gebhart/patrepeval huggingface dataset:
A hit-and-run system for targeted genetic manipulations in yeast (1992)

Journal Article A hit-and-run system for targeted genetic manipulations in yeast Get access Joaquim Roca, Joaquim Roca Search for other works by this author on: Oxford Academic PubMed Google Scholar Marc R. Gartenberg, Marc R. Gartenberg Search for other works by this author on: Oxford Academic PubMed Google Scholar Yasuji Oshima, Yasuji Oshima 1Department of Fermentation Technology, Faculty of Engineering, Osaka University2-1 Yamadaoka, Suita-shi, Osaka 565, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar James C. Wang James C. Wang * * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 20, Issue 17, 11 September 1992, Pages 4671–4672, https://doi.org/10.1093/nar/20.17.4671 Published: 11 September 1992 Article history Received: 26 May 1992 Published: 11 September 1992
Reductive Coupling and Polymerization of Unsaturated Amides. II. Effect of Substituents1 (1954)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReductive Coupling and Polymerization of Unsaturated Amides. II. Effect of Substituents1H. R. Snyder and Robert E. PutnamCite this: J. Am. Chem. Soc. 1954, 76, 7, 1893–1898Publication Date (Print):April 1, 1954Publication History Published online1 May 2002Published inissue 1 April 1954https://pubs.acs.org/doi/10.1021/ja01636a047https://doi.org/10.1021/ja01636a047research-articleACS PublicationsRequest reuse permissionsArticle Views116Altmetric-Citations3LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Deletion of the BCSP31 gene of Brucella abortus by replacement (1991)

The 31-kDa salt-extractable immunogenic protein, BCSP31, was deleted from several Brucella abortus strains by replacement with a marker gene encoding resistance to the antibiotics kanamycin and neomycin. The BCSP31 gene replacement plasmids, constructed with ColE1-derived vectors, were introduced by electroporation into B. abortus strain 19 (S19), into a rough variant of B. abortus S19, and into B. abortus S2308, and antibiotic-resistant transformants were isolated. B. abortus S19 is an attenuated strain used as a vaccine for prevention of bovine brucellosis in the United States, and B. abortus S2308 is a commonly used challenge strain. The antibiotic-resistant isolates were all obtained by recombination; none were spontaneous mutants. Loss of the gene encoding BCSP31 and presence of the marker gene were confirmed by Southern analysis. Vector sequences were either absent or linked to the genome, indicating that ColE1-derived plasmids are not maintained in B. abortus. Survival of B. abortus mutant strains in the macrophagelike cell line J774 and in HeLa cells was examined and shown to be indistinguishable from that of the parental strain.
Distribution and elimination of protein therapeutics: A review (2012)

It was 1980s when the first therapeutic protein was launched in the market. It was recombinant DNAderived insulin. Since its inception, within the worldwide pharmaceutical sector, protein therapeutics has been enjoying the fastest growth, notably for the last few years. As a result it is assumed that the treatment methodology with the conventional drug therapy will be shifted towards therapeutic proteins in near future. It made revolution in the treatment of chronic diseases like cancer, diabetes, cardiovascular diseases. The major segments in protein therapeutics are monoclonal antibody, insulin, granulocyte-colony stimulating factor (G-CSF), coagulation factors etc. In this review paper we will discuss the general aspects of protein therapeutics with their advantages over small-molecule drugs, functional classification of therapeutic proteins and their uses. The pharmacokinetics of protein therapeutics, especially from the distribution and elimination characteristics of therapeutic proteins will be discussed in brief with relevant examples. The major challenges and future perspectives will also be presented in short. DOI: http://dx.doi.org/10.3329/sjps.v4i2.10433 S. J. Pharm. Sci. 4(2) 2011: 01-12
Printable hydraulics: A method for fabricating robots by 3D co-printing solids and liquids (2016)

This paper introduces a novel technique for fabricating functional robots using 3D printers. Simultaneously depositing photopolymers and a non-curing liquid allows complex, pre-filled fluidic channels to be fabricated. This new printing capability enables complex hydraulically actuated robots and robotic components to be automatically built, with no assembly required. The technique is showcased by printing linear bellows actuators, gear pumps, soft grippers and a hexapod robot, using a commercially-available 3D printer. We detail the steps required to modify the printer and describe the design constraints imposed by this new fabrication approach.
URINARY TRACT SUBSTITUTION1 (1961)

