gebhart/patrepeval huggingface dataset:
Towards fast solid state DNA sequencing (2003)

The current most widely used method for DNA sequencing is the chain termination method or Sanger technique. Many attempts are being made to improve upon this method particularly with regard to the elimination of the latter stage of electrophoresis. Using the ion sensitive field effect transistor and low power signal processing techniques, the possibility of intelligent solid state DNA sequencing is explored.
Utility of KL-6/MUC1 in the clinical management of interstitial lung diseases (2012)

Interstitial lung diseases (ILDs) are a diverse group of pulmonary disorders characterized by various patterns of inflammation and fibrosis in the interstitium of the lung. Because injury and/or regeneration of type II pneumocytes are prominent histological features of ILDs, substances derived from type II pneumocytes have been the focus of research investigating potential biomarkers for ILD. One important biomarker for ILD is the high-molecular-weight glycoprotein, Krebs von den Lungen-6 (KL-6). KL-6 is now classified as a human MUC1 mucin protein, and regenerating type II pneumocytes are the primary cellular source of KL-6/MUC1 in the affected lungs of patients with ILD. KL-6/MUC1 is detectable in the serum of patients with ILD, and extensive investigations performed primarily in Japan have revealed that serum KL-6/MUC1 is elevated in 70-100% of patients with various ILDs, including idiopathic interstitial pneumonias, collagen vascular disease-associated interstitial pneumonia, hypersensitivity pneumonia, radiation pneumonitis, drug-induced ILDs, acute respiratory distress syndrome, pulmonary sarcoidosis, and pulmonary alveolar proteinosis. The results from these various studies have supported the utility of KL-6/MUC1 as a serum biomarker for detecting these various ILDs. Moreover, KL-6/MUC1 serum levels have been demonstrated to be useful for evaluating disease activity and predicting the clinical outcomes of various ILD types. Based on these observations, we believe that KL-6/MUC1 is currently one of the best and most reliable serum biomarkers available for ILD management.
Targeting Cancer: The Challenges and Successes of Structure-Based Drug Design Against the Human Purinome (2006)

Purine-binding proteins are of critical importance to all living organisms. Approximately 13% of the human genome is devoted to coding for purine-binding proteins. Given their importance, purine-binding proteins are attractive targets for chemotherapeutic intervention against a variety of disease states, particularly cancer. Modern computational and biophysical techniques, combined together in a structure-based drug design approach, aid immensely in the discovery of inhibitors of these targets. This review covers the process of modern structure-based drug design and gives examples of its use in discovery and development of drugs that target purine-binding proteins. The targets reviewed are human purine nucleoside phosphorylase, human epidermal growth factor receptor kinase, and human kinesin spindle protein.
Construction, characterization, and mammalian expression of an immunotoxin consisting of ranpirnase (Rap) fused to a humanized anti-EGP-1 antibody, hRS7, as a potential therapeutic for prostate cancer (2005)

