gebhart/patrepeval huggingface dataset:
Optimization of Codon Usage Enhances the Immunogenicity of a DNA Vaccine Encoding Mycobacterial Antigen Ag85B (2005)

In spite of its many other benefits, DNA vaccine is limited in its application by its insufficient immunogenicity. One promising approach for enhancing its immunogenicity is to maximize its expression in the immunized host. In the current study, we investigated whether codon optimization of the mycobacterial antigen Ag85B gene could enhance the expression and immunogenicity of the Ag85B DNA vaccine. We generated a synthetic humanized Ag85B (hAg85B) gene in which codon usage was optimized for expression in human cells. DNA plasmids with codon-optimized hAg85B increased the level of protein expression in vitro and in vivo. DNA vaccine with hAg85B induced stronger Th1-like and cytotoxic T-cell immune responses in BALB/c mice and generated higher protective immunity in a BALB/c mouse model of Mycobacterium tuberculosis aerosol infection than did the DNA vaccine with wild-type Ag85B. Therefore, our results suggest that codon optimization of mycobacterial antigens (e.g., Ag85B) could improve protein expression and thereby enhance the immunogenicity of DNA vaccines against M. tuberculosis.
Deep Visual-Semantic Alignments for Generating Image Descriptions (2016)

We present a model that generates natural language descriptions of images and their regions. Our approach leverages datasets of images and their sentence descriptions to learn about the inter-modal correspondences between language and visual data. Our alignment model is based on a novel combination of Convolutional Neural Networks over image regions, bidirectional Recurrent Neural Networks (RNN) over sentences, and a structured objective that aligns the two modalities through a multimodal embedding. We then describe a Multimodal Recurrent Neural Network architecture that uses the inferred alignments to learn to generate novel descriptions of image regions. We demonstrate that our alignment model produces state of the art results in retrieval experiments on Flickr8K, Flickr30K and MSCOCO datasets. We then show that the generated descriptions outperform retrieval baselines on both full images and on a new dataset of region-level annotations. Finally, we conduct large-scale analysis of our RNN language model on the Visual Genome dataset of 4.1 million captions and highlight the differences between image and region-level caption statistics.
Metabolic reprogramming orchestrates cancer stem cell properties in nasopharyngeal carcinoma (2014)

Cancer stem cells (CSCs) represent a subpopulation of tumor cells endowed with self-renewal capacity and are considered as an underlying cause of tumor recurrence and metastasis. The metabolic signatures of CSCs and the mechanisms involved in the regulation of their stem cell-like properties still remain elusive. We utilized nasopharyngeal carcinoma (NPC) CSCs as a model to dissect their metabolic signatures and found that CSCs underwent metabolic shift and mitochondrial resetting distinguished from their differentiated counterparts. In metabolic shift, CSCs showed a greater reliance on glycolysis for energy supply compared with the parental cells. In mitochondrial resetting, the quantity and function of mitochondria of CSCs were modulated by the biogenesis of the organelles, and the round-shaped mitochondria were distributed in a peri-nuclear manner similar to those seen in the stem cells. In addition, we blocked the glycolytic pathway, increased the ROS levels, and depolarized mitochondrial membranes of CSCs, respectively, and examined the effects of these metabolic factors on CSC properties. Intriguingly, the properties of CSCs were curbed when we redirected the quintessential metabolic reprogramming, which indicates that the plasticity of energy metabolism regulated the balance between acquisition and loss of the stemness status. Taken together, we suggest that metabolic reprogramming is critical for CSCs to sustain self-renewal, deter from differentiation and enhance the antioxidant defense mechanism. Characterization of metabolic reprogramming governing CSC properties is paramount to the design of novel therapeutic strategies through metabolic intervention of CSCs.
Improved multipass optics for diode laser spectroscopy (1993)

Feedback between optical elements can be a major source of noise when trying to attain high sensitivity in infrared absorption experiments. We find that a conventional White-cell optical arrangement introduces étaloning fringes that modulate the peak-to-peak amplitude of our signals by 1 part in 16 666, a fractional change of 6×10−5. Although relatively small, this ‘‘noise’’ is systematic and adds coherently with averaging, obscuring interesting absorption features. An easily constructed multipass optical system suited for performing high-resolution infrared spectroscopy in molecular beams is described. The design is based on a variation of the White cell and has been optimized for use with lead salt diode lasers. One of the key components in the improved design is the addition of an oscillating mirror for spoiling optical feedback generated by laser scatter and/or poor mode coupling of the laser to the multipass optics.
An in vitro investigation of the astringency property of certain anhidrotic solutions. (1985)