SUMMARY In three groups of dogs, portions of the urinary tract have been removed and replaced by aortic homografts and plastic materials. The three groups were those in which the upper hemisphere of the bladder was removed (Group 1), where the whole bladder and lower ureters were removed (Group 2), and where one ureter only was removed (Group 3). When aortic homografts were used the results were unsatisfactory. When plastic materials were used, some satisfactory functional results were obtained in the first two groups, but the results in the third group were poor. There is no evidence in these experiments that bladder muscle fibres regenerate or take any part in the development of the re‐formed urinary tract.
Revisiting Catalysis by Chymotrypsin Family Serine Proteases Using Peptide Substrates and Inhibitors with Unnatural Main Chains (1999)

Chymotrypsin family serine proteases play essential roles in key biological and pathological processes and are frequently targets of drug discovery efforts. This large enzyme family is also among the most advanced model systems for detailed studies of enzyme mechanism and structure/function relationships. Productive interactions between these enzymes and their substrates are widely believed to mimic the "canonical" interactions between serine proteases and "standard" inhibitors observed in numerous protease-inhibitor complexes. To test this central hypothesis we have synthesized and characterized a series of peptide analogs, based on model substrates and inhibitors of trypsin, that contain unnatural main chains. These results call into question a long accepted theory regarding the interaction of chymotrypsin family serine proteases with substrates and suggest that the canonical interactions observed between these enzymes and standard inhibitors may represent nonproductive rather than productive, substrate-like interactions.
Nanocrystal targeting in vivo (2002)

Inorganic nanostructures that interface with biological systems have recently attracted widespread interest in biology and medicine. Nanoparticles are thought to have potential as novel intravascular probes for both diagnostic (e.g., imaging) and therapeutic purposes (e.g., drug delivery). Critical issues for successful nanoparticle delivery include the ability to target specific tissues and cell types and escape from the biological particulate filter known as the reticuloendothelial system. We set out to explore the feasibility of in vivo targeting by using semiconductor quantum dots (qdots). Qdots are small (<10 nm) inorganic nanocrystals that possess unique luminescent properties; their fluorescence emission is stable and tuned by varying the particle size or composition. We show that ZnS-capped CdSe qdots coated with a lung-targeting peptide accumulate in the lungs of mice after i.v. injection, whereas two other peptides specifically direct qdots to blood vessels or lymphatic vessels in tumors. We also show that adding polyethylene glycol to the qdot coating prevents nonselective accumulation of qdots in reticuloendothelial tissues. These results encourage the construction of more complex nanostructures with capabilities such as disease sensing and drug delivery.
Sleep apnea syndrome. Can it induce hemodynamic changes? (1975)

Of 250 patients referred to the Stanford Sleep Disorders Clinic, 35 were diagnosed for a sleep induced apnea syndrome. Thirty of them (27 adults and 3 children) were nonobese and complained of a sleep disorder. In 12 patients (9 adults and 3 children) extensive cardiorespiratory workups were done during sleep and wakefulness. Three types of sleep induced apnea syndrome were identified: diaphragmatic (or central), obstructive and mixed. The diaphragmatic type was predominant in sleep apnea insomnia; obstructive was predominant in sleep apnea hypersomnia. Hemodynamic changes were documented during sleep. Tracheostomy, done in two cases, improved the sleep induced symptomatology.
Multimodal semi-supervised learning for image classification (2010)

In image categorization the goal is to decide if an image belongs to a certain category or not. A binary classifier can be learned from manually labeled images; while using more labeled examples improves performance, obtaining the image labels is a time consuming process. We are interested in how other sources of information can aid the learning process given a fixed amount of labeled images. In particular, we consider a scenario where keywords are associated with the training images, e.g. as found on photo sharing websites. The goal is to learn a classifier for images alone, but we will use the keywords associated with labeled and unlabeled images to improve the classifier using semi-supervised learning. We first learn a strong Multiple Kernel Learning (MKL) classifier using both the image content and keywords, and use it to score unlabeled images. We then learn classifiers on visual features only, either support vector machines (SVM) or least-squares regression (LSR), from the MKL output values on both the labeled and unlabeled images. In our experiments on 20 classes from the PASCAL VOC'07 set and 38 from the MIR Flickr set, we demonstrate the benefit of our semi-supervised approach over only using the labeled images. We also present results for a scenario where we do not use any manual labeling but directly learn classifiers from the image tags. The semi-supervised approach also improves classification accuracy in this case.
Carbon nanotube‐sensor‐integrated microfluidic platform for real‐time chemical concentration detection (2009)

