gebhart/patrepeval huggingface dataset:
Distinguishing between Zika and Spondweni viruses (2016)

The Spondweni serogroup includes Zika and Spondweni viruses. Both viruses have been historically misidentified and their diseases have been misdiagnosed due to their serological cross-reactivity and similar clinical presentations. Early case reports indicate a subset of patients present with clinical manifestations suggestive of serious illness. Flaviviruses have a high serological cross-reactivity. Before the advent of genetic sequencing, serological assays such as virus neutralization and hemaglutination-inhibition were used to differentiate virus species. Much of the early work differentiating flaviviruses into various serogroups was later confirmed by sequencing and phylogenetic analyses. Historically, serological assays (neutralization and complement fixation tests) were also used to determine evidence of prior infection and geographic distribution. Both viruses in the Spondweni serogroup exhibit serological cross-reactivity and cause non-specific febrile illness in humans, making diagnosis challenging in regions where both viruses circulate. Zika virus was first isolated in Uganda in 1947 (strain MR-766) (1) and Spondweni virus (strain Chuku) was first isolated in Nigeria in 1952. (2) Cross-reactivity in neutralization tests led to the misidentification of the Spondweni virus Chuku strain as a strain of Zika virus. (2-5) This misidentification led to additional studies where this strain of Spondweni virus was reported as Zika virus, a confusion that continues to the present day, although the misidentification of this isolate was clarified and widely reported in 1964. (3-5) Consequently, early clinical case reports from Nigeria, (2) studies involving the experimental infection of a human volunteer, (6) vector competence studies in Aedes aegypti mosquitoes (6) and experimental infections in non-human primates, (7) all involved Spondweni virus (strain Chuku) rather than Zika virus. This cross-reactivity means that the results of early serosurveys--in which only one serological assay was used to screen. blood samples from people or animals living in regions where both viruses circulate--are difficult to interpret. (2,8) Both Zika and Spondweni viruses are primarily transmitted to humans through the bite of an infective mosquito, and the majority of infections are asymptomatic. In symptomatic Zika and Spondweni virus cases, signs and symptoms appear as early as three days post-infection. (6,9) The typical clinical presentation of a Zika virus infection is now well established. The most commonly reported signs and symptoms from 195 patients between 1964 and 2016 are rash (67.2%), fever (63.6%), arthralgia (28.7%), myalgia (23.6%), headache (21.5%), conjunctivitis (20.5%), retroorbital pain (11.3%), oedema (9.7%), pruritus (7.7%) and fatigue (7.2%). (9) Less is known regarding the clinical presentation of Spondweni virus infections. The six well documented cases of Spondweni virus infections report signs and symptoms of fever (100%), headache (83.3%), nausea (83.3%), myalgia (66. …
PROTECTING EXTERNALLY SUPPLIED SOFTWARE IN SMALL COMPUTERS (1981)

The increasing decentralization of computing resources and the proliferation of personal and small business computers create new problems in computer security. One such problem is the protection of externally supplied software, i.e., software supplied by other than the users/owners of these small computers. In the case of personal and small business computers, proprietary software serves as the primary example. In distributed systems comprised of autonomously managed nodes, members of the user community may act as vendors of external software in a less formal context. In these contexts dual security requirements arise: vendors require encapsulation of their software to prevent release and to detect modification of information, whereas users require confinement of external software in order to control its access to computer resources. The protection mechanisms developed to support mutually suspicious subsystems in centralized systems are not directly applicable here because of differences in the computing environment, e.g., the need to protect external subsystems from physical attacks mounted by owners of these small computers. This thesis employs two tools to achieve the security requirements of vendors of external software: tamper-resistance models (TRMs) and cryptographic techniques. External software can be confined in two ways: through the use of a secure operating system in conjunction with a TRM supplied by a third-party or by providing separate processors for vendors and users and employing some simple hardware to implement access control for the user.
Experimental Approbation of Selective Laser Melting of Powders by the Use of Non-Gaussian Power Density Distributions (2014)

