by Bcr-Abl. Mutation at tyrosine 207, a residue conserved in c-Crk, abrogates all in vivo tyrosine phosphorylation of Crkl. Despite this loss of phosphotyrosine, mutation at this site enhanced Crkl function as measured by complex formation with SH2 binding proteins, signal transduction to Jun Kinase, and fibroblast transformation. These observations implicate Crkl in cellular adhesion and demonstrate that Y207 functions as a negative regulatory site.
GLP-1 Tablet in Type 2 Diabetes in Fasting and Postprandial Conditions (1997)

Potentially therapeutic plasma levels of GLP-1 were achieved after administration of a single buccal tablet in type 2 diabetic patients. The peptide had a marked glucose-lowering effect during the first 2 h. This new GLP-1 tablet may become a feasible alternative treatment for type 2 diabetic patients, although a more prolonged pharmacokinetic profile is required.
Use of Continuous Human Lung Cell Culture for Adenovirus Isolation (1995)

Adenovirus sensitivity, TCD50 value and mean time to cytopathic effect (CPE) were compared in Madin-Darby canine kidney (MDCK), rhesus monkey kidney (RhMK), human lung carcinoma (A549) and in newly identified continuous human lung (CHL) cell cultures. High-titer stock and positive original specimens were inoculated in culture. Patients specimens were also placed in shell-vial cultures. A549 and CHL cells demonstrated comparable sensitivity, however the former generally produced CPE earlier. Sensitivity was respectively reduced and poor in RhMK and MDCK cultures, as expected in cells of nonhuman origin. The performance of CHL for adenoviruses and other pathogens makes them a useful addition in diagnostic virology laboratories.
Over-Expression of the Functional Interleukin-11α Receptor in the Development of B-Cell Chronic Lymphocytic Leukemia (2001)

Several cytokines have been found to play a role in the pathogenesis of B-CLL. In the present study using reverse-transcriptase polymerase chain reaction (RT-PCR), FACS analysis and immunofluorescence we have shown the constitutive expression of IL-11 and IL-11R alpha in B-chronic lymphocytic leukemia (B-CLL). The expression level of IL-11R alpha in B-CLL cells is much higher than in PBL of normal donors. Recombinant human IL-11 (rhIL-11) activates B-CLL cells, leading to morphologic alterations of the cells and increase in cell number and size. Short-term cultivation in the presence of rhIL-11 did not lead to quantitative changes in the ratio of the living vs apoptotic and dead cells. However, in contrast to rhIL-6, pretreatment with rhIL-11, did not cause B-CLL cells to be resistant to the action of dexamethasone. These data suggest an essential role for the IL-11/IL11 R alpha system in the pathogenesis of the malignant B-CLL cells.
Packaging of Proteases and Proteoglycans in the Granules of Mast Cells and Other Hematopoietic Cells (1995)

Mouse mast cell protease 7 (mMCP-7) is a tryptase stored in the secretory granules of mast cells. At the granule pH of 5.5, mMCP-7 is fully active and is bound to heparin-containing serglycin proteoglycans. to understand the interaction of mMCP-7 with heparin inside and outside the mast cell, this trytase was first studied by comparative protein modeling. The "pro" form of mMCP-7 was then expressed in insect cells and studied by site-directed mutagenesis. Although mMCP-7 lacks known linear sequences of amino acis that interact with heparin, the three-dimensional model of mMCP-7 revealed an area on the surface of the folded protein away from the substrate-binding site that exhibits a strong positive electrostatic potential at the acidic pH of the granule. In agreement with this calculation, recombinant pro-mMCP-7 bound to a heparin-affinity column at pH 5.5 and readily dissociated from the column at pH > 6.5. Site-directed mutagenesis confirmed the prediction that the conversion of His residues 8,68, and 70 in the positively charged region into Glu prevents the binding of pro-mMCP-7 to heparin. Because the binding requires positively charged His residues, native mMCP-7 is able to dissociate from the protease/proteoglycan macromolecular complex when the complex is exocytosed from bone marrow-derived mast cells into a neutral pH environment. Many hematopoietic effector cells store positively charged proteins in granules that contain serglycin proteoglycans. The heparin/mMCP-7 interaction, which depends on the tertiary structure of the tryptase, may be representative of a general control mechanism by which hematopoietic cells maximize storage of properly folded, enzymatically active proteins in their granules.
Multiplexed immunohistochemistry, imaging, and quantitation: A review, with an assessment of Tyramide signal amplification, multispectral imaging and multiplex analysis (2014)

Tissue sections offer the opportunity to understand a patient's condition, to make better prognostic evaluations and to select optimum treatments, as evidenced by the place pathology holds today in clinical practice. Yet, there is a wealth of information locked up in a tissue section that is only partially accessed, due mainly to the limitations of tools and methods. Often tissues are assessed primarily based on visual analysis of one or two proteins, or 2-3 DNA or RNA molecules. Even while analysis is still based on visual perception, image analysis is starting to address the variability of human perception. This is in contrast to measuring characteristics that are substantially out of reach of human perception, such as parameters revealed through co-expression, spatial relationships, heterogeneity, and low abundance molecules. What is not routinely accessed is the information revealed through simultaneous detection of multiple markers, the spatial relationships among cells and tissue in disease, and the heterogeneity now understood to be critical to developing effective therapeutic strategies. Our purpose here is to review and assess methods for multiplexed, quantitative, image analysis based approaches, using new multicolor immunohistochemistry methods, automated multispectral slide imaging, and advanced trainable pattern recognition software. A key aspect of our approach is presenting imagery in a workflow that engages the pathologist to utilize the strengths of human perception and judgment, while significantly expanding the range of metrics collectable from tissue sections and also provide a level of consistency and precision needed to support the complexities of personalized medicine.
A Separate and Special Place—The Queen Elizabeth Hospital Barbara Lazenby Craig and Ronald K. MacLeod (1987)

