gebhart/patrepeval huggingface dataset:
Neutralizing antibodies can initiate genome release from human enterovirus 71 (2014)

Antibodies were prepared by immunizing mice with empty, immature particles of human enterovirus 71 (EV71), a picornavirus that causes severe neurological disease in young children. The capsid structure of these empty particles is different from that of the mature virus and is similar to "A" particles encountered when picornaviruses recognize a potential host cell before genome release. The monoclonal antibody E18, generated by this immunization, induced a conformational change when incubated at temperatures between 4 °C and 37 °C with mature virus, transforming infectious virions into A particles. The resultant loss of genome that was observed by cryo-EM and a fluorescent SYBR Green dye assay inactivated the virus, establishing the mechanism by which the virus is inactivated and demonstrating that the E18 antibody has potential as an anti-EV71 therapy. The antibody-mediated virus neutralization by the induction of genome release has not been previously demonstrated. Furthermore, the present results indicate that antibodies with genome-release activity could also be produced for other picornaviruses by immunization with immature particles.
CYCLIC CHANGES IN THE CONCENTRATION OF PROSTAGLANDIN F<sub>2α</sub> IN HUMAN UTERINE FLUSHINGS (1978)

Prostaglandin F2alpha (PGF2alpha) was measured by radioimmunoassay in uterine flushings obtained from 41 women at various stages of the menstrual cycle. The concentration of PGF2alpha changed significantly during the cycle, with highest values in the mid secretory phase of the cycle (mean 9.1 ng/ml of uterine flushing, range 3.9 to 16.0 ng/ml, n = 9). The still unresolved role of intrauterine PGF2alpha is discussed in relation to luteolysis, myometrial contractility and implantation.
Joint Rate Control Algorithm for Low-Delay MPEG-4 Object-Based Video Encoding (2009)

This paper proposes an improved rate control algorithm for jointly encoding multiple arbitrarily shaped video objects in the context of low-delay MPEG-4 compliant video coding. The algorithm provides adequate mechanisms for dealing with deviations between the ideal and the actual behavior of video scene encoders, notably: 1) compensation mechanisms (e.g., rate control decisions) that are able to track these deviations and compensate them to allow a stable and efficient operation of the encoder, and 2) adaptation mechanisms (e.g., estimation of model parameters) that are able to instantaneously represent the actual behavior of the encoder and its rate controller. The proposed solution efficiently allocates the available resources, i.e., target bit rate and bitstream buffer space, aiming at maximizing the average scene quality and minimizing quality fluctuations along time and among the various video objects. The results show that this solution outperforms the usual reference solutions, notably those specified in the rate control informative annex of the MPEG-4 visual standard.
Efficient Execution Replay for ATHAPASCAN-0 Parallel Programs (1999)

ATHAPASCAN-0 programs are executed by a network of communicating threads evolving dynamically. Within the same node, threads communicate through shared memory and synchronization primitives. Between two different nodes, threads communicate by message passing. Execution replay of ATHAPASCAN-0 programs addresses the non-determinism arising from synchronization races, from promiscuous messages received from non specified source and from the varying number of operations testing the completion of non blocking ATHAPASCAN-0 primitives. The execution replay mechanism is mainly control-base- d since, in addition to recording the results of test operations, only the order of accesses to synchronization functions and the order of arrival of promiscuous messages need to be recorded. The efficiency of the recording comes from the use of Lamport clocks to reduce drastically the number of records associated to synchronization operations and from the reduction to a single record of the information necessary to reproduce a series of unsuccessful tests.
The interaction of shockwaves with a vapour bubble in boiling histotripsy: The shock scattering effect (2020)

Boiling histotripsy is a High Intensity Focused Ultrasound (HIFU) technique which uses a number of short pulses with high acoustic pressures at the HIFU focus to induce mechanical tissue fractionation. In boiling histotripsy, two different types of acoustic cavitation contribute towards mechanical tissue destruction: a boiling vapour bubble and cavitation clouds. An understanding of the mechanisms underpinning these phenomena and their dynamics is therefore paramount to predicting and controlling the overall size of a lesion produced for a given boiling histotripsy exposure condition. A number of studies have shown the effects of shockwave heating in generating a boiling bubble at the HIFU focus and have studied its dynamics under boiling histotripsy insonation. However, not much is known about the subsequent production of cavitation clouds that form between the HIFU transducer and the boiling bubble. The main objective of the present study is to examine what causes this bubble cluster formation after the generation of a boiling vapour bubble. A numerical simulation of 2D nonlinear wave propagation with the presence of a bubble at the focus of a HIFU field was performed using the k-Wave MATLAB toolbox for time domain ultrasound simulations, which numerically solves the generalised Westervelt equation. The numerical results clearly demonstrate the appearance of the constructive interference of a backscattered shockwave by a bubble with incoming incident shockwaves. This interaction (i.e., the reflected and inverted peak positive phase from the bubble with the incoming incident rarefactional phase) can eventually induce a greater peak negative pressure field compared to that without the bubble at the HIFU focus. In addition, the backscattered peak negative pressure magnitude gradually increased from 17.4 MPa to 31.6 MPa when increasing the bubble size from 0.2 mm to 1.5 mm. The latter value is above the intrinsic cavitation threshold of -28 MPa in soft tissue. Our results suggest that the formation of a cavitation cloud in boiling histotripsy is a threshold effect which primarily depends (a) the size and location of a boiling bubble, and (b) the sum of the incident field and that scattered by a bubble.
Fractionation of asparagine-linked oligosaccharides by serial lectin-Agarose affinity chromatography. A rapid, sensitive, and specific technique. (1982)