679 Introduction: We describe construction, expression and characterization of a novel immunotoxin involving ranpirnase (Rap), an amphibian ribonuclease (RNase) isolated from the oocytes of Rana pipiens (Northern leopard frog), as the toxin moiety, and an internalizing humanized monoclonal antibody (mAb), hRS7, as the tumor-targeting agent. Rap is a single-chain protein of 104 amino acids (MW ∼12 kDa) exhibiting cytostatic and cytotoxic effects on a variety of tumor cell lines in vitro as well as antitumor activity in vivo. Previous studies indicated that cytotoxicity of Rap is enhanced more than 10,000-fold when the enzyme is chemically conjugated to an internalizing antibody. The murine mAb RS7-3G11 reacts with epithelial glycoprotein-1 (EGP-1). A high frequency of EGP-1 expression has been observed in a variety of tumor types, including lung, stomach, bladder, breast, ovary, uterus and prostate, with limited presence on normal human tissues. The intended therapeutic application for the immunotoxin is prostate cancer. The Rap molecule contains a putative glycosylation site N69-V70-T71, and when it is expressed in mammalian cultures, the Rap molecule is glycosylated. To obtain a non-glycosylated form of Rap, N69 has been mutated to Q. The basic design of the immunotoxin, 2L-Rap(N69Q)-hRS7-γ1, consists of two N69Q-mutated Rap molecules, each connected via a flexible linker to the N-terminus of one light chain of the hRS7 antibody. Methods: The Rap gene was inserted at the N-terminus of the light chain in the expression vector of hRS7. Sp2/0 mouse myeloma cells were transfected, and positive clones were identified by ELISA screening. The fusion protein was purified by protein A column chromatography and characterized by a variety of techniques, including SE-HPLC, SDS-PAGE, and an in vitro transcription translation (IVTT) assay using the luciferase reporter system. Results: The purified protein was shown to be a single peak by SE-HPLC. The EC50 of RNase activity, as measured by the IVTT assay, was 1400 pM for 2L-Rap(N69Q)-hRS7 and 30 pM for free Rap. Conclusion: A novel immunotoxin for targeting prostate cancer has been developed and expressed in a mammalian system. This will now permit testing in appropriate prostate cancer systems.
Percutaneous splanchnic nerve radiofrequency ablation for chronic abdominal pain (2005)

Although preliminary data regarding RFA ablation of splanchnic nerves are encouraging, further trials are also needed comparing percutaneous splanchnic nerve ablation with opioid analgesia and coeliac plexus blockade.
PCRless library mutagenesis via oligonucleotide recombination in yeast (2010)

The directed evolution of biomolecules with new functions is largely performed in vitro, with PCR mutagenesis followed by high-throughput assays for desired activities. As synthetic biology creates impetus for generating biomolecules that function in living cells, new technologies are needed for performing mutagenesis and selection for directed evolution in vivo. Homologous recombination, routinely exploited for targeted gene alteration, is an attractive tool for in vivo library mutagenesis, yet surprisingly is not routinely used for this purpose. Here, we report the design and characterization of a yeast-based system for library mutagenesis of protein loops via oligonucleotide recombination. In this system, a linear vector is co-transformed with single-stranded mutagenic oligonucleotides. Using repair of nonsense codons engineered in three different active-site loops in the selectable marker TRP1 as a model system, we first optimized the recombination efficiency. Single-loop recombination was highly efficient, averaging 5%, or 4.0×10(5) recombinants. Multiple loops could be simultaneously mutagenized, although the efficiencies dropped to 0.2%, or 6.0×10(3) recombinants, for two loops and 0.01% efficiency, or 1.5×10(2) recombinants, for three loops. Finally, the utility of this system for directed evolution was tested explicitly by selecting functional variants from a mock library of 1:10(6) wild-type:nonsense codons. Sequencing showed that oligonucleotide recombination readily covered this large library, mutating not only the target codon but also encoded silent mutations on either side of the library cassette. Together these results establish oligonucleotide recombination as a simple and powerful library mutagenesis technique and advance efforts to engineer the cell for fully in vivo directed evolution.
Packet-switched on-chip interconnection network for system-on-chip applications (2005)

Increasing complexity of a system-on-chip design demands efficient on-chip interconnection architecture such as on-chip network to overcome limitations of bus architecture. In this brief, we propose a packet-switched on-chip interconnection network architecture, through which multiple processing units of different clock frequencies can communicate with each other without global synchronization. The architecture is analyzed in terms of area and energy consumption, and implementation issues on building blocks are addressed for cost-effective design. A test chip is implemented using 0.38-/spl mu/m CMOS technology, and measured its operation at 800 MHz to demonstrate its feasibility.
Homeostasis and Self-Tolerance in the Immune System: Turning Lymphocytes off (1998)

The immune system responds in a regulated fashion to microbes and eliminates them, but it does not respond to self-antigens. Several regulatory mechanisms function to terminate responses to foreign antigens, returning the immune system to a basal state after the antigen has been cleared, and to maintain unresponsiveness, or tolerance, to self-antigens. Here, recent advances in understanding of the molecular bases and physiologic roles of the mechanisms of immune homeostasis are examined.
Fuzzy Logic and Neural Network Control Systems for Backing up a Truck and a Trailer (2011)