Compounds effective in vivo in the rat as anhidrotic wee found to precipitate egg white protein. There was little correlation between the effectiveness of a compound as an antiperspirant and its ability to precipitate protein. Lanthanum chloride was an exception since it was found to be the most effective anhidrotic in the rat and also produced the highest levels of precipitate. The addition of calcium or magnesium chloride increased the quantity of protein precipitated by the anhidrotic solutions, in contrast to their effect in vivo.
Laboratory evaluation of a method proposed by Gnam for measuring the temperature of rotating parts (1948)

A therm oco uple application s uggested by Gnam for m ea surin g the temperature o f rotating parts without slip rings or telemetering has been investigated. A rota ting circui t, con isting of a thermoco uple in series wi th t he rotor coil s of a converter, and a stationary circuit, co nsistin g of the tator coils of t he converter and a transformer, are linked mag netieally . One t herm ocouple junction is fi xed to the rotating part whose temperature is to be measured, an d the othe r pro t rude from a hollow shaft in to a furnace. The temperat ure of the rotating part is stationary circui t, a s d etermined by an oscilloscope , used as a null inclicator. Full-scale appl ication of t hi system eems p ract icable.
Product Data Exchange (1994)

Part 1 First generation methods for CAD data exchange: the ad hoc solution CAD and CAD data exchange. Part 2 Second generation methods: the neutral format early versions of IGES 1979-83 the proliferation of product data exchange initiatives further developments related initiatives. Part 3 Complementary initiatives and infrastructure problems with product data exchange testing sets and application protocols conformance testing. Part 4 The third generation: STEP the history of STEP andassociated activities a brief description of step the way forward.
Numerical Simulation of the Shock Compression of Microscale Reactive Particle Systems (2005)

The shock compression of Reactive Particle Metal Mixtures (RPMMs) is studied at the microscale by direct numerical simulation. Mixture microstructures are rendered explicitly, providing spatial resolution of the coupled thermal, mechanical, and chemical responses at the particle level during shock compression. A polymer-bonded aluminum-iron oxide thermite system is the focus of this work; however, the computational methods developed here may be extended to other reactive particle systems. Shock waves are propagated through the mixtures in finite element simulations, where Eulerian formulations are used to handle the highly-dynamic nature of particulate shock compression. Thermo-mechano-chemical responses are computed for a set of mixture classes (20% and 50% epoxy content by weight) subjected to a range of dynamic loading conditions (particle velocities ranging from 0.300??00 km/s). Two critical sub-problems are addressed: (i) the calculation of Hugoniot data for variable mixture compositions and (ii) the prediction of sites that experience microscale reaction initiation. Hugoniot calculations are in excellent agreement with experimental data. Microscale reaction initiation sites are predicted in certain load cases for each mixture class, although such predictions cannot currently be validated by experimental methods.
Complexity of the early genetic response to growth factors in mouse fibroblasts. (1988)

Genes whose expression is growth factor regulated are likely to be important components in the mechanisms controlling cell proliferation and differentiation. With the aim of identifying some of those genes, a lambda cDNA library was prepared with poly(A)+ RNA from quiescent NIH 3T3 cells stimulated with serum for 4 h in the presence of cycloheximide. Differential screening of approximately 200,000 recombinant phage plaques revealed 2,540 clones that cross hybridized preferentially with [32P]cDNA derived from RNA of stimulated cells rather than with cDNA derived from nonstimulated cells. Cross hybridization of these clones identified 82 independent sequences, including c-fos and c-myc. Seventy-one clones were further studied. Analysis of the changes in transcription and mRNA levels after serum stimulation demonstrated that the kinetics and extent of the induction vary dramatically between the different genes. Cycloheximide in all cases superinduced the mRNA levels by two mechanisms, inhibiting the shutoff of transcription and prolonging the half-lives of the mRNAs. Our results showed that induction of proliferation is accompanied by the onset of a complex genetic program.
A Simple Set Model of Requirements Representation (2002)

A successful information systems development (ISD) depends on a complete, correct, and consistent set of requirements specification. In this paper, we present a set model of requirements representation to present functional and non-functional requirements in a systematic and schematic manner. Because the nature of the set operation is mathematical and methodological, requirements representation becomes scholastic and structured. In this paper, we first describe an incremental and iterative process model of requirements analysis where a spiral of requirements acquisition, articulation, and analysis is defined. We then depict a set-oriented data and process model to abstract the analyzed require ments into a hierarchical structure. We further delineate the set model to represent the abstracted functional and non-functional requirements. The main advantage of the simple set model is that it provides a set of tractable requirements specification that allows devel opers to test if the specification is complete, correct, and consistent. A simple example is prepared as an illustration of this approach to show the meaning, values, and feasibility.
Clinical Trials of Primary and Secondary Prevention of Thrombosis and Restenosis (1995)