Experimental results on laser beam modulation at selective laser melting (SLM) are presented. The modulation is a possible way to improve the efficiency of the SLM process. The optical diagnostics shows the energy loss up to 30%. This could be a consequence of high thermal gradients in the melt pool resulted by the Gaussian power density distribution. The Gaussian distribution can be changed to the flat-top one or to the inverse-Gaussian (donut) one. An experimental stand with a 200W laser source was developed. Twenty single tracks for each of the three modes were obtained for a Co-Cr alloy. The samples were studied by scanning electronic microscopy (SEM) on irregularity. Optical diagnostics by high velocity camera (HVC) shows that the use of the non-Gaussian laser beam distributions can significantly reduce the width of the free-of-powder consolidation zone, which is considered as the main reason for irregularity of single tracks. A better metallurgical bonding of the single tracks with the substrate was obtained by the use of the flat-top laser beam. Both of these facts show a significant influence of the laser beam energy distribution on the energy loss at SLM, especially for high power laser sources. The observed escape of granules shows a possible influence of the dynamic factor. The use of the non-Gaussian distributions can enhance 3D parts, for example, improve the geometrical tolerance and decrease the residual porosity.
IMPORT AND ROUTING OF NUCLEUS-ENCODED CHLOROPLAST PROTEINS (1996)

Most chloroplast proteins are nuclear encoded, synthesized as larger precursor proteins in the cytosol, posttranslationally imported into the organelle, and routed to one of six different compartments. Import across the outer and inner envelope membranes into the stroma is the major means for entry of proteins destined for the stroma, the thylakoid membrane, and the thylakoid lumen. Recent investigations have identified several unique protein components of the envelope translocation machinery. These include two GTP-binding proteins that appear to participate in the early events of import and probably regulate precursor recognition and advancement into the translocon. Localization of imported precursor proteins to the thylakoid membrane and thylakoid lumen is accomplished by four distinct mechanisms; two are homologous to bacterial and endoplasmic reticulum protein transport systems, one appears unique, and the last may be a spontaneous mechanism. Thus chloroplast protein targeting is a unique and surprisingly complex process. The presence of GTP-binding proteins in the envelope translocation machinery indicates a different precursor recognition process than is present in mitochondria. Mechanisms for thylakoid protein localization are in part derived from the prokaryotic endosymbiont, but are more unusual and diverse than expected.
Essential and nonessential amino acid composition of pigs from birth to 145 kilograms of body weight, and comparison to other studies. (1998)

The amino acid composition of the body components (carcass, hair, whole blood, and a composite of the other body tissues) were determined from a total of 81 crossbred pigs at 10 weight intervals from birth to 145 kg body weight. Body component amino acid compositions (g/100 g protein) were multiplied by their respective protein contents, resulting in calculated whole-body amino acid compositions. From 8.5 to 145 kg body weight, the amino acid compositions were similar within each body component but differed between body components. There was a higher concentration of carcass lysine, arginine, and histidine (P < .01) in the carcass, and isoleucine (P < .12), threonine (P < .15), and methionine (P < .08) tended to be higher than in the composite of the other body tissue. Whole blood was, however, higher in leucine, valine, and lysine, and hair was higher in cystine than the carcass. The relative concentration of lysine in the whole body increased to about 37 kg body weight and reached a plateau, whereas the other essential amino acids increased to 8.5 kg and then reached a plateau. Tryptophan, however, decreased from birth to 8.5 kg and then remained at a similar concentration to 145 kg body weight. Whole-body amino acid composition of pigs in our study was generally similar to that noted in other scientific reports, but there was a wide variation in amino acid values between studies.
Camptothecin and taxol: discovery to clinic--thirteenth Bruce F. Cain Memorial Award Lecture. (1995)