Today, computer control systems have achieved a highest position of their applicability through large scale industries to smaller activities such as controlling a movement of an object. Especially many researches are being carried out to develop control systems to automate the movements of vehicles as it is performed by a human being. This paper presents control systems to control the backing up motion of a truck and trailer vehicle into a particular location such as a loading dock. Salient feature of these systems is that it can be applied to any vehicle system which has a trailer attached to it. Two separate control systems are used to achieve the desired goal. In the first approach, the system uses fuzzy logic while the second approach uses an artificial neural network for the same purpose. The proposed controllers are tested for different initial positions and orientations of the truck and the trailer using a simulation model implemented with the MATLAB tool boxes. Comparisons of the results obtained are also presented. Under the conditions considered for the simulation it is observed that the fuzzy logic based control system is capable of controlling the vehicle within a larger area than that of the neural network based control system.
Total Syntheses of 2,4-Diamino-2,4-dideoxy-l-arabinose and 2,4-Diamino-2,4-dideoxy-l-ribose (1996)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTTotal Syntheses of 2,4-Diamino-2,4-dideoxy-l-arabinose and 2,4-Diamino-2,4-dideoxy-l-ribosePaola Soro, Gloria Rassu, Pietro Spanu, Luigi Pinna, Franca Zanardi, and Giovanni CasiraghiView Author Information Istituto per l'Applicazione delle Tecniche Chimiche Avanzate del CNR, Via Vienna 2, I-07100 Sassari, Italy, Dipartimento di Chimica dell'Università, Via Vienna 2, I-07100 Sassari, Italy, and Dipartimento Farmaceutico dell'Università, Viale delle Scienze, I-43100 Parma, Italy Cite this: J. Org. Chem. 1996, 61, 15, 5172–5174Publication Date (Web):July 26, 1996Publication History Received6 February 1996Published online26 July 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/jo960246fhttps://doi.org/10.1021/jo960246fbrief-reportACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views236Altmetric-Citations18LEARN 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 SUBJECTS:Amides,Carbohydrates,Nitrogen,Reaction products,Reagents Get e-Alerts
The principal axes transformation--a method for image registration. (1990)

We have developed a computational technique suitable for registration of sets of image data covering the whole brain volume which are translated and rotated with respect to one another. The same computational method may be used to register pairs of tomographic brain images which are rotated and translated in the transverse section plane. The technique is based on the classical theory of rigid bodies, employing as its basis the principal axes transformation. The performance of the method was studied by simulation and with image data from PET, XCT, and MRI. It was found that random errors in determining the brain contour are well tolerated. Progressively coarser axial sampling of data sets led to some degradation, but acceptable performance was obtained with axial sampling distances up to 10 mm. Given adequate digital sampling of the object volume, we conclude that registration by the principal axes transformation can be accomplished with typical errors in the range of approximately 1 mm. The advantages of the technique are simplicity and speed of computation.
[Traumatic hyphema caused by eye injuries]. (2005)

