gebhart/patrepeval huggingface dataset:
A Potent Malaria Transmission Blocking Vaccine Based on Codon Harmonized Full Length Pfs48/45 Expressed in Escherichia coli (2009)

Malaria caused by Plasmodium falciparum is responsible for nearly 1 million deaths annually. Although much progress has been made in the recent past, the development of a safe, effective and affordable malaria vaccine has remained a challenge. A vaccine targeting sexual stages of the parasite will not only reduce malaria transmission by female Anopheles mosquitoes, but also reduce the spread of parasites able to evade immunity elicited by vaccines targeting pre-erythrocytic and erythrocytic asexual stages. We focused our studies on Pfs48/45, a protein expressed in the sexual stages developing within an infected person and one of the most promising transmission-blocking vaccine targets. Functional immunogenicity of Pfs48/45 protein requires proper disulfide bond formation, consequently evaluation of the immunogenicity of recombinant full-length Pfs48/45 has been hampered by difficulties in expressing properly folded protein to date. Here we present a strategy involving harmonization of codons for successful recombinant expression of full length Pfs48/45 in Escherichia coli. The purified protein, designated CH-rPfs48/45, was recognized by monoclonal antibodies directed against reduction-sensitive conformational epitopes in the native protein. Immunogenicity evaluation in mice revealed potent transmission blocking activity in membrane feeding assays of antisera elicited by CH-rPfs48/45 formulated in three different adjuvants, i.e. Alum, Montanide ISA-51 and complete Freund's adjuvant. More importantly, CH-rPfs48/45 formulated with Montanide ISA-51 when administered to nonhuman primates (Olive baboons, Papio anubis) resulted in uniformly high antibody responses (ELISA titers >2 million) in all five animals. Sera from these animals displayed greater than 93% blocking activity in membrane feeding assays after a single immunization, reaching nearly complete blocking after a booster dose of the vaccine. The relative ease of expression and induction of potent transmission blocking antibodies in mice and nonhuman primates provide a compelling rationale and basis for development of a CH-rPfs48/45 based malaria transmission blocking vaccine.
A comparison of simulation based and scan chain implemented fault injection (2002)

This paper compares two fault injection techniques: scan chain implemented fault injection (SCIFI), i.e. fault injection in a physical system using built in test logic, and fault injection in a VHDL software simulation model of a system. The fault injections were used to evaluate the error detection mechanisms included in the Thor RISC microprocessor, developed by Saab Ericsson Space AB. The Thor microprocessor uses several advanced error detection mechanisms including control flow checking, stack range checking and variable constraint checking. A newly developed tool called FIMB UL (Fault Injection and Monitoring using BUilt in Logic), which uses the Test Access Port (TAP) of the Thor CPU to do fault injection, is presented. The simulations were carried out using the MEFISTO-C tool and a highly detailed VHDL model of the Thor processor. The results show that the larger fault set available in the simulations caused only minor differences in the error detection distribution compared to SCIFI and that the overall error coverage was lower using SCIFI (90-94% vs. 94-96% using simulation based fault injection).
Heteroduplex mobility assay and phylogenetic analysis of V3 region sequences of human immunodeficiency virus type 1 isolates from Gulu, northern Uganda. The Italian-Ugandan Cooperation AIDS Program (1995)

