gebhart/patrepeval huggingface dataset:
Fluid and Pharmacological Dynamics in a Subcutaneous Chamber Implanted in Rats (1973)

Antibiotic dynamics in the fluid obtained from subcutaneously implanted chambers in rats were similar to those observed in serum following single intramuscular injections of carbenicillin.
The Drosophila odz/ten-m gene encodes a type I, multiply cleaved heterodimeric transmembrane protein (2002)

The product of the Drosophila melanogaster odd Oz (odz)/Tenascin-major (ten-m) pair-rule gene consists of eight epidermal growth factor (EGF)-like repeats followed by a novel 1800 amino acid polypeptide stretch unique to proteins of the Odz/Ten-m family. The structure and membrane orientation of this large enigmatic protein was characterized by raising and employing antibodies directed against discrete Odz polypeptide regions. Protein-modifying reagents impermeable to the plasma membrane were used in concert with the battery of antibodies to demonstrate that Odz is a type I transmembrane protein with the vast C-terminal portion in the intracellular space, and with the EGF repeats deployed extracellularly. The polypeptide was shown to undergo multiple cleavages at discrete intracellular and extracellular sites, and its extreme C-terminus was shown to undergo either processing at a very large number of sites or programmed degradation. The polypeptide is presented at the cell surface with additional post-translational modifications, and as two subunits of previously cleaved Odz joined by cysteine disulphide bridges maintaining their association. The model derived for the Odz protein is discussed in light of other models proposed for proteins of the Odz/Ten-m family, and in terms of functional implications.
Efficient search of a sequence of words in a large text file (2014)

Searching a specific word or sequence of words, or quotations in a large text document is generally performed by string matching algorithms. Specific word can be more efficiently searched by using suitable hash functions on a hash table where the words of the large text file are organized in order. In this paper, we present a new technique of efficient search of a sequence of words in a large text file using the concept of hashing and linked list. For building the hash table, the words are organized in order. The number of occurrences and positions of each word and positions of its next words are added to the record of each word in the hash table. Any word can be searched using a simple hash function and the subsequent word can be located using the position of next word since this information is available with the record of current word making the hash table as a linked list of words. Since the text file is large, there would be redundancy of hash functional values. Therefore, hash function is used only to locate the upper and lower bounds of the first word. Then an algorithm like binary-search method is used to find the word in the table. We provide our methodology of building the hash table and search techniques. Plausible tests are carried out with simple examples to demonstrate how the algorithms work. Time and space complexities are also computed to show the efficiency of the method.
Etudes technologiques, expérimentales et par simulation pour la commutation optique sur InP (2001)

Ce travail s'est déroulé à l'IEMN et fait suite à une thèse également soutenue dans l'équipe optoélectronique de l'IEMN, sur la réalisation de matrices de commutation sur InP. Notre étude a été soutenue par la direction Générale des Armées et suivi par THALES systèmes aéroportés. Initialement, le travail effectué était essentiellement technologique, destiné à rendre plus fiable et reproductible le procédé de réalisation de ces composants. Diverses modifications du procédé ont donc été établies dans ce but. La vérification des composants finaux a révélé un bon contrôle des dimensions caractéristiques des composants dans la limite des inhomogénéités sur plaque, inhérentes au matériel utilisé pour la fabrication. Malgré ces améliorations du process nous n'avons pu réaliser la fonction de commutation 4x4 qui n'avait pu être atteinte dans les travaux précédents pour cause d'un problème technologique invoqué et maintenant résolu ! De ce fait nous avons donné une autre orientation à notre travail, en abordant les problèmes plus amont de la conception des composants.
Development and Preclinical Testing of a Vaccine for 3,4‐Methylenedioxypyrovalerone (( R,S )‐MDPV) Substance Use Disorders (2018)

