gebhart/patrepeval huggingface dataset:
Targeting of Synthetic Gene Delivery Systems (2003)

Safe, efficient, and specific delivery of therapeutic genes remains an important bottleneck for the development of gene therapy. Synthetic, nonviral systems have a unique pharmaceutical profile with potential advantages for certain applications. Targeting of the synthetic vector improves the specificity of gene medicines through a modulation of the carriers' biodistribution, thus creating a dose differential between healthy tissue and the target site. The biodistribution of current carrier systems is being influenced to a large extent by intrinsic physicochemical characteristics, such as charge and size. Consequently, such nonspecific interactions can interfere with specific targeting, for example, by ligands. Therefore, a carrier complex should ideally be inert, that is, free from intrinsic properties that would bias its distribution away from the target site. Strategies such as coating of DNA carrier complexes with hydrophilic polymers have been used to mask some of these intrinsic targeting effects and avoid nonspecific interactions. Preexisting endogenous ligand-receptor interactions have frequently been used for targeting to certain cell types or tumours. Recently exogenous ligands have been derived from microorganisms or, like antibodies or phage-derived peptides, developed de novo. In animal models, such synthetic vectors have targeted remote sites such as a tumour. Furthermore, the therapeutic proof of the concept has been demonstrated for fitting combinations of synthetic vectors and therapeutic gene.
Noise Resilient Recovery Algorithm for Compressed Sensing (2014)

In this article, we discuss a novel greedy algorithm for the recovery of compressive sampled signals under noisy conditions. Most of the greedy recovery algorithms proposed in the literature require sparsity of the signal to be known or they estimate sparsity, for a known representation basis, from the number of measurements. These algorithms recover signals when noise level is significantly low. We propose Entropy minimization based Matching Pursuit (EMP) which has the capability to reject noise even when noise level is comparable to that of signal level. The proposed algorithm can cater to compressible signals and signals for which sparsity is not known in advance. Simulation study of the proposed scheme shows improved robustness to white Gaussian noise in comparison with the conventional greedy recovery algorithms.
Sequence of a full-length cDNA for rat lung .beta.-galactoside-binding protein: primary and secondary structure of the lectin (1988)

A full-length cDNA for rat lung beta-galactoside lectin (subunit Mr approximately 14,000, lectin 14K) was cloned and the nucleotide sequence determined. The deduced amino acid sequence agrees with the amino acid composition and direct amino acid sequence analysis of purified rat lung lectin peptides. We found that the amino-terminal alanine is blocked with an acetyl group. Comparison of the amino acid sequence with other proteins shows a high degree of homology only with other vertebrate lectin sequences, supporting the suggestion that these lectins may constitute a unique class of vertebrate proteins. The amino acid composition and sequence of lectin peptides, the sequence of lectin cDNA, and isoelectric focusing of purified lectin indicate that rat lung lectin 14K is composed predominantly of a single protein. In addition, rat uterus lectin 14K was found to be the same protein as that present in lung. We characterized the secondary and tertiary structure of rat lung lectin 14K by circular dichroism, by analytical ultracentrifugation, and by computer analysis of its primary structure. Results of these experiments suggest that lectin 14K is primarily a hydrophilic protein with an asymmetric, elongated structure consisting of approximately equal amounts of alpha helix, beta sheet, beta turn, and random coil. We found that Cys-2 and Cys-130 react most rapidly with iodoacetamide; one or both of these residues may be primarily responsible for the thiol requirement of lectin activity.
Characterization of a multifunctional α2,3-sialyltransferase from Pasteurella dagmatis (2013)