In the primary prevention of arterial disease, there may be a role for anti-oxidant vitamins and for oestrogen replacement therapy in postmenopausal women. For the secondary prevention of thrombotic complications of atherosclerosis, aspirin has proven efficacious in reducing both mortality and morbidity. Patients with ischaemic heart disease and moderately elevated serum cholesterol benefit from simvastatin administration. Heparin and oral anticoagulants are the mainstay in the primary and secondary prevention of venous thrombosis. More potent antithrombotic compounds, the direct thrombin inhibitors and the glycoprotein IIb-IIIa antagonists, are mainly being evaluated in emergency coronary medicine. Preliminary results are encouraging but haemorrhagic problems need to be solved. The trend toward a decrease in late restenosis following coronary angioplasty using a IIb-IIIa antagonizing Fab fragment may prove to be a major therapeutic breakthrough.
Continuous blood pressure prediction from pulse transit time using ECG and PPG signals (2016)

High blood pressure (BP) is the most common cause of death and disability in the world, and is the largest contributor to heart and kidney disease. Current methods of measuring and monitoring blood pressure require either invasive procedures or intermittent inflation of a cuff to restrict blood flow. Thus a non-invasive method for continuous blood pressure monitoring is needed. Pulse transit time (PTT), has been reported to be highly correlated with blood pressure but data examining the effect of posture and activity on PTT based BP estimation are very limited. In this paper, PTT was computed using the windowed correlation between ECG and PPG signals. Continuous blood pressure was estimated using a previously published linear regression model. In fourteen healthy subjects, BP was estimated using PTT in 5 different positions (recumbent, seated, standing, walking, cycling) for each subject according to a preset protocol. Accuracy was increased when sparsified, preprocessed PPG signals were used. Furthermore, the observed errors of PTT measurement were within 1% of manual PTT measurement. The Root-Mean-Squared Errors (RMSE) in systolic and diastolic blood pressure between the reference standard oscillometric cuff-based device and the estimated BP from PTT were lowest when seated or standing and highest when walking or cycling. The mean difference ±standard deviation (SD) of the difference between the PTT-based estimated systolic BP and the reference standard was 0.07±5.8 mmHg in the seated position; however, this increased to 4.4±20.9 and 10.2±16.0 when walking and cycling respectively. Therefore, PTT-based BP estimation was reasonably accurate while stationary but not during motion and further improvements in estimation are required before its use for the estimation of ambulatory BP.
Compile-Time Query Optimization for Big Data Analytics (2019)

Many emerging programming environments for large-scale data analysis, such as Map-Reduce, Spark, and Flink, provide Scala-based APIs that consist of powerful higher-order operations that ease the development of complex data analysis applications. However, despite the simplicity of these APIs, many programmers prefer to use declarative languages, such as Hive and Spark SQL, to code their distributed applications. Unfortunately, most current data analysis query languages are based on the relational model and cannot effectively capture the rich data types and computations required for complex data analysis applications. Furthermore, these query languages are not well-integrated with the host programming language, as they are based on an incompatible data model. To address these shortcomings, we introduce a new query language for data-intensive scalable computing that is deeply embedded in Scala, called DIQL, and a query optimization framework that optimizes and translates DIQL queries to byte code at compile-time. In contrast to other query languages, our query embedding eliminates impedance mismatch as any Scala code can be seamlessly mixed with SQL-like syntax, without having to add any special declaration. DIQL supports nested collections and hierarchical data and allows query nesting at any place in a query. With DIQL, programmers can express complex data analysis tasks, such as PageRank and matrix factorization, using SQL-like syntax exclusively. The DIQL query optimizer uses algebraic transformations to derive all possible joins in a query, including those hidden across deeply nested queries, thus unnesting nested queries of any form and any number of nesting levels. The optimizer also uses general transformations to push down predicates before joins and to prune unneeded data across operations. DIQL has been implemented on three Big Data platforms, Apache Spark, Apache Flink, and Twitter's Cascading/Scalding, and has been shown to have competitive performance relative to Spark DataFrames and Spark SQL for some complex queries. This paper extends our previous work on embedded data-intensive query languages by describing the complete details of the formal framework and the query translation and optimization processes, and by providing more experimental results that give further evidence of the performance of our system.
Molecular characterization of a puromycin‐insensitive leucyl‐specific aminopeptidase, PILS‐AP (2000)