Synthetic cathinones like 3,4‐methylenedioxypyrovalerone (( R,S )‐MDPV) are medically dangerous psychoactive drugs which at high doses produce psychosis, cardiovascular toxicity, and death. The goal for these studies was to develop and test a vaccine for treating (( R,S )‐MDPV) substance use disorders. A racemic MDPV conjugate vaccine was developed from a hapten structure capable of generating antibodies that bind with high affinity to ( R,S )‐MDPV and other potent synthetic cathinones. We hypothesized that treatment with an optimized MDPV vaccine could produce high affinity antibodies against ( R,S )‐MDPV capable of mitigating the pharmacological effects of ( R,S )‐MDPV. An ( R,S )‐MDPV‐like hapten was conjugated to different carrier proteins, mixed with Sigma Adjuvant System, and used to immunize male Sprague Dawley rats (n=5/group). The immunochemical characteristics of the rats' immune response was then evaluated. The K D value as determined by radioimmunoassay for ( R,S )‐MDPV binding was 2.5 ± 1.9 nM, which demonstrated production of high affinity antibodies. The K D value for the individual ( R )‐ and ( S )‐MDPV binding was 0.71 ± 0.8 nM and 2.8 ± 2.3 nM, respectively. These similar K D values for the MDPV enantiomers indicates antibodies for both enantiomers contribute to the high binding of ( R,S )‐MDPV. The rat antisera also showed similar high affinity binding of ( R,S )‐α‐pyrrolidinovalerophenone (α‐PVP). No significant cross reactivity was detected with over‐the‐counter medications like (+)‐pseudoephedrine, neurotransmitters (dopamine, norepinephrine, epinephrine, and serotonin), or non‐cathinone drugs of abuse (cocaine, morphine, phencyclidine, (+)‐methamphetamine, (+)‐MDMA, and (−)‐MDMA). Moreover, the vaccination protocol produced high serum antibody titers, determined by rapid equilibrium dialysis, from 5 weeks after the start of immunizations until termination of the rats 3 months later. Finally, locomotor studies of control and vaccinated rats were conducted to test the vaccine's efficacy using a series of increasing doses of ( R,S )‐MDPV (0.3–5.6 mg/kg, sc, 2 days apart). The immunized rats displayed significantly (p&lt;0.05) lower MDPV‐induced locomotor activity and a significantly shorter duration of action compared to controls. In conclusion, active vaccination with an ( R,S )‐MDPV conjugate vaccine produced very high affinity antibodies against ( R,S )‐MDPV; and the vaccinated rats showed significantly reduced ( R,S )‐MDPV‐induced locomotor effects compared to controls. Support or Funding Information Funded by NIDA grants DA039195 and T32 GM106999 This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
Precise memory leak detection for java software using container profiling (2013)

A memory leak in a Java program occurs when object references that are no longer needed are unnecessarily maintained. Such leaks are difficult to detect because static analysis typically cannot precisely identify these redundant references, and existing dynamic leak detection tools track and report fine-grained information about individual objects, producing results that are usually hard to interpret and lack precision. In this article we introduce a novel container-based heap-tracking technique, based on the fact that many memory leaks in Java programs occur due to incorrect uses of containers, leading to containers that keep references to unused data entries. The novelty of the described work is twofold: (1) instead of tracking arbitrary objects and finding leaks by analyzing references to unused objects, the technique tracks only containers and directly identifies the source of the leak, and (2) the technique computes a confidence value for each container based on a combination of its memory consumption and its elements' staleness (time since last retrieval), while previous approaches do not consider such combined metrics. Our experimental results show that the reports generated by the proposed technique can be very precise: for two bugs reported by Sun, a known bug in SPECjbb 2000, and an example bug from IBM developerWorks, the top containers in the reports include the containers that leak memory.
Exploiting telecommunications to deliver real time transport information (1998)

This paper reviews our research in the use of novel telecommunications services to collate and provide both personalised and community wide, time critical, transport information. The objective is to explore opportunities offered by telecommunications to improve the efficiency and use of transport services. Innovative uses of advanced Internet technologies coupled with information delivery using messaging technologies, such as pagers and mobile phones are described. We outline the impact of recent advances in server based applications on the management and delivery of dynamic information. We review an Internet based application that takes real time bus location data and predicts arrival times, delivered using a variety of novel telecommunication services.
A Patch Prior for Dense 3D Reconstruction in Man-Made Environments (2012)