Camptothecin and taxol are secondary metabolites found, respectively, in the wood bark of Camptotheca acuminata, a native of China, and Taxus brevifolia, found in the northwest Pacific coastal region of the United States. The compounds were isolated guided by bioassay on various extracts and chromatographic fractions. Their unique and hitherto unknown structures were elucidated by nuclear magnetic resonance, mass spectrometry, and X-ray analysis. Both compounds have unique mechanisms of antitumor activity; camptothecin uniquely inhibits an enzyme, topoisomerase I, involved in DNA replication. Taxol binds to a protein, tubulin, thus inhibiting cell division. Taxol has been called the best new anticancer agent developed from natural products, showing particular efficacy against ovarian cancer. Camptothecin and analogues singly or combined with cisplatin show efficacy against solid tumors, breast, lung, and colorectal, which hitherto have been unaffected by most cancer chemotherapeutic agents.
Scalable in-situ qubit calibration during repetitive error detection (2016)

We present a method to optimize qubit control parameters during error detection which is compatible with large-scale qubit arrays. We demonstrate our method to optimize single or two-qubit gates in parallel on a nine-qubit system. Additionally, we show how parameter drift can be compensated for during computation by inserting a frequency drift and using our method to remove it. We remove both drift on a single qubit and independent drifts on all qubits simultaneously. We believe this method will be useful in keeping error rates low on all physical qubits throughout the course of a computation. Our method is O(1) scalable to systems of arbitrary size, providing a path towards controlling the large numbers of qubits needed for a fault-tolerant quantum computer
A contingent replication assay for the detection of protein-protein interactions in animal cells. (1991)

We have developed a sensitive and rapid assay system termed the contingent replication assay (CRA) for selecting cDNAs with desired functional properties from a cDNA library. The system functions in animal cells and permits enrichment of the desired cDNA in small-scale and convenient experiments. The assay can be used for the enrichment of proteins that activate transcription from conditional enhancers, bind to specific DNA sequences, or interact with target proteins of interest. In this communication we report the application of this assay to study protein-protein interactions in animal cells.
Isolation and renaturation of bio-active proteins expressed in Escherichia coli as inclusion bodies. (1992)

Over-expression of recombinant proteins in Escherichia coli often results in the formation of insoluble and inactive material as inclusion bodies. Within the last years specific methods and strategies have been developed to produce bio-active proteins from these inclusion bodies. These methods include (i) isolation and purification of inclusion bodies, (ii) solubilization and reduction of the insoluble material, and (iii) renaturation of the proteins including formation of native disulphide bonds. Inclusion bodies are isolated from E. coli cells after desintegration of cells by mechanic forces. Due to their stability, inclusion bodies may be purified by washing with detergent solutions or low concentrations of denaturant. High concentrations of urea and guanidine hydrochloride are used in combination with reducing reagents such as 2-mercaptoethanol or dithiothreitol to reduce and solubilize proteins from inclusion bodies. After purification of solubilized materials, proteins are renatured and native disulphide bonds are formed by either air oxidation or glutathione reoxidation starting from reduced material, or by disulphide interchange starting from mixed disulphides containing peptides. Final yield of renatured proteins is raised by low concentrations of proteins and by adding low concentrations of denaturant during renaturation.
New C‐5 Substituted Pyrrolotriazine Dual Inhibitors of EGFR and HER2 Protein Tyrosine Kinases. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Person location and person tracking ‐ Technologies, risks and policy implications (2001)

Many long‐standing technologies embody the ability to locate and track people. During the last couple of decades of the twentieth century, new technologies have been developed which greatly increase those capabilities. The nature of these technologies is described, and the processes identified whereby they are being applied to the serious detriment of civil freedoms. Implications are drawn for technology‐using organisations, for technology providers, for standards developers, for policy makers, and for privacy and data protection commissioners.
Biotination of proteins in vivo. A post-translational modification to label, purify, and study proteins. (1990)