A new multifunctional α2,3-sialyltransferase has been discovered in Pasteurella dagmatis. The enzyme, in short PdST, was identified from the P. dagmatis genome by sequence similarity with sialyltransferases of glycosyltransferase family GT-80. In addition to its regioselective sialyltransferase activity (5.9 U/mg; pH 8.0), purified PdST is alternatively active at low pH as α2,3-sialidase (0.5 U/mg; pH 4.5) and α2,3-trans-sialidase (1.0 U/mg; pH 4.5). It also shows cytidine-5'-monophosphate N-acetyl-neuraminic (CMP-Neu5Ac) hydrolase activity (3.7 U/mg; pH 8.0) when no sialyl acceptor substrate is present in the reaction. After sialyltransferase PmST1 from P. multocida, PdST is the second member of family GT-80 to display this remarkable catalytic promiscuity. A unique feature of PdST, however, is a naturally occurring Ser-to-Thr substitution within a highly conserved Y(112)DDGS(116) sequence motif. In PmST1, the equivalent Ser(143) is involved in binding of the CMP-Neu5Ac donor substrate. Reversion of the natural mutation in a T116S-PdST variant resulted in a marked increase in α2,3-trans-sialidase side activity (4.0 U/mg; pH 4.5), whereas the major sialyltransferase activity was lowered (3.8 U/mg; pH 8.0). The Michaelis-Menten constant for CMP-Neu5Ac was decreased 4-fold in T116S mutant when compared with wild-type PdST (KM=1.1 mM), indicating that residue 116 of PdST contributes to a delicate balance between substrate binding and catalytic activity. D-Galactose and various β-D-galactosides function as sialyl acceptors from CMP-Neu5Ac, whereas other hexoses (e.g. D-glucose) are inactive. Structure comparison was used to rationalize the particular acceptor substrate specificity of PdST in relation to other GT-80 sialyltransferases that show strict α2,3-regioselectivity, but are flexible in using α/β-galactosides for sialylation.
Role of Antibiotic Penetration Limitation in <i>Klebsiella pneumoniae</i> Biofilm Resistance to Ampicillin and Ciprofloxacin (2000)

The penetration of two antibiotics, ampicillin and ciprofloxacin, through biofilms developed in an in vitro model system was investigated. The susceptibilities of biofilms and corresponding freely suspended bacteria to killing by the antibiotics were also measured. Biofilms of Klebsiella pneumoniae were developed on microporous membranes resting on agar nutrient medium. The susceptibilities of planktonic cultures and biofilms to 10 times the MIC were determined. Antibiotic penetration through biofilms was measured by assaying the concentration of antibiotic that diffused through the biofilm to an overlying filter disk. Parallel experiments were performed with a mutant K. pneumoniae strain in which beta-lactamase activity was eliminated. For wild-type K. pneumoniae grown in suspension culture, ampicillin and ciprofloxacin MICs were 500 and 0.18 microgram/ml, respectively. The log reductions in the number of CFU of planktonic wild-type bacteria after 4 h of treatment at 10 times the MIC were 4.43 +/- 0.33 and 4.14 +/- 0.33 for ampicillin and ciprofloxacin, respectively. Biofilms of the same strain were much less susceptible, yielding log reductions in the number of CFU of -0.06 +/- 0.06 and 1.02 +/- 0.04 for ampicillin and ciprofloxacin, respectively, for the same treatment. The number of CFU in the biofilms after 24 h of antibiotic exposure was not statistically different from the number after 4 h of treatment. Ampicillin did not penetrate wild-type K. pneumoniae biofilms, whereas ciprofloxacin and a nonreactive tracer (chloride ion) penetrated the biofilms quickly. The concentration of ciprofloxacin reached the MIC throughout the biofilm within 20 min. Ampicillin penetrated biofilms formed by a beta-lactamase-deficient mutant. However, the biofilms formed by this mutant were resistant to ampicillin treatment, exhibiting a 0.18 +/- 0.07 log reduction in the number of CFU after 4 h of exposure and a 1.64 +/- 0.33 log reduction in the number of CFU after 24 h of exposure. Poor penetration contributed to wild-type biofilm resistance to ampicillin but not to ciprofloxacin. The increased resistance of the wild-type strain to ciprofloxacin and the mutant strain to ampicillin and ciprofloxacin could not be accounted for by antibiotic inactivation or slow diffusion since these antibiotics fully penetrated the biofilms. These results suggest that some other resistance mechanism is involved for both agents.
Ultrasensitive electrochemical detection of DNA hybridization using Au/Fe3O4 magnetic composites combined with silver enhancement (2010)