We analyzed peripheral blood mononuclear cells from 19 asymptomatic seropositive pregnant women from the district of Gulu in northern Uganda. A 700-bp fragment of the human immunodeficiency virus type 1 (HIV-1) env gene, including the V3-V5 region, was successfully amplified by PCR from 10 samples (52.6%) and was subsequently subjected to both a heteroduplex mobility assay for genetic screening and subtyping and DNA sequence analysis (approximately 300 bp) for nucleotide comparison and phylogenetic studies. The results show the presence of HIV-1 A and D subtypes (or clades) in this rural area, with the prevalence of the A subtype (8 of 10) being greater than that of the D (2 of 10) subtype, which is unlike what was previously reported for Uganda. By pairwise comparison analysis, the percentage of sequence divergence among samples within each subtype is low (the average intrasubtype divergence is 15.8%), but it is significantly higher between the two subtypes (the average intersubtype divergence is 23%). At the amino acid level, the two HIV-1 subtypes show distinct tetramers at the apex of the V3 loop and, in particular, GPGQ in clade A and GPGR in clade D. In addition, 10 of the 19 viral samples (52.6%) have been isolated in vitro. Nine of the samples have been classified as rapid/high, which reflects a high in vitro replication capacity for the HIV-1 field isolates from this country, even for those obtained from seropositive asymptomatic individuals. These observations, despite being made on the basis of a limited sample size, show a modest degree of genetic divergence among samples isolated in the last 4 years in this country by comparison with those based on the 1990 data on HIV-1 isolates from Kampala. The results reported here are, therefore, extremely relevant for Uganda, which is one of the selected World Health Organization field sites for future HIV-1 vaccine evaluation programs.
A distinct class of vertebrate collagen genes encodes chicken type IX collagen polypeptides. (1985)

Type IX collagen is a disulfide-bonded protein first isolated from hyaline cartilage. The structure of this collagen is unusual in that the molecules contain three triple-helical domains interspersed with noncollagenous regions. The molecules are heterotrimers composed of three genetically distinct polypeptide chains. In our laboratory, cDNAs specific for two of these polypeptide chains have recently been isolated. Here we report on the isolation of genomic clones by use of these cDNAs as probes for screening a chicken genomic library. Nucleotide sequence analysis of these clones shows that the exon structure of type IX collagen genes is fundamentally different from the exon structure of the genes for the fibrillar collagen types I-III. Whereas the sizes of exons in fibrillar collagen genes are related to a basic 54-base-pair coding unit, the exons of type IX collagen genes show a large variation in size and do not appear to be related to a 54-base-pair unit. We propose, therefore, that type IX collagen genes belong to a class of vertebrate collagen genes distinct from that of fibrillar collagens.
Beyond Field Effect: Analysis of Shrunken Centroids in Normal Esophageal Epithelia Detects Concomitant Esophageal Adenocarcinoma (2007)

BACKGROUND AND AIMS: Because of the extremely low neoplastic progression rate in Barrett's esophagus, it is difficult to diagnose patients with concomitant adenocarcinoma early in their disease course. If biomarkers existed in normal squamous esophageal epithelium to identify patients with concomitant esophageal adenocarcinoma, potential applications would be far-reaching. The aim of the current study was to identify global gene expression patterns in normal esophageal epithelium capable of revealing simultaneous esophageal adenocarcinoma, even located remotely in the esophagus. METHODS: Tissues comprised normal esophageal epithelia from 9 patients with esophageal adenocarcinoma, 8 patients lacking esophageal adenocarcinoma or Barrett's, and 6 patients with Barrett's esophagus alone. cDNA microarrays were performed, and pattern recognition in each of these subgroups was achieved using shrunken nearest centroid predictors. RESULTS: Our method accurately discriminated normal esophageal epithelia of 8/8 patients without esophageal adenocarcinoma or Barrett's esophagus and of 6/6 patients with Barrett's esophagus alone from normal esophageal epithelia of 9/9 patients with Barrett's esophagus and concomitant esophageal adenocarcinoma. Moreover, we identified genes differentially expressed between the above subgroups. Thus, based on their corresponding normal esophageal epithelia alone, our method accurately diagnosed patients who had concomitant esophageal adenocarcinoma. CONCLUSIONS: These global gene expression patterns, along with individual genes culled from them, represent potential biomarkers for the early diagnosis of esophageal adenocarcinoma from normal esophageal epithelia. Genes discovered in normal esophagus that are differentially expressed in patients with vs. without esophageal adenocarcinoma merit further pursuit in molecular genetic, functional, and therapeutic interventional studies.
Basic Principles of Protease‐Catalyzed Peptide Bond Formation (1985)