Post-translational modification of proteins with biotin provides the means to specifically label proteins in vivo and to purify proteins from crude cell lysates. The carboxyl-terminal protein segments modified by reaction with biotin ligase are strongly conserved in nature. We have demonstrated that the proteins encoded by translational gene fusions of a number of heterologous proteins to these carboxyl-terminal sequences become biotinated in vivo. The minimum size of the protein segment needed to allow biotination of fusion proteins is 75 amino acids. This biotination sequence, although of bacterial origin, functions in Saccharomyces cerevisiae as well as in Escherichia coli. Fusion proteins are readily labeled with [3H]biotin in vivo and the labeling is highly specific due to the scarcity (less than 5) of biotinated protein species. Biotinated fusion proteins can be readily purified in native form by binding to columns of monomeric avidin followed by elution with buffers containing biotin. Alternatively, proteins can be purified in a denatured form in presence of 1% sodium dodecyl sulfate or 8 M urea. Thus, this technology allows purification by affinity chromatography of any protein to which a biotination sequence can be attached. The ability to specifically label a protein in vivo should have utility in studies such as intracellular protein trafficking and cytoskeletonal dynamics.
Assessment of the human faecal microbiota: I. Measurement and reproducibility of selected enzymatic activities (2012)

Optimal measurement of these core activities of the microbiota required a sufficient quantity of rapidly chilled or frozen specimens collected in phosphate buffered saline at pH7·0. Application of these methods to clinical and epidemiologic research could provide insights on how the intestinal microbiota affects human health.
Increased Protection against Pneumococcal Disease by Mucosal Administration of Conjugate Vaccine plus Interleukin-12 (2003)

Streptococcus pneumoniae is a common cause of respiratory tract infections, its main entry route being the nasal mucosa. The recent development of pneumococcal polysaccharide conjugate vaccines has led to a dramatic improvement in protection against invasive disease in infants and children, but these vaccines have been found to be only 50 to 60% protective against bacterial carriage. In this study, we investigated the efficacy of intranasal (i.n.) conjugate vaccine delivery using interleukin-12 (IL-12) as a mucosal adjuvant. Immunized mice treated with IL-12 demonstrated increased expression of lung and splenic gamma interferon and IL-10 mRNAs; high levels of antibody, particularly serum immunoglobulin G2a (IgG2a) and respiratory IgA; and significantly increased opsonic activity. After intraperitoneal challenge with type 3 pneumococci, there was 75% survival of i.n. vaccinated mice compared to 0% survival of unvaccinated mice. In addition, after i.n. challenge with type 14 pneumococci, vaccinated mice possessed fewer bacterial colonies in the upper respiratory tract than unvaccinated mice. However, no significant difference in type 14 carriage was observed between vaccinated and unvaccinated groups following intramuscular vaccination, the typical route of vaccination in humans. Using mice with a genetic disruption in IgA expression, it was found that pneumococcus-specific IgA played a significant role in the clearance of bacteria from the upper respiratory tract. We conclude that i.n vaccination in the presence of IL-12 is able to enhance systemic and mucosal immune responses to pneumococci and efficiently protect against both invasive infection and bacterial carriage.
Prevalence of Frequent Headache in a Population Sample (1998)

Frequent headache is common in the general population and is more prevalent in Caucasians and in those with less than a high school education. Chronic tension-type headache is more common than frequent headache with migrainous features, though the latter is more disabling. Although more common in females than males, the female preponderance of frequent headache is less marked than in migraine. The sex ratio varies by frequent headache subtype.
Synthesis of 6′-Aminohexyl 2-Acetamido-2-deoxy-D-galactoside Isomers and a Unique Isomerization Catalyzed by Ion Exchange Resin (1986)