Dense 3D reconstruction in man-made environments has to contend with weak and ambiguous observations due to texture-less surfaces which are predominant in such environments. This challenging task calls for strong, domain-specific priors. These are usually modeled via regularization or smoothness assumptions. Generic smoothness priors, e.g. total variation are often not sufficient to produce convincing results. Consequently, we propose a more powerful prior directly modeling the expected local surface-structure, without the need to utilize expensive methods such as higher-order MRFs. Our approach is inspired by patch-based representations used in image processing. In contrast to the over-complete dictionaries used e.g. for sparse representations our patch dictionary is much smaller. The proposed energy can be optimized by utilizing an efficient first-order primal dual algorithm. Our formulation is in particular very natural to model priors on the 3D structure of man-made environments. We demonstrate the applicability of our prior on synthetic data and on real data, where we recover dense, piece-wise planar 3Dmodels using stereo and fusion of multiple depth images.
Is Methylphenidate Like Cocaine? (1995)

We speculate that because the experience of the high is associated with the fast uptake of cocaine and methylphenidate in the brain, the slow clearance of methylphenidate from the brain may serve as a limiting factor in promoting its frequent self-administration.
Implementation of a neural network-based digital beamformer for a umts smart antenna (2005)

In typical UMTS mobile propagation environments, the interference level due to several user's transmission is the main constraint factor of the system. Smart antennas are an efficient solution to reduce the interference level, thus increasing the number of users allowed in the system. The beamformer module of the adaptive antenna uses the information obtained from the array output to maximize the desired user's signal and minimize the interference's power, by properly combining the received signals. Typically, well-known adaptive algorithms are used to compute the optimum beamforming weights. An interesting alternative to traditional adaptive algorithms are artificial neural networks, specially for real-time implementation in a DSP. A digital beamformer based on a radial basis function neural network is presented in this paper, and its main features are studied. Its performance is compared to the results obtained with typical and optimal beamformers.
In Vitro Validation of the Therapeutic Potential of Dendrimer-Based Nanoformulations against Tumor Stem Cells (2022)

Tumor cells with stem cell properties are considered to play major roles in promoting the development and malignant behavior of aggressive cancers. Therapeutic strategies that efficiently eradicate such tumor stem cells are of highest clinical need. Herein, we performed the validation of the polycationic phosphorus dendrimer-based approach for small interfering RNAs delivery in in vitro stem-like cells as models. As a therapeutic target, we chose Lyn, a member of the Src family kinases as an example of a prominent enzyme class widely discussed as a potent anti-cancer intervention point. Our selection is guided by our discovery that Lyn mRNA expression level in glioma, a class of brain tumors, possesses significant negative clinical predictive value, promoting its potential as a therapeutic target for future molecular-targeted treatments. We then showed that anti-Lyn siRNA, delivered into Lyn-expressing glioma cell model reduces the cell viability, a fact that was not observed in a cell model that lacks Lyn-expression. Furthermore, we have found that the dendrimer itself influences various parameters of the cells such as the expression of surface markers PD-L1, TIM-3 and CD47, targets for immune recognition and other biological processes suggested to be regulating glioblastoma cell invasion. Our findings prove the potential of dendrimer-based platforms for therapeutic applications, which might help to eradicate the population of cancer cells with augmented chemotherapy resistance. Moreover, the results further promote our functional stem cell technology as suitable component in early stage drug development.
Coulometric Diffusion Layer Titrations Using the Ring-Disk Electrode with Amperometric End Point Detection. (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCoulometric Diffusion Layer Titrations Using the Ring-Disk Electrode with Amperometric End Point Detection.Stanley. Bruckenstein and D. C. JohnsonCite this: Anal. Chem. 1964, 36, 11, 2186–2187Publication Date (Print):October 1, 1964Publication History Published online1 May 2002Published inissue 1 October 1964https://doi.org/10.1021/ac60217a004Request reuse permissionsArticle Views39Altmetric-Citations12LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (229 KB) Get e-Alertsclose Get e-Alerts
Improved sensitivity, safety, and rapidity of COVID-19 tests by replacing viral storage solution with lysis buffer (2021)