We present a general technique for fractionating cell-derived asparagine-linked oligosaccharides on the basis of oligosaccharide structure. This procedure has been applied to the study of [2-3H]mannose-labeled mouse lymphoma cells (BW5147). The fractionation scheme involves serial chromatography on concanavalin A-Sepharose, pea lectin-Sepharose, and leukoagglutinating phytohemagglutinin-agarose. Approximately 85% of the labeled glycopeptides was retained on one or more of the affinity columns. The various fractions eluted from the columns contain relatively pure populations of glycopeptides which were used for structural analysis. The recovery of the glycopeptides was quantitative. The procedure was used to estimate the overall spectrum of Asn-linked oligosaccharides synthesized by the lymphoma cell line. We conclude that serial lectin-agarose affinity chromatography is a rapid, sensitive, and specific technique for fractionating and analyzing Asn-linked oligosaccharides. A general fractionation scheme employing additional lectins is presented.
ELECTROTRICHOGENESIS: FURTHER EVIDENCE OF EFFICACY AND SAFETY ON EXTENDED USE (1992)

These data represent a subset of data from the original 36-week study conducted by Maddin et al., which was in itself a preliminary study of a pulsed electrical stimulation device in male subjects alone. The extension phase of this study, which is summarized here, was undertaken to gather data on longer-term efficacy and safety and to study clinical effects in control subjects who were then switched to active treatment. Thirteen subjects had active treatment for 70 weeks, and 14 subjects were included in the crossover group, which had sham treatment for 36 weeks followed by active treatment for 30 additional weeks. On average, terminal hair counts increased from 82 to 276 in the active treatment group. Among those in the crossover group, a mild increase, from 124 to 160, was observed during the sham treatment period and a more notable increase, from 160 to 249, occurred during the subsequent active treatment period. The results presented here provide evidence of the efficacy and safety of this device during extended use; however, the generalizability of these findings is limited by the small subset of subjects for whom complete data are available.
RecA protein of Escherichia coli has a third essential role in SOS mutator activity (1990)

The DNA damage-inducible SOS response of Escherichia coli includes an error-prone translesion DNA replication activity responsible for SOS mutagenesis. In certain recA mutant strains, in which the SOS response is expressed constitutively, SOS mutagenesis is manifested as a mutator activity. Like UV mutagenesis, SOS mutator activity requires the products of the umuDC operon and depends on RecA protein for at least two essential activities: facilitating cleavage of LexA repressor to derepress SOS genes and processing UmuD protein to produce a fragment (UmuD') that is active in mutagenesis. To determine whether RecA has an additional role in SOS mutator activity, spontaneous mutability (tryptophan dependence to independence) was measured in a family of nine lexA-defective strains, each having a different recA allele, transformed or not with a plasmid that overproduces either UmuD' alone or both UmuD' and UmuC. The magnitude of SOS mutator activity in these strains, which require neither of the two known roles of RecA protein, was strongly dependent on the particular recA allele that was present. We conclude that UmuD'C does not determine the mutation rate independently of RecA and that RecA has a third essential role in SOS mutator activity.
Design and implementation of a pilot orientation program for new NASA engineering employees (1993)

This paper describes the design and field testing of an orientation program for new employees of NASA Lewis Research Center's Engineering Directorate. A group of new employees designed the program using a series of TQM analysis techniques. The program objectives were: provide consistent treatment for new employees; assist management and clerical staff with their responsibility for orientation; introduce the employee to as many facets of the organization as possible; allow the employee to feel like a member of the organization as early as possible; maximize the use of existing services; and use up-to-date information. The major aspects of the program included: training of management and clerical staff; lab tours and briefings describing the organization; shepherding, using senior employees as shepherds; a handbook of information about the center and the directorate; a package of information about northeast Ohio; and social activities involving the new employees and shepherds. The program was tested on a pilot group of six new employees over a four month period and was considered to be highly successful by both the employees and management. Aspects of the program have subsequently been adopted for center-wide use.
The SKS1 protein kinase is a multicopy suppressor of the snf3 mutation of Saccharomyces cerevisiae (1996)