This paper presents the development of a chemical sensor employing electronic-grade carbon nanotubes (EG-CNTs) as the active sensing element for sodium hypochlorite detection. The sensor, integrated in a PDMS-glass microfluidic chamber, was fabricated by bulk aligning of EG-CNTs between gold microelectrode pairs using dielectrophoretic technique. Upon exposure to sodium hypochlorite solution, the characteristics of the carbon nanotube chemical sensor were investigated at room temperature under constant current mode. The sensor exhibited responsivity, which fits a linear logarithmic dependence on concentration in the range of 1/32 to 8 ppm, a detection limit lower than 5 ppb, while saturating at 16 ppm. The typical response time of the sensor at room temperature is on the order of minutes and the recovery time is a few hours. In particular, the sensor showed an obvious sensitivity to the volume of detected solution. It was found that the activation power of the sensor was extremely low, i.e. in the range of nanowatts. These results indicate great potential of EG-CNT for advanced nanosensors with superior sensitivity, ultra-low power consumption, and less fabrication complexity.
Biotransformation of Various Alkanes Using theEscherichia coliExpressing an Alkane Hydroxylase System fromGordoniasp. TF6 (2004)

Biotransformation using alkane-oxidizing bacteria or their alkane hydroxylase (AH) systems have been little studied at the molecular level. We have cloned and sequenced genes from Gordonia sp. TF6 encoding an AH system, alkB2 (alkane 1-monooxygenase), rubA3 (rubredoxin), rubA4 (rubredoxin), and rubB (rubredoxin reductase). When expressed in Escherichia coli, these genes allowed the construction of biotransformation systems for various alkanes. Normal alkanes with 5 to 13 carbons were good substrates for this biotransformation, and oxidized to their corresponding 1-alkanols. Surprisingly, cycloalkanes with 5 to 8 carbons were oxidized to their corresponding cycloalkanols as well. This is the first study to achieve biotransformation of alkanes using the E. coli expressing the minimum component genes of the AH system. Our biotransformation system has facilitated assays and analysis leading to improvement of AH systems, and has indicated a cycloalkane oxidation pathway in microorganisms for the first time.
The importance of steroid hormones in prostate cancer. (1992)

Steroid hormones have an important role in prostate biology. Androgens are crucial for the normal development of the prostate gland and in maintaining its functional state in the adult. It seems that the prolonged presence of androgens might also be an important factor in the development of prostate cancer. In addition, androgens and oestrogens appear to play some part in the development of benign prostatic hyperplasia, although the exact nature of their role has not been clearly defined. Stimulation of prostate cancer growth by androgens is well established, with androgen withdrawal therapy constituting the most effective therapy in men with prostate cancer. Additive steroid therapy of metastatic prostate cancer with oestrogens or progestins has also proven effective. The effects of androgens on prostate cancer cell growth might be mediated through modulation of growth factor expression and alteration of growth factor receptor levels. Androgen response can be modulated by the expression of mutated oncogenes such as ras. Androgen independence can occur through a loss of AR expression or mutation of the AR; however, the patterns of AR expression in normal prostatic tissue from development to adulthood and in cancer are now just beginning to be described. Other steroids, such as the retinoids, show promise as preventive agents, possibly through the modulation of growth factors.
Prevalence of high blood cholesterol among US adults. An update based on guidelines from the second report of the National Cholesterol Education Program Adult Treatment Panel (1993)

Substantial progress has been made in reducing the prevalence of high blood cholesterol; yet a large proportion of all adults, approximately 29%, require dietary intervention for high blood cholesterol.
Conformational influence of the ribose 2'-hydroxyl group: Crystal structures of DNA-RNA chimeric duplexes (1993)

We have crystallized three double-helical DNA-RNA chimeric duplexes and determined their structures by X-ray crystallography at resolutions between 2 and 2.25 A. The two self-complementary duplexes [r(G)d(CGTATACGC)]2 and [d(GCGT)r(A)d(TACGC)]2, as well as the Okazaki fragment d(GGGTATACGC).r(GCG)d(TATACCC), were found to adopt A-type conformations. The crystal structures are non-isomorphous, and the crystallographic environments for the three chimeras are different. A number of intramolecular interactions of the ribose 2'-hydroxyl groups contribute to the stabilization of the A-conformation. Hydrogen bonds between 2'-hydroxyls and 5'-oxygens or phosphate oxygens, in addition to the previously observed hydrogen bonds to 1'-oxygens of adjacent riboses and deoxyriboses, are observed in the DNA-RNA chimeric duplexes. The crystalline chimeric duplexes do not show a transition between the DNA A- and B-conformations. CD spectra suggest that the Okazaki fragment assumes an A-conformation in solution as well. In this molecule the three RNA residues may therefore lock the complete decamer in the A-conformation. Crystals of an all-DNA strand with the same sequence as the self-complementary chimeras show a morphology which is different from those of the chimera crystals. Moreover, the oligonucleotide does not match any of the sequence characteristics of DNAs usually adopting the A-conformation in the crystalline state (e.g., octamers with short alternating stretches of purines and pyrimidines). In DNA-RNA chimeric duplexes, it is therefore possible that a single RNA residue can drive the conformational equilibrium toward the A-conformation.
Conceptual Stage in Designing Multimedia for Tele Learning (2001)