Conducting numerous, rapid, and reliable PCR tests for SARS-CoV-2 is essential for our ability to monitor and control the current COVID-19 pandemic. Here, we tested the sensitivity and efficiency of SARS-CoV-2 detection in clinical samples collected directly into a mix of lysis buffer and RNA preservative, thus inactivating the virus immediately after sampling. We tested 79 COVID-19 patients and 20 healthy controls. We collected two samples (nasopharyngeal swabs) from each participant: one swab was inserted into a test tube with Viral Transport Medium (VTM), following the standard guideline used as the recommended method for sample collection; the other swab was inserted into a lysis buffer supplemented with nucleic acid stabilization mix (coined NSLB). We found that RT-qPCR tests of patients were significantly more sensitive with NSLB sampling, reaching detection threshold 2.1±0.6 (Mean±SE) PCR cycles earlier then VTM samples from the same patient. We show that this improvement is most likely since NSLB samples are not diluted in lysis buffer before RNA extraction. Re-extracting RNA from NSLB samples after 72 hours at room temperature did not affect the sensitivity of detection, demonstrating that NSLB allows for long periods of sample preservation without special cooling equipment. We also show that swirling the swab in NSLB and discarding it did not reduce sensitivity compared to retaining the swab in the tube, thus allowing improved automation of COVID-19 tests. Overall, we show that using NSLB instead of VTM can improve the sensitivity, safety, and rapidity of COVID-19 tests at a time most needed.
ChemInform Abstract: HOMONUCLEOSIDE PHOSPHONIC ACIDS ‐ I. A GENERAL SYNTHESIS OF ISOSTERIC PHOSPHONATE ANALOGS OF NUCLEOSIDE 3′‐PHOSPHATES (1984)

Abstract Die Titelverbindungen (VI l) werden ausgehend von dem Keton (I) gewonnen: Das aus diesem über die Stufen (III), (IVa)′‐(IVe) erhältliche Acetat (Va) wird (mit HCl) in die Halogenose (‐Vb) übergeführt, die unmittelbar mit entsprechenden Basen (als Hg‐ bzw. ClHg‐Derivate eingesetzt) unter Bildung der voll geschützten Nucleoside (VI) kondensiert werden.
A 32nm 8.3GHz 64-entry &#x00D7; 32b variation tolerant near-threshold voltage register file (2010)

This paper describes a 64-entry × 32b 1-read, 1-write ported register file with measured 8.3GHz operation consuming 83mW, fabricated in 1.0V 32nm CMOS. Contention-free shared keeper circuits combined with variation tolerant dual-ended transmission gate write memory cells enable 300mV Vcc-min reduction and measured scalable near-threshold voltage operation to 340mV with energy efficiency of 550GOPS/W.
Comparative Genomics and Biosynthetic Potential Analysis of Two Lichen-Isolated Amycolatopsis Strains (2018)

Actinomycetes have been extensively exploited as one of the most prolific secondary metabolite-producer sources and continue to be in the focus of interest in the constant search of novel bioactive compounds. The availability of less expensive next generation genome sequencing techniques has not only confirmed the extraordinary richness and broad distribution of silent natural product biosynthetic gene clusters among these bacterial genomes, but also has allowed the incorporation of genomics in bacterial taxonomy and systematics. As part of our efforts to isolate novel strains from unique environments, we explored lichen-associated microbial communities as unique assemblages to be studied as potential sources of novel bioactive natural products with application in biotechnology and drug discovery. In this work, we have studied the whole genome sequences of two new <i>Amycolatopsis</i> strains (CA-126428 and CA-128772) isolated from tropical lichens, and performed a comparative genomic analysis with 41 publicly available <i>Amycolatopsis</i> genomes. This work has not only permitted to infer and discuss their taxonomic position on the basis of the different phylogenetic approaches used, but has also allowed to assess the richness and uniqueness of the biosynthetic pathways associated to primary and secondary metabolism, and to provide a first insight on the potential role of these bacteria in the lichen-associated microbial community.
Pyrolytic Carbon Coating Enhances Teflon and Dacron Fabric Compatibility with Endothelial cell Growth (1991)