Saccharomyces cerevisiae strains carrying snf3 are defective in high affinity glucose transport, and thus are unable to grow fermentatively on media with low concentrations of glucose. A multicopy suppressor of the snf3 growth defect, SKS1 (suppressor kinase of snf3), was found to encode a putative ser/thr protein kinase homologous to Ran1p, a kinase that regulates the switch between meiosis and vegetative growth in Schizosaccharomyces pombe. Overexpression of the SKS1 open reading frame is sufficient for suppression of the growth defects of snf3 mutants. Disruption of the open reading frame eliminates this suppression; as does the mutation of the consensus ATP binding site of Sks1p. A DDSE (DNA dependent snf3 suppressor element) was found to be present in the SKS1 promoter region. The suppression by this DDSE occurs in the absence of SKS1 coding region, that is, the DDSE can suppress a snf3 sks1 double null mutant which fails to grow fermentatively on low glucose as a snf3 mutant does. Both SKS1 and its DDSE can additionally suppress the growth defects of grr1 mutants, which are also impaired in high affinity glucose transport. The snf3 genomic suppressors, rgt1, RGT2 and ssn6, are also capable of suppressing snf3 associated growth defects in a strain lacking sks1.
Secure deduplication of general computations (2015)

The world's fast-growing data has become highly concentrated on enterprise or cloud storage servers. Data deduplication reduces redundancy in this data, saving storage and simplifying management. While existing systems can deduplicate computations on this data by memoizing and reusing computation results, they are insecure, not general, or slow.

This paper presents UNIC, a system that securely deduplicates general computations. It exports a cache service that allows applications running on behalf of mutually distrusting users on local or remote hosts to memoize and reuse computation results. Key in UNIC are three new ideas. First, through a novel use of code attestation, UNIC achieves both integrity and secrecy. Second, it provides a simple yet expressive API that enables applications to deduplicate their own rich computations. This design is much more general and flexible than existing systems that can deduplicate only specific types of computations. Third, UNIC explores a cross-layer design that allows the underlying storage system to expose data deduplication information to the applications for better performance.

Evaluation of UNIC on four popular open-source applications shows that UNIC is easy to use, fast, and with little storage overhead.
Current starved delay element with symmetric load (2006)

Variable delay elements are often used in different types of high-speed integrated circuits, mainly intended for delay compensation, skew equalization, etc. These circuits are normally realized as hybrid, composed of digital and analog controlled parts. The digital part is used for coarse-grain, while the analog for fine-grain delay variation. Efficient analog delay element architecture is proposed in this paper. The proposal is based on modification of the standard current starved delay element solution. An analytical equation that corresponds to the delay of the circuit is given also. In terms of control voltage, the proposed circuit has a linear delay transfer function in the whole range of regulation. Improvement is achieved at a cost of small hardware overhead in respect to the standard solution. Delay linearity error is less than 1% and the agreement between analytical model and simulation results is good, i.e. the error is less than 5%.
One-step process takes H/sub 2/S from gas stream (1986)

A novel, one-step process selectively removes hydrogen sulfide from sourgases and converts dissolved hydrogen sulfide directly to sulfur in a bubble tower filled with a sweetener solution. The sweetener is a proprietary formulation consisting of an alkaline solution of oxidizing and buffering agents. Oxidation of hydrogen sulfide to sulfur is achieved by a liquid-phase oxidation technique. Various sour gas sweetening processes have been used for a number of years. Incentives for use of the one-step process include: 1. Improved economics for hydrogen sulfide removal based on cost-performance evaluations. 2. Simplicity of operation. 3. Low capital cost requirements for the gas processing plant. 4. Adaptability to existing process equipment. 5. Low toxicity and nonhazardous waste characteristics of the spent slurry generated by the hydrogen sulfide reaction. This article presents the current understanding of hydrogen sulfide oxidation chemistry in nitrite solutions, as well as research and field data related to the one-step process. The field data provide quantifiable proof that the one-step process is a viable economical alternative for hydrogen sulfide removal in properly designed and operated equipment.
HIGH-PURITY GLASSES BASED ON ARSENIC CHALCOGENIDES (2001)

Low impurity content is the essential requirement to many applications of vitreous arsenic chalcogenides as a material for optoelectronics. Investigations carried out in last ten years in-creased the knowledge volume about the nature and origin of impurities in chalcogenide glasses, their effect on glass properties, especially on the transmittance in middle IR region and on radiation strength. These properties are most sensitive to impurity presence. The mini-mum calculated content of impurities, leading to observation of impurity contribution to the property value, is 0.1- 100 ppb at. for different impurity groups. The effective methods of preparations and analysis of high- purity glasses are developed. The best glass samples con-tain the impurities of widespread metals and silicon on the level of 0.1 ppm wt., optically ac-tive hydrogen- 0.2-0.05 ppm at., oxygen and carbon- 0.5- 1 ppm wt., submicron size het-erogeneous inclusions- 104- 5*106 cm-3. Impurity content in the glasses of ordinary quality is 10- 100 times higher. The presence of impurities should be taken into account while investi-gating both well-known and developed properties and applications of glasses.
Current limiting switching by squeezing arcs into narrow insulating slots (1992)