Abstract The 6-aminohexyl α- and β-pyranosides and β-furanoside of 2-acetamido-2-deoxy-D-galactose (N-acetyl-D-galactosamine) were prepared. N-Acetyl-D-galactosamine was reacted with acetyl chloride in the cold. The per-O-acetyl 1-chloro derivative was then reacted with 6-(N-trifluoroacetyl) aminohexanol in the presence of mercuric cyanide. Glycoside products were isolated by gel chroraatography, de-O-acetylated, and de-N-trifluoroacety-lated. The β-pyranoside, which is the major product, was obtained in 29% overall yield, as well as the β-furanoside. The α-pyranoside was prepared in 70% overall yield by reacting 2-acetamido-1, 3, 4, 6-tetra-O-acetyl-2-deoxy-α-D-galacto-pyranose, which is a byproduct of the above synthetic scheme (22%), with 6-(N-trifluoroacetyl)aminohexanol in the presence of boron trifluoride etherate. A strong cation exchange resin (Dowex 50X8, H+ form) catalyzed interconversion of the β-furanoside and the β-pyranoside, with the latter predominating at equilibrium. The α-pyranoside was not produced in any appreciable amount in the Dowex-catalyzed isomerization. Although the allyl β-pyranoside and β-furanoside of N-acetyl-D-galactosamine also isomerized under similar conditions, the competing hydrolysis of the glycosidic bond occurred to a greater extent. A possible mechanizm for the isomerization is discussed.
Probe set algorithms: is there a rational best bet? (2006)

Affymetrix microarrays have become a standard experimental platform for studies of mRNA expression profiling. Their success is due, in part, to the multiple oligonucleotide features (probes) against each transcript (probe set). This multiple testing allows for more robust background assessments and gene expression measures, and has permitted the development of many computational methods to translate image data into a single normalized "signal" for mRNA transcript abundance. There are now many probe set algorithms that have been developed, with a gradual movement away from chip-by-chip methods (MAS5), to project-based model-fitting methods (dCHIP, RMA, others). Data interpretation is often profoundly changed by choice of algorithm, with disoriented biologists questioning what the "accurate" interpretation of their experiment is. Here, we summarize the debate concerning probe set algorithms. We provide examples of how changes in mismatch weight, normalizations, and construction of expression ratios each dramatically change data interpretation. All interpretations can be considered as computationally appropriate, but with varying biological credibility. We also illustrate the performance of two new hybrid algorithms (PLIER, GC-RMA) relative to more traditional algorithms (dCHIP, MAS5, Probe Profiler PCA, RMA) using an interactive power analysis tool. PLIER appears superior to other algorithms in avoiding false positives with poorly performing probe sets. Based on our interpretation of the literature, and examples presented here, we suggest that the variability in performance of probe set algorithms is more dependent upon assumptions regarding "background", than on calculations of "signal". We argue that "background" is an enormously complex variable that can only be vaguely quantified, and thus the "best" probe set algorithm will vary from project to project.
Penetration of timolol eye drops into human aqueous humour: the first hour. (1985)

Samples of aqueous humour were removed from 26 eyes at the start of cataract extraction. Two drops of timolol 0.5% had been instilled into the conjunctival sac 12-71 minutes before operation. Analysis by gas chromatography showed a mean timolol concentration of 55.46 ng/mg, with a range of 8 to 100 ng/mg.
Lagrangian-Eulerian advection of noise and dye textures for unsteady flow visualization (2002)

A new hybrid scheme, called Lagrangian-Eulerian advection (LEA), that combines the advantages of the Eulerian and Lagrangian frameworks is applied to the visualization of dense representations of time-dependent vector fields. The algorithm encodes the particles into a texture that is then advected. By treating every particle equally, we can handle texture advection and dye advection within a single framework. High temporal and spatial correlation is achieved through the blending of successive frames. A combination of particle and dye advection enables the simultaneous visualization of streamlines, particle paths and streak-lines. We demonstrate various experimental techniques on several physical flow fields. The simplicity of both the resulting data structures and the implementation suggest that LEA could become a useful component of any scientific visualization toolkit concerned with the display of unsteady flows.