Compatibility with endothelial cell attachment and growth appears to be an important requisite of vascular prosthetic materials, possibly influencing thrombosis, pseudointimal hyperplasia, and accelerated atherosclerosis at the site of blood-material interaction. Since deposition of pyrolytic carbon (PC) on prosthetic surfaces has been associated with enhanced hemocompatibility, in the present study we assessed whether a thin layer (0.5 microns) of PC deposited onto materials such as knitted Teflon and Dacron enhanced endothelial cell attachment and growth. Cultured human umbilical vein endothelial cells (HUVEC) were seeded at a density of 4.5 x 10(4) cells/cm2 on PC-coated and uncoated grafts. In order to quantify endothelial cell attachment on the fabrics, the area of Teflon and Dacron fabrics covered by endothelial cells was estimated on day 2 after seeding using the point counting method in scanning electron micrographs. Subsequently, on days 2 and 4 after seeding, endothelial cell proliferation was measured both as number of endothelial cells and as total proteins of the endothelial cells covering the fabrics. On day 2 endothelial cell growth on PC-coated fabrics was greater (mean +/- SE; area 42.3 +/- 9.9 mm2, n = 6; cell number 3.9 x 10(4) +/- 3.03 x 10(3) cells, n = 4; total proteins 14.9 +/- 1.2 micrograms, n = 4) than on uncoated fabrics (area 10.6 +/- 4.6 mm2, n = 6; cell number 2.9 x 10(4) +/- 4.3 x 10(3) cells, n = 4; total proteins 11.3 +/- 1.7 micrograms, n = 4; P less than 0.001, less than 0.05 and less than 0.05, respectively).(ABSTRACT TRUNCATED AT 250 WORDS)
Forms and accumulation of copper and zinc in a sandy typic hapludalf soil after long-term application of pig slurry and deep litter (2013)

Successive applications of pig slurry and pig deep litter may lead to an accumulation of copper (Cu) and zinc (Zn) fractions in the soil profile. The objective of this study was to evaluate the Cu and Zn forms and accumulation in a Sandy Typic Hapludalf soil after long-term application of pig slurry and deep litter. In March 2010, eight years after initiating an experiment in Braço do Norte, Santa Catarina (SC), Brazil, on a Sandy Typic Hapludalf soil, soil samples were collected from the 0-2.5, 2.5-5.0, 5-10 and 10-15 cm layers in treatments consisting of no manure application (control) and with applications of pig slurry and deep litter at two levels: the single and double rate of N requirement for maize and black oat succession. The soil was dried, ground in an agate mortar and analyzed for Cu and Zn contents by 0.01 mol L-1 EDTA and chemically fractionated to determine Cu and Zn. The applications of Pig deep litter and slurry at doses equivalent to 90 kg ha-1 N increased the contents of available Cu and Zn in the surface soil layer, if the double of this dose was applied in pig deep litter or double this dose in pig slurry, Cu and Zn migrated to a depth of 15 cm. Copper is accumulated mainly in the organic and residual fractions, and zinc preferentially in the fraction linked to clay minerals, especially in the surface soil layers.
Recurrent Early Thrombus Formation in HeartMate II Left Ventricular Assist Device (2013)

Left ventricular assist devices are becoming an established treatment for end-stage heart failure. In spite of their proven benefit, pump thrombosis remains a significant complication. Here we describe the challenging management of a patient with recurrent pump thrombosis.
Rapid detection of vancomycin-resistant enterococci (1994)

Campylobacter blood agar with clindamycin incubated in 6% CO2 served as a medium to both screen for vancomycin resistance and select for presumptive enterococci. Colonies that grew on the medium were specifically identified as enterococci within 30 min by the pyroglutamyl-beta-naphthylamide and rapid bile esculin tests. The combination of a selective medium plus rapid enzyme substrate tests offered an inexpensive means to enumerate vancomycin-resistant enterococci from specimens by using readily available reagents.