Abstract The stereospecific formation of peptide bonds under mild conditions and without side reactions is still a formidable task in peptide synthesis. One approach that springs to mind, namely the use of the naturally occurring catalyst involved in the biosynthesis of proteins, the ribosomal peptidyl transferase, cannot be realized in practice. The fact, however, that the natural cleavage of proteins is carried out by other enzymes, namely the proteases, together with the reversibility of these cleavage reactions in principle, has led to an interesting synthetic concept. Proteases normally catalyze the enzymatic degradation of proteins and peptides by hydrolytic cleavage of the peptide bond in an exergonic reaction. The use of physicochemical principles in order to influence the equilibrium, the concentration of products, and the kinetic parameters of the reaction results in the successful application of the catalytic properties of proteases to peptide synthesis. The purpose of this review is to describe and summarize the methods used in such approaches and to attempt a systematic categorization. The principles are applied to the synthesis of such practically relevant products as aspartame and human insulin.
Yggdrasil: An Optimized System for Training Deep Decision Trees at Scale (2016)

Deep distributed decision trees and tree ensembles have grown in importance due to the need to model increasingly large datasets. However, PLANET, the standard distributed tree learning algorithm implemented in systems such as \xgboost and Spark MLlib, scales poorly as data dimensionality and tree depths grow. We present Yggdrasil, a new distributed tree learning method that outperforms existing methods by up to 24x. Unlike PLANET, Yggdrasil is based on vertical partitioning of the data (i.e., partitioning by feature), along with a set of optimized data structures to reduce the CPU and communication costs of training. Yggdrasil (1) trains directly on compressed data for compressible features and labels; (2) introduces efficient data structures for training on uncompressed data; and (3) minimizes communication between nodes by using sparse bitvectors. Moreover, while PLANET approximates split points through feature binning, Yggdrasil does not require binning, and we analytically characterize the impact of this approximation. We evaluate Yggdrasil against the MNIST 8M dataset and a high-dimensional dataset at Yahoo; for both, Yggdrasil is faster by up to an order of magnitude.
Potent Neutralization of Influenza A Virus by a Single-Domain Antibody Blocking M2 Ion Channel Protein (2011)

Influenza A virus poses serious health threat to humans. Neutralizing antibodies against the highly conserved M2 ion channel is thought to offer broad protection against influenza A viruses. Here, we screened synthetic Camel single-domain antibody (VHH) libraries against native M2 ion channel protein. One of the isolated VHHs, M2-7A, specifically bound to M2-expressed cell membrane as well as influenza A virion, inhibited replication of both amantadine-sensitive and resistant influenza A viruses in vitro, and protected mice from a lethal influenza virus challenge. Moreover, M2-7A showed blocking activity for proton influx through M2 ion channel. These pieces of evidence collectively demonstrate for the first time that a neutralizing antibody against M2 with broad specificity is achievable, and M2-7A may have potential for cross protection against a number of variants and subtypes of influenza A viruses.
A single-season epidemic with respiratory syncytial virus subgroup B2 during 10 epidemic years, 1978 to 1988 (1991)

Respiratory syncytial virus strains isolated from infants and children hospitalized with acute respiratory tract disease in Huntington, W. Va., from July 1979 through June 1988 were categorized by subgroup by using two panels of monoclonal antibodies specific for subgroup A and subgroup B. Of 405 strains tested, 319 (78.8%) were subgroup A, 73 (18.0%) were subgroup B1, and 13 (3.2%) were subgroup B2. The subgroup B2 strains occurred as a single-season epidemic during the epidemiologic year July 1980 to June 1981, except for one strain isolated in the epidemiologic year 1978 to 1979. Subgroup B strains were associated with significantly fewer bronchiolitis illnesses than subgroup A strains. The severity of illnesses caused by subgroup B1 and B2 strains was the same.
Peptidoglycan hydrolases-potential weapons against Staphylococcus aureus (2012)