A novel method is described for the highly effective amplifying electrochemical response of DNA based on oligonucleotides functionalized with Au/Fe(3)O(4) nanocomposites by the aid of silver (Ag) enhancement. Via electrostatic layer-by-layer (LBL) assembly, the prepared Fe(3)O(4) nanoparticles form nano-clusters coated with a bilayer composed of polystyrene sulfonate sodium salt (PSS) and poly(diallyldimethylammonium chloride) (PDDA), which are in favor of adsorbing lots of gold nanoparticles (AuNPs) on the surface. The application of magnetic Fe(3)O(4) made the procedures much more simple, convenient and feasible. The resulting composites were then used as labels via the Au-S bond for the DNA hybridization, followed by catalytic deposition of silver on the gold tags. Such an assay is then combined with a sensitive anodic stripping voltammetry (ASV) measurement of multiple silver nanoparticle tracers. A 27-mer sequence DNA target is detected at a glassy carbon (GC) electrode with a detection limit down to ca. 100 aM, which is 800 times lower than that obtained using gold nanoparticles only as labels in the control experiments. This Fe(3)O(4)/PSS/PDDA/Au composite offers a great promising future for the ultrasensitive detection of other biorecognition events.
Robust feature matching in 2.3µs (2009)

In this paper we present a robust feature matching scheme in which features can be matched in 2.3 μs. For a typical task involving 150 features per image, this results in a processing time of 500 μs for feature extraction and matching. In order to achieve very fast matching we use simple features based on histograms of pixel intensities and an indexing scheme based on their joint distribution. The features are stored with a novel bit mask representation which requires only 44 bytes of memory per feature and allows computation of a dissimilarity score in 20 ns. A training phase gives the patch-based features invariance to small viewpoint variations. Larger viewpoint variations are handled by training entirely independent sets of features from different viewpoints. A complete system is presented where a database of around 13,000 features is used to robustly localise a single planar target in just over a millisecond, including all steps from feature detection to model fitting. The resulting system shows comparable robustness to SIFT and Ferns while using a tiny fraction of the processing time, and in the latter case a fraction of the memory as well.
A Robust Indoor Positioning System Based on the Procrustes Analysis and Weighted Extreme Learning Machine (2015)

Indoor positioning system (IPS) has become one of the most attractive research fields due to the increasing demands on location-based services (LBSs) in indoor environments. Various IPSs have been developed under different circumstances, and most of them adopt the fingerprinting technique to mitigate pervasive indoor multipath effects. However, the performance of the fingerprinting technique severely suffers from device heterogeneity existing across commercial off-the-shelf mobile devices (e.g., smart phones, tablet computers, etc.) and indoor environmental changes (e.g., the number, distribution and activities of people, the placement of furniture, etc.). In this paper, we transform the received signal strength (RSS) to a standardized location fingerprint based on the Procrustes analysis, and introduce a similarity metric, termed signal tendency index (STI), for matching standardized fingerprints. An analysis of the capability of the proposed STI to handle device heterogeneity and environmental changes is presented. We further develop a robust and precise IPS by integrating the merits of both the STI and weighted extreme learning machine (WELM). Finally, extensive experiments are carried out and a performance comparison with existing solutions verifies the superiority of the proposed IPS in terms of robustness to device heterogeneity.
The Automated Palomar 60 Inch Telescope (2006)

We have converted the Palomar 60-inch telescope (P60) from a classical night assistant-operated telescope to a fully robotic facility. The automated system, which has been operational since September 2004, is designed for moderately fast (t <~ 3 minutes) and sustained (R <~ 23 mag) observations of gamma-ray burst afterglows and other transient events. Routine queue-scheduled observations can be interrupted in response to electronic notification of transient events. An automated pipeline reduces data in real-time, which is then stored on a searchable web-based archive for ease of distribution. We describe here the design requirements, hardware and software upgrades, and lessons learned from roboticization. We present an overview of the current system performance as well as plans for future upgrades.
Screening for Resistance to<i>Sclerotinia trifoliorum</i>in Alfalfa by Inoculation of Excised Leaf Tissue (1996)