The design of educational WWW-based hypermedia is often seen as a process of gradually progressing from content into interaction design. In the final shaping of the hyperlinks, menus and orientation pages, too many decisions are normally made at the same time. This article presents a four-stage design process that gives more attention to the conceptual and metaphoric aspects to be covered. Schematic representations are proposed as the main devices to validate design steps. A repertoire of concept mapping tools is discussed. The full sequence of conceptual, metaphoric, structural and navigational design is finally integrated as a scaffolding method for project teams in WWW-based hypermedia developing projects. The conceptual exploration method was applied and evaluated in the 1977 Summer School of Nova University at Lauderdale, Florida.
Studies on Anti-inflammatory Agents. XXXI. Studies on the Synthesis and Anti-inflammatory Activity of Xanthenyl- and Benzopyranopyridinylacetic Acid Derivatives (1976)

A series of xanthenyl- and benzopyranopyridinylacetic acid derivatives were synthesized by various methods, and the relationship between their structure and anti-inflammatory activity was assayed by the method of ultraviolet erythema. It was thereby found that 2-(5H-[1]benzopyrano[2, 3-b]pyridin-7-yl)propionic acid (IV-2) had the most potent anti-inflammatory activity.
Enhancing Tolerance to Short-Chain Alcohols by Engineering the Escherichia coli AcrB Efflux Pump to Secrete the Non-native Substrate n-Butanol (2013)

The microbial conversion of sugars to fuels is a promising technology, but the byproducts of biomass pretreatment processes and the fuels themselves are often toxic at industrially relevant levels. One promising solution to these problems is to engineer efflux pumps to secrete fuels and inhibitory chemicals from the cell, increasing microbial tolerance and enabling higher fuel titer. Toward that end, we used a directed evolution strategy to generate variants of the Escherichia coli AcrB efflux pump that act on the non-native substrate n-butanol, enhancing growth rates of E. coli in the presence of this biofuel by up to 25%. Furthermore, these variants confer improved tolerance to isobutanol and straight-chain alcohols up to n-heptanol. Single amino acid changes in AcrB responsible for this phenotype were identified. We have also shown that both the chemical and genetic inactivation of pump activity eliminate the tolerance conferred by AcrB pump variants, supporting our assertion that the variants secrete the non-native substrates. This strategy can be applied to create an array of efflux pumps that modulate the intracellular concentrations of small molecules of interest to microbial fuel and chemical production.
Hardware/software partitioning for multi-function systems (1997)

We are interested in optimizing the design of multi-function embedded systems that run a pre-specified set of applications, such as multi-standard audio/video codecs and multi-system phones. Such systems usually have stringent performance constraints and tend to have mixed hardware-software implementations. The current state of the art in the hardware/software codesign of such systems is to design for each application separately. This often leads to application-specific sub-optimal decisions and inconsistent mappings of nodes in different applications. We use these as the guiding principles to formulate, as a codesign problem, the design and synthesis of an efficient hardware-software implementation for a multi-function embedded system. Our solution methodology is to first identify nodes that represent similar functionality across different applications. Such common nodes are characterized by several metrics. These metrics are quantified and used by a hardware/software partitioning tool to map nodes to the same resource as far as possible. We demonstrate how this is achieved by modifying a traditional partitioning algorithm (GCLP) used to partition single applications. The overall result of the system-level partitioning process is (1) a hardware or software mapping and (2) a schedule for execution for each node within the application set. On an example set consisting of three video applications, we show that the solution obtained by the use of our method is 38% smaller than that obtained when each application is considered independently.
A fast encoding method for lattice codes and quantizers (1983)

In an earlier paper the authors described a very fast method which, for the root lattices <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">A_{n}, D_{n}, E_{n}</tex> , their duals and certain other lattices, finds the closest lattice point to an arbitrary point of the underlying space. If the lattices are used as codes for a Gaussian channel, the algorithm provides a fast decoding procedure, or if they are used as vector quantizers the algorithm performs the analog-to-digital conversion efficiently. The present paper offers a solution to the inverse problem for the same lattices (the encoding problem for channel codes or the digital-to-analog part of quantizing), namely, given an integer <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</tex> , to find the kth code vector, and to the closely related problem of finding the index <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</tex> of a given code vector.
Functional correlates of α2A-adrenoceptor gene polymorphism in the HANE study (1999)

We propose that alleles at the alpha(2A)-adrenoceptor locus might contribute to interindividual differences in the regulation of human lipid and glucose metabolism.