Bacteria of the genus Staphylococcus are common pathogens responsible for a broad spectrum of human and animal infections and belong to the most important etiological factors causing food poisoning. Because of rapid increase in the prevalence of isolation of staphylococci resistant to many antibiotics, there is an urgent need for the development of new alternative chemotherapeutics. A number of studies have recently demonstrated the strong potential of peptidoglycan hydrolases (PHs) to control and treat infections caused by this group of bacteria. PHs cause rapid lysis and death of bacterial cells. The review concentrates on enzymes hydrolyzing peptidoglycan of staphylococci. Usually, they are characterized by high specificity to only Staphylococcus aureus cell wall components; however, some of them are also able to lyse cells of other staphylococci, e.g., Staphylococcus epidermidis-human pathogen of growing importance and also other groups of bacteria. Some PHs strengthen the bactericidal or bacteriostatic activity of common antibiotics, and as a result, they should be considered as component of combined therapy which could definitely reduced the development of bacterial resistance to both enzymes and antibiotics. The preliminary research revealed that most of these enzymes can be produced using heterologous, especially Escherichia coli expression systems; however, still much effort is required to develop more efficient and large-scale production technologies. This review discusses current state on knowledge with emphasis on the possibilities of application of PHs in the context of therapeutics for infections caused by staphylococci.
Canned speech for tactical voice message systems (2003)

Various aspects of canned speech generation were examined. In this approach, brief tactical messages are generated by concatenating the speech waveforms corresponding to the individual words. According to the tests conducted, listeners unanimously preferred canned speech over synthetic speech generated by a text-to-speech converter. They selected canned speech not only for its higher intelligibility, but they also felt that canned speech was more natural. Some listeners thought that canned speech was originally recorded as sentences rather than individual words strung together. The data rate required to transmit canned speech is very low (well below 100 b/s). Such a low-data-rate voice encoding technique is essential when the network is congested. Future voice communication should be designed in such a manner that no voice messages are preempted because any voice call might be delivering vital tactical information. With the availability of low-cost, high-density memory devices, canned speech generation is practical in many applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A New Method for Revealing Striations in High-Resistive Floating-Zone Silicon Crystals (1972)

Striations were revealed by preferential etching of preannealed longitudinal crystal slices taken from high‐resistive floating‐zone silicon crystals. The required preannealing treatment was carried out at a temperature between 1000° and 1200°C in a tubular furnace. A model for the mechanism of striation revealing is proposed. The influence of such striations on the performance of planar diodes is briefly discussed.
Enhancing Hemicellulose Recovery and the Enzymatic Hydrolysis of Cellulose by Adding Lignosulfonates during the Two-Stage Steam Pretreatment of Poplar (2015)

To enhance overall sugar recovery, poplar was steam pretreated in two stages. First, under mild pretreatment conditions (160 °C, 15 min) using various acid catalysts (H2SO4, SO2, oxalic, citric) to assess optimum hemicellulose recovery, followed by an uncatalyzed, second pretreatment (200 °C, 5 min), to facilitate enzymatic hydrolysis of the cellulose. The first stage solubilized and recovered about 50% of the xylan, as compared to the 30% obtained in the more severe, single-stage pretreatment. As surfactants are known to increase hemicellulose accessibility during pretreatments, lignosulfonates were added to birch xylan and poplar, increasing xylose yields and retaining 60 mmol/kg strong acid groups, even after the second pretreatment stage and extensive washing, suggesting that lignosulfonates adsorbed to the substrate and enhanced cellulose accessibility. This was confirmed by the increased water retention values and Direct Orange dye adsorption. A two-stage steam pretreatment, incorporating lignosulfonate addition, increased cellulose hydrolysis from 75 to 92%.
Interactions of α-Melanotropin and Agouti on B16 Melanoma Cells: Evidence for Inverse Agonism of Agouti (1997)

alpha-Melanocyte-stimulating hormone (alpha-MSH, alpha-melanotropin) and agouti control the switch between eumelanin and pheomelanin synthesis in mammalian melanocytes. Here we investigated interactions between alpha-MSH, agouti protein, cAMP elevating agents and phorbol ester on mouse B16 melanoma cells. Agouti (Kd 3.7 nmol/l) and alpha-MSH (Kd 2.3 nmol/l) had similar affinities to the MC1 melanocortin receptor. Both alpha-MSH and agouti induced MC1 receptor down-regulation. Agouti antagonized melanogenesis induced by alpha-MSH, forskolin, cholera toxin (CT), and pertussis toxin (PT). It also reduced the constitutive melanin formation of long-term cultures. Cell proliferation was inhibited by agouti (43% at 100 nM). This effect was reversed by alpha-MSH, forskolin, or CT. B16-G4F cells, a cell variant that lacks the MC1 receptor, did not respond to agouti. From these results we conclude that agouti shows the characteristics of an inverse agonist acting through the MC1 receptor.
Squeezing-enhanced fiber Mach-Zehnder interferometer for low-frequency phase measurement (2017)