Excised leaf tissues of alfalfa were inoculated with Sclerotinia trifoliorum to determine whether leaf-inoculation techniques may be used to screen for heritable and effective resistance to the pathogen. Leaf tissues were placed on water agar in petri plates, inoculated with mycelia of S. trifoliorum, and incubated at 17°C. Host responses were evaluated according to the rate and extent of necrosis that developed during 1 week. One thousand plants of cultivar Delta were screened for resistance by successive inoculation of excised unifoliate leaves, first trifoliate leaflets, and disks of tissue from later leaves. The five plants considered most resistant were intercrossed, and progeny were compared with those of five plants selected for susceptibility, five selected at random, and the parent cultivar. Progeny of resistant plants had significantly (P = 0.05) less severe disease than did progenies of susceptible and random plants and the parent cultivar when evaluated by inoculation of unifoliate leaves, first trifoliate leaflets, leaf disks, excised stems, and whole plants. In field experiments with natural infection during two growing seasons, progeny of resistant plants had less severe disease and produced significantly (P = 0.05) higher yields of forage through the first or second harvests than did progenies of susceptible and random plants and the parent cultivar. These results establish that inoculation of excised leaf tissue is an effective and efficient means to screen for resistance to S. trifoliorum in alfalfa.
Address compression through base register caching (1990)

The paper presents a technique to reduce processor-to-memory address bandwidth by exploiting temporal and spatial locality in address reference streams. Higher order portions of address words are cached in base registers at both the processor and memory. This makes it possible to transmit small register indexes between processor and memory instead of the high order address bits themselves. Trace driven simulations indicate that base register caching reduces processor-to-memory address bandwidth up to 60% without appreciable loss in performance. >
Measuring vertex centrality in co-occurrence graphs for online social tag recommendation (2009)

Abstract. We present a social tag recommendation model for collaborative bookmarking systems. This model receives as input a bookmark of a web page or scientific publication, and automatically suggests a set of social tags useful for annotating the bookmarked document. Analysing and processing the bookmark textual contents- document title, URL, abstract and descriptions- we extract a set of keywords, forming a query that is launched against an index, and retrieves a number of similar tagged bookmarks. Afterwards, we take the social tags of these bookmarks, and build their global co-occurrence sub-graph. The tags (vertices) of this reduced graph that have the highest vertex centrality constitute our recommendations, which are finally ranked based on TF-IDF and personalisation based techniques.
Phase I and II studies of intravenous Rexin-G as monotherapy for stage IVb gemcitabine-resistant pancreatic cancer. (2010)

4149 Background: To evaluate (1) the safety and antitumor activity of Rexin-G, and (2) the cumulative toxicity and sustained efficacy of Rexin-G continuance in gemcitabine-resistant Stage IVb pancreas cancer. Methods: Fifteen patients were given escalating doses of 1, 2 or 3 × 10e11 cfu of Rexin-G i.v. 2 to 3 times a week for 4 weeks. A phase II component was incorporated by adaptive design, and additional cycles were given if there was ≤ grade 1 toxicity. The estimated tumor burden was determined by PET-CT scan using the formula: S [Target Lesions (cm) + (No. of Non- Target Lesions + (20*))] × 10e9. Note: (20*) indicates ascites, pleural effusion, and/or
Implementation of the CDC translational informatics platform - from genetic variants to the national Swedish Rheumatology Quality Register (2013)

Research and clinical database integration is a real challenge and a road-block in translational research. Through this research we addressed the challenges and demonstrated the usefulness of CDC. We adhered to ethical regulations pertaining to patient data, and we determined that the existing software solutions cannot meet the translational research needs at hand. We used RA as a test case since we have ample data on active and longitudinal cohort.
RSFQ logic/memory family: a new Josephson-junction technology for sub-terahertz-clock-frequency digital systems (1991)

Recent developments concerning the rapid single-flux-quantum (RSFQ) circuit family are reviewed. Elementary cells in this circuit family can generate, pass, memorize, and reproduce picosecond voltage pulses with a nominally quantized area corresponding to transfer of a single magnetic flux quantum across a Josephson junction. Functionally, each cell can be viewed as a combination of a logic gate and an output latch (register) controlled by clock pulses, which are physically similar to the signal pulses. Hand-shaking style of local exchange by the clock pulses enables one to increase complexity of the LSI RSFQ systems without loss of operating speed. The simplest components of the RSFQ circuitry have been experimentally tested at clock frequencies exceeding 100 GHz, and an increase of the speed beyond 300 GHz is expected as a result of using an up-to-date fabrication technology. This review includes a discussion of possible future developments and applications of this novel, ultrafast digital technology.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
KDA-a tool for automatic design evaluation and refinement using the blackboard model of control (1988)