Most historical reviews of hospitals fall into a pattern of humble beginnings, extraordinary efforts to achieve a place in the world of health, and finally-I with maturity-new struggles that confront the institution. This book follows that pattern. Beginning in 1874 as the Toronto Home for Incurables for the purpose of affording maintenance, nursing, and medical and surgical aid to persons suffering from incurable disease, the hospital gradually increased its capacity until, in 1978, it was a two-site hospital with more than 600 beds and fresh problems.
Regulation of Antinucleoprotein IgG by Systemic Vaccination and Its Effect on Influenza Virus Clearance (2011)

Seasonal influenza epidemics recur due to antigenic drift of envelope glycoprotein antigens and immune evasion of circulating viruses. Additionally, antigenic shift can lead to influenza pandemics. Thus, a universal vaccine that protects against multiple influenza virus strains could alleviate the continuing impact of this virus on human health. In mice, accelerated clearance of a new viral strain (cross-protection) can be elicited by prior infection (heterosubtypic immunity) or by immunization with the highly conserved internal nucleoprotein (NP). Both heterosubtypic immunity and NP-immune protection require antibody production. Here, we show that systemic immunization with NP readily accelerated clearance of a 2009 pandemic H1N1 influenza virus isolate in an antibody-dependent manner. However, human immunization with trivalent inactivated influenza virus vaccine (TIV) only rarely and modestly boosted existing levels of anti-NP IgG. Similar results were observed in mice, although the reaction could be enhanced with adjuvants, by adjusting the stoichiometry among NP and other vaccine components, and by increasing the interval between TIV prime and boost. Importantly, mouse heterosubtypic immunity that had waned over several months could be enhanced by injecting purified anti-NP IgG or by boosting with NP protein, correlating with a long-lived increase in anti-NP antibody titers. Thus, current immunization strategies poorly induce NP-immune antibody that is nonetheless capable of contributing to long-lived cross-protection. The high conservation of NP antigen and the known longevity of antibody responses suggest that the antiviral activity of anti-NP IgG may provide a critically needed component of a universal influenza vaccine.
Learning hyperparameter optimization initializations (2015)

Hyperparameter optimization is often done manually or by using a grid search. However, recent research has shown that automatic optimization techniques are able to accelerate this optimization process and find hyperparameter configurations that lead to better models. Currently, transferring knowledge from previous experiments to a new experiment is of particular interest because it has been shown that it allows to further improve the hyperparameter optimization. We propose to transfer knowledge by means of an initialization strategy for hyperparameter optimization. In contrast to the current state of the art initialization strategies, our strategy is neither limited to hyperparameter configurations that have been evaluated on previous experiments nor does it need meta-features. The initial hyperparameter configurations are derived by optimizing for a meta-loss formally defined in this paper. This loss depends on the hyperparameter response function of the data sets that were investigated in past experiments. Since this function is unknown and only few observations are given, the meta-loss is not differentiable. We propose to approximate the response function by a differentiable plug-in estimator. Then, we are able to learn the initial hyperparameter configuration sequence by applying gradient-based optimization techniques. Extensive experiments are conducted on two meta-data sets. Our initialization strategy is compared to the state of the art for initialization strategies and further methods that are able to transfer knowledge between data sets. We give empirical evidence that our work provides an improvement over the state of the art.
Poly-l-glutamic acid (PGA) Aided Inhibitors of Apoptotic Protease Activating Factor 1 (Apaf-1):  An Antiapoptotic Polymeric Nanomedicine (2006)

An antiapoptotic polymeric nanomedicine, PGA-peptoid 1, has been developed by the conjugation of a novel apoptotic protease activating factor 1 (Apaf-1) inhibitor (peptoid 1) to poly-L-glutamic acid (PGA). Full structural and biophysical characterization of the conjugate by different techniques has been accomplished. This macromolecule clearly enhances the antiapoptotic activity of peptoid 1 in different cell models.
Hardware emulation of Memristor based Ternary Content Addressable Memory (2017)

MTCAM (Memristor Ternary Content Addressable Memory) is a special purpose storage medium in which data could be retrieved based on the stored content. Using Memristors as the main storage element provides the potential of achieving higher density and more efficient solutions than conventional methods. A key missing item in the validation of such approaches is the wide spread availability of hardware emulation platforms that can provide reliable and repeatable performance statistics. In this paper, we present a hardware MTCAM emulation based on 2-Transistors-2Memristors (2T2M) bit-cell. It builds on a bipolar memristor model with storing and fetching capabilities based on the actual current-voltage behaviour. The proposed design offers a flexible verification environment with quick design revisions, high execution speeds and powerful debugging techniques. The proposed design is modeled using VHDL and prototyped on Xilinx Virtex® FPGA.