The family M1 of Zn-dependent aminopeptidases comprises members of closely related enzymes which are known to be involved in a variety of physiologically important processes. On the basis of two highly conserved peptide motifs, we have identified a new member of this family by PCR amplification and cDNA-library screening. The longest ORF encodes a protein of 930 residues. It contains the HEXXH(X)18E Zn-binding motif and displays high homology to the other M1 family members except for its N-terminus for which a signal sequence of 20 residues can be predicted. This interpretation was supported by expressing fusion proteins formed with green fluorescent protein which localized to intracellular vesicles in COS-7 and BHK cells. Northern-blot analysis revealed ubiquitous expression of a major 3. 1-kb transcript. For enzymatic studies, the complete protein was expressed in Sf 9 insect cells. When aminoacyl beta-naphthylamides were used as substrates, efficient hydrolysis was only observed for Leu (and to a lesser extent Met). The activity was inhibited by chelators of bivalent cations and by other known aminopeptidase inhibitors, but surprisingly puromycin was without effect. This newly identified puromycin-insensitive leucyl-specific aminopeptidase is a signal-sequence-bearing member of family M1 and may be another example of the small subset of substrate-specific peptidases.
Zn2+ Inhibits Coronavirus and Arterivirus RNA Polymerase Activity In Vitro and Zinc Ionophores Block the Replication of These Viruses in Cell Culture (2020)

Increasing the intracellular Zn2+ concentration with zinc-ionophores like pyrithione (PT) can efficiently impair the replication of a variety of RNA viruses, including poliovirus and influenza virus. For some viruses this effect has been attributed to interference with viral polyprotein processing. In this study we demonstrate that the combination of Zn2+ and PT at low concentrations (2 µM Zn2+ and 2 µM PT) inhibits the replication of SARS-coronavirus (SARS-CoV) and equine arteritis virus (EAV) in cell culture. The RNA synthesis of these two distantly related nidoviruses is catalyzed by an RNA-dependent RNA polymerase (RdRp), which is the core enzyme of their multiprotein replication and transcription complex (RTC). Using an activity assay for RTCs isolated from cells infected with SARS-CoV or EAV—thus eliminating the need for PT to transport Zn2+ across the plasma membrane—we show that Zn2+ efficiently inhibits the RNA-synthesizing activity of the RTCs of both viruses. Enzymatic studies using recombinant RdRps (SARS-CoV nsp12 and EAV nsp9) purified from E. coli subsequently revealed that Zn2+ directly inhibited the in vitro activity of both nidovirus polymerases. More specifically, Zn2+ was found to block the initiation step of EAV RNA synthesis, whereas in the case of the SARS-CoV RdRp elongation was inhibited and template binding reduced. By chelating Zn2+ with MgEDTA, the inhibitory effect of the divalent cation could be reversed, which provides a novel experimental tool for in vitro studies of the molecular details of nidovirus replication and transcription.
Non-Chromate Conversion Coatings for Magnesium Die Castings (1997)

<div class="htmlview paragraph">Hexavalent chromium-containing baths have traditionally been used as pre-treatments on magnesium alloys. Environmentally friendly alternatives to these baths are being investigated. One alternative seems to be a phosphate-permanganate treatment consisting of a mixture of sodium dihydrogenphosphate and potassium permanganate. The phosphate-permanganate treatment has shown equivalent performance to a standard chrome pickle, both as stand-alone corrosion protection and as a base for subsequent coating. Phosphate-permanganate treatments must be combined with a deoxidizing process to be successful. Another alternative is a fluorozirconate treatment. The paint base properties of fluorozirconate are quite close to what is obtained using a chrome pickle.</div>
Determination of amide, urea, and nitrile compounds using alkali-fusion reaction gas chromatography (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination of amide, urea, and nitrile compounds using alkali-fusion reaction gas chromatographyStanley P. Frankoski and Sidney. SiggiaCite this: Anal. Chem. 1972, 44, 12, 2078–2080Publication Date (Print):October 1, 1972Publication History Published online1 May 2002Published inissue 1 October 1972https://pubs.acs.org/doi/10.1021/ac60320a024https://doi.org/10.1021/ac60320a024research-articleACS PublicationsRequest reuse permissionsArticle Views122Altmetric-Citations19LEARN 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
Heterogeneity of human neutrophil phagolysosomes: functional consequences for candidacidal activity (1984)

Opsonized yeast phase Candida albicans, incubated with human neutrophils, are internalized into two classes of phagosomes. One class, termed “unsealed vacuoles,” comprises approximately 40% of the total and maintains functional communication to the cell's exterior that is sufficient to permit ingress of dyes, such as trypan or methylene blue. The remaining cell-associated yeasts are contained in “sealed vacuoles,” completely sequestered from the external milieu. Approximately 71.8% of C albicans within sealed vacuoles are rendered nonviable within 60 minutes, whereas only 14.5% of organisms within unsealed vacuoles are killed during this time. We conclude that vacuolar sealing mechanisms are imperfectly developed in normal human neutrophils and that incompletely sealed vacuoles support antimicrobial processes substantially less well than do completely sealed ones.