For low-voltage circuit breakers, arc breaking by squeezing the arc in a narrow insulating slot is an alternative to the conventional technique of using arc chutes with steel plates. The performance of a switching device based on this principle was experimentally investigated. The influence of slot dimensions, switching speed, insulating material, and other test parameters on the arc breaking characteristics was determined. By using a simplified arc model, the curves of arc voltage and arc current can be simulated. There is a good agreement between the experimental and the calculated results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Security in Cloud Computing : A Security Assessment of Cloud Computing Providers for an Online Receipt Storage (2010)

Considerations with regards to security issues and demands must be addressed before migrating an application into a cloud computing environment. Different vendors, Microsoft Azure, Amazon Web Services and Google AppEngine, provide different capabilities and solutions to the individual areas of concern presented by each application. Through a case study of an online receipt storage application from the company dSafe, a basis is formed for the evaluation. The three cloud computing vendors are assessed with regards to a security assessment framework provided by the Cloud Security Alliance and the application of this on the case study. Finally, the study is concluded with a set of general recommendations and the recommendation of a cloud vendor. This is based on a number of security aspects related to the case study's existence in the cloud. With dSafe's high demands of data locality, integrity and security, Google AppEngine is discarded as an option due to the lack of focus on business related applications, whilst Microsoft Azure is the recommended cloud vendor - closely followed by Amazon Web Services - due to its suitable technical solutions with regards to existing implementation, risk mitigation capabilities and audit results.
The Effects of Genetic Polymorphisms of <i>IL‐1</i> and <i>TNF‐A</i> on <i>Helicobacter pylori</i>–Induced Gastroduodenal Diseases in Korea (2006)

The IL-1Beta-511 T-carrier polymorphism has a negative effect on the development of H. pylori-positive BGU, and high frequency of IL-1RN 2/2 was found in the H. pylori-positive relatives of GC patients, which suggest that this genetic polymorphism could play some role in the H. pylori-induced gastroduodenal diseases in Korea.
Selective Removal of N‐Heterocyclic Aromatic Contaminants from Fuels by Lewis Acidic Metal–Organic Frameworks (2011)

Bring in the cleaner! Metal–organic frameworks (MOFs) are able to separate nitrogen and sulfur contaminants from fuel, which may lead to the production of cleaner fuels (see picture; ppmw=parts per million by weight). The separation ability is shown to originate from the Lewis acidity of the metal sites in the MOFs. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Photodynamic therapy: Combined modality approaches targeting the tumor microenvironment (2006)

Improvements in PDT tumor responsiveness may be achieved by employing combined modality regimens targeting malignant cells as well as treatment-induced angiogenesis and/or inflammation.
Rapid Drug Susceptibility Testing of Drug-Resistant Mycobacterium tuberculosis Isolates Directly from Clinical Samples by Use of Amplicon Sequencing: a Proof-of-Concept Study (2016)

Increasingly complex drug-resistant tuberculosis (DR-TB) is a major global health concern and one of the primary reasons why TB is now the leading infectious cause of death worldwide. Rapid characterization of a DR-TB patient's complete drug resistance profile would facilitate individualized treatment in place of empirical treatment, improve treatment outcomes, prevent amplification of resistance, and reduce the transmission of DR-TB. The use of targeted next-generation sequencing (NGS) to obtain drug resistance profiles directly from patient sputum samples has the potential to enable comprehensive evidence-based treatment plans to be implemented quickly, rather than in weeks to months, which is currently needed for phenotypic drug susceptibility testing (DST) results. In this pilot study, we evaluated the performance of amplicon sequencing of Mycobacterium tuberculosis DNA from patient sputum samples using a tabletop NGS technology and automated data analysis to provide a rapid DST solution (the Next Gen-RDST assay). One hundred sixty-six out of 176 (94.3%) sputum samples from the Republic of Moldova yielded complete Next Gen-RDST assay profiles for 7 drugs of interest. We found a high level of concordance of our Next Gen-RDST assay results with phenotypic DST (97.0%) and pyrosequencing (97.8%) results from the same clinical samples. Our Next Gen-RDST assay was also able to estimate the proportion of resistant-to-wild-type alleles down to mixtures of ≤1%, which demonstrates the ability to detect very low levels of resistant variants not detected by pyrosequencing and possibly below the threshold for phenotypic growth methods. The assay as described here could be used as a clinical or surveillance tool.