We propose and experimentally demonstrate a quantum-enhanced fiber Mach-Zehnder interferometer for low-frequency phase measurement beyond the shot-noise limit using a high-frequency squeezing technique. The local oscillator field is amplitude-modulated in the MHz range and is then demodulated to avoid the technical noise that occurs at low frequencies. After measurement of the phase noise at a frequency of tens of kHz, an improvement of ∼2 dB relative to the shot-noise level is achieved. Additionally, the amplitude modulation depth has no significant effect on the phase noise improvement of the interferometer when deployed in our experimental configuration. The current scheme introduces a quantum technique into the fiber-based measurements, particularly for the low frequency range, and this scheme has potential applications in the high-precision fiber sensing of temperature, strain, and various other parameters.
Short Notices (1961)

Short Notices Get access E. MILLER E. MILLER St. John's CollegeCambridge Search for other works by this author on: Oxford Academic Google Scholar The English Historical Review, Volume LXXVI, Issue CCCI, October 1961, Pages 699-a–699, https://doi.org/10.1093/ehr/LXXVI.CCCI.699-a Published: 01 October 1961
Hypervalent Iodine(III) Sulfonate Mediated Synthesis of Quinoxalines in Liquid PEG‐400 (2009)

Abstract PEG‐400[poly(ethylene glycol‐400)] is used as a “green” recyclable solvent in the one‐pot synthesis of quinoxalines by reaction with aryl ketones, hypervalent Iodine(III) Sulfonate, and o ‐phenylenediamines. Significant rate enhancements and improved yields have been observed.
Analysis of Effectiveness of Retrieval in Clustered Files (1977)

article Free Access Share on Analysis of Effectiveness of Retrieval in Clustered Files Authors: C. T. Yu Department of Computer Science, University of Alberta, Edmonton, Canada T6G 2E1 Department of Computer Science, University of Alberta, Edmonton, Canada T6G 2E1View Profile , W. S. Luk Department of Computer Science, University of Alberta, Edmonton, Canada T6G 2E1 Department of Computer Science, University of Alberta, Edmonton, Canada T6G 2E1View Profile Authors Info & Claims Journal of the ACMVolume 24Issue 4Oct. 1977 pp 607–622https://doi.org/10.1145/322033.322039Published:01 October 1977Publication History 12citation294DownloadsMetricsTotal Citations12Total Downloads294Last 12 Months1Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Secure and noise-free holographic encryption with a quick-response code (2014)

In holographic encryption, double random-phase encoding in the Fresnel domain (DRPEiFD) is a prevalent encryption method because it is lensless and secure. However, noises bring adverse effects during decryption. In this letter, we introduce quick-response (QR) coding during encryption to resist noises. We transform the original information into a QR code and then encrypt the code as a hologram through DRPEiFD. To retrieve the input, we decrypt the hologram in the opposite manner to the encryption and subsequently obtain a QR code with noises. By scanning this code with proper applications in smartphones, we can obtain a noise-free retrieval. Numerical experiments and images scanned by a smartphone are shown to validate our proposed method.
The glyoxysomal 3‐ketoacyl‐CoA thiolase precursor from <i>Brassica napus</i> has enzymatic activity when synthesized in <i>Escherichia coli</i> (1997)

Glyoxysomal 3-ketoacyl-CoA thiolase is the last enzyme in the beta-oxidation of fatty acids in plant glyoxysomes. A full-length cDNA of the glyoxysomal 3-ketoacyl-CoA thiolase from Brassica napus and a truncated version, lacking the N-terminal targeting signal were cloned in a T7 promoter-based vector. Both recombinant proteins were expressed in Escherichia coli and activity was measured. Full-length and truncated 3-ketoacyl-CoA thiolase have comparable activity in E. coli. Moreover, full-length 3-ketoacyl-CoA thiolase was purified from E. coli and N-terminal sequencing of the protein confirmed that the precursor form indeed is enzymatically active.