Interest in applying knowledge-based techniques in software engineering is growing, but little has yet been accomplished in the area of software design. This paper discusses the use of the blackboard model of control for design evaluation and refinement, and describes KDA (Knowledge-based Design Assistant) which has been built to demonstrate the applicability of this idea; the tool's architecture and example sessions are included and explained.
Design of system-on-a-chip test access architectures under place-and-route and power constraints (2000)

Test access is a difficult problem encountered in the testing of core-based system-on-a-chip (SOC) designs. Since embedded cores in an SOC are not directly accessible via chip inputs and outputs, special access mechanisms are required to test them at the system level. We propose test access architectures based on integer linear programming (ILP) that incorporate place-and-route constraints arising from the functional interconnections between cores, as well as system-level constraints on power consumption. As a case study, we apply the ILP models to two representative SOCs, and solve them using a public-domain ILP software package.
Ethanol as Hydrogen Donor: Highly Efficient Transfer Hydrogenations with Rhodium(I) Amides (2008)

Catalysts take to the bottle: Rhodium amides with a saw-horse structure serve as very efficient catalysts for the transfer hydrogenation of ketones and activated olefins using ethanol as hydrogen donor. Under mild conditions, the corresponding alcohols and ethyl acetate are formed with high efficiency, with a turnover frequency above 500 000 h−1.
DNA sequence and units of transcription of the conjugative transfer gene complex (trs) of Staphylococcus aureus plasmid pGO1 (1993)

The conjugative transfer genes of 52-kb staphylococcal R plasmid pGO1 were localized to a single BglII restriction fragment and cloned in Escherichia coli. Sequence analysis of the 13,612-base transfer region, designated trs, identified 14 intact open reading frames (ORFs), 13 of which were transcribed in the same direction. Each ORF identified was preceded by a typical staphylococcal ribosomal binding sequence, and 10 of the 14 proteins predicted to be encoded by these ORFs were seen when an E. coli in vitro transcription-translation system was used. Functional transcription units were identified in a Staphylococcus aureus host by complementation of Tn917 inserts that abolished transfer and by Northern (RNA) blot analysis of pGO1 mRNA transcripts. These studies identified three complementation groups (trsA through trsC, trsD through trsK, and trsL-trsM) and four mRNA transcripts (trsA through trsC [1.8 kb], trsA-trsB [1.3 kb], trsL-trsM [1.5 kb], and trsN [400 bases]). No definite mRNA transcript was seen for the largest complementation group, trsD through trsK (10 kb). Comparison of predicted trs-encoded amino acid sequences to those in the data base showed 20% identity of trsK to three related genes necessary for conjugative transfer of plasmids in gram-negative species and 32% identity of trsC to a gene required for conjugative mobilization of plasmid pC221 from staphylococci.
Collective embedding for neural context-aware recommender systems (2019)

Context-aware recommender systems consider contextual features as additional information to predict user's preferences. For example, the recommendations could be based on time, location, or the company of other people. Among the contextual information, time became an important feature because user preferences tend to change over time or be similar in the near future. Researchers have proposed different models to incorporate time into their recommender system, however, the current models are not able to capture specific temporal patterns. To address the limitation observed in previous works, we propose Collective embedding for Neural Context-Aware Recommender Systems (CoNCARS). The proposed solution jointly model the item, user and time embeddings to capture temporal patterns. Then, CoNCARS use the outer product to model the user-item-time correlations between dimensions of the embedding space. The hidden features feed our Convolutional Neural Networks (CNNs) to learn the non-linearities between the different features. Finally, we combine the output from our CNNs in the fusion layer and then predict the user's preference score. We conduct extensive experiments on real-world datasets, demonstrating CoNCARS improves the top-N item recommendation task and outperform the state-of-the-art recommendation methods.