Hyphema is a common consequence of mechanical ocular trauma. Blood in the anterior chamber (hyphema)can occur after blunt or lacerating trauma. Traumatic hyphema is a diagnostic and therapeutic emergency. Major complications of hyphema include secondary hemorrhage, secondary glaucoma, corneal staining and disturbances in visual acuity. The aim of our study was the retrospective analysis of patients with posttraumatic hyphema. According to a prospective protocol we studied 428 patients who were examined and treated at the Emergency Department of Department of Ophthalmology Medical University of Gdansk between 1998-2004 years (ears). Data obtained included age and sex. 81% of patients were man, 19% of patients were women. Mean age of patients with ocular hyphema 6-72 years. We determined initial and final visual acuities (visual acuity - distance Snellen acuity test), intraocular pressure measurement, biomicroscopy, fundus indirect ophthalmology, gonioscopy and US- examinations (sometimes). Data obtained also were: slitlamp examinations for hyphema size, hyphema grading and corneal clarity. Most hyphemas were small, occupying less than one- third of the volume of the anterior chamber. The most common associated injuries to the eye hyphema included corneal oedema, glaucoma (secondary glaucoma), cataract and mydriasis. Traumatic hyphema is therapeutic emergency. More preventive efforts (hospitalization) were necessary, especially for children. In our study we observed 89% patients with traumatic hyphema due to non - penetrating eye injury. The assault were responsible for hyphema in 30.1% of cases and traffic accidents in 38.7% of all hyphemas. Treatment of the hyphema is generally topical. Outcome is good (in more cases), if medical treatment was quickly instituted. Surgical treatment must be reserved for a special cases, but it needs more further investigations.
Efflux Pump Blockers in Gram-Negative Bacteria: The New Generation of Hydantoin Based-Modulators to Improve Antibiotic Activity (2016)

Multidrug resistant (MDR) bacteria are an increasing health problem with the shortage of new active antibiotic agents. Among effective mechanisms that contribute to the spread of MDR Gram-negative bacteria are drug efflux pumps that expel clinically important antibiotic classes out of the cell. Drug pumps are attractive targets to restore the susceptibility toward the expelled antibiotics by impairing their efflux activity. Arylhydantoin derivatives were investigated for their potentiation of activities of selected antibiotics described as efflux substrates in Enterobacter aerogenes expressing or not AcrAB pump. Several compounds increased the bacterial susceptibility toward nalidixic acid, chloramphenicol and sparfloxacin and were further pharmacomodulated to obtain a better activity against the AcrAB producing bacteria.
Bulk superconductivity at 36 K inLa1.8Sr0.2CuO4 (1987)

We report the results of resistivity and magnetic susceptibility measurements in ${\mathrm{La}}_{2\mathrm{\ensuremath{-}}\mathrm{x}}$${\mathrm{Sr}}_{\mathrm{x}}$${\mathrm{CuO}}_{4}$ for x\ensuremath{\le}0.3. The x=0.2 sample shows a superconducting transition at 36.2 K with a width of 1.4 K. The associated dc diamagnetic susceptibility (Meissner effect) is a large fraction (60%--70%) of the ideal value. We estimate the density of states from critical-field and resistivity data and suggest, by analogy to ${\mathrm{BaPb}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$${\mathrm{Bi}}_{\mathrm{x}}$${\mathrm{O}}_{3}$, that conventional phonon-mediated superconductivity can account for the high ${\mathrm{T}}_{\mathrm{c}}$ in this class of materials.
Activation of ATP-sensitive K+(KATP) channels by H2O2underlies glutamate-dependent inhibition of striatal dopamine release (2003)

In many cells, ATP-sensitive K+ channels (KATP channels) couple metabolic state to excitability. In pancreatic beta cells, for example, this coupling regulates insulin release. Although KATP channels are abundantly expressed in the brain, their physiological role and the factors that regulate them are poorly understood. One potential regulator is H2O2. We reported previously that dopamine (DA) release in the striatum is modulated by endogenous H2O2, generated downstream from glutamatergic alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-receptor activation. Here we investigated whether H2O2-sensitive KATP channels contribute to DA-release modulation by glutamate and gamma-aminobutyric acid (GABA). This question is important because DA-glutamate interactions underlie brain functions, including motor control and cognition. Synaptic DA release was evoked by using local electrical stimulation in slices of guinea pig striatum and monitored in real time with carbon-fiber microelectrodes and fast-scan cyclic voltammetry. The KATP-channel antagonist glibenclamide abolished the H2O2-dependent increase in DA release usually seen with AMPA-receptor blockade by GYKI-52466 [1-(4-aminophenyl)-4-methyl-7,8-methylenedioxy-5H-2,3-benzodiazepine hydrochloride] and the decrease in DA release seen with GABA-type-A-receptor blockade by picrotoxin. In contrast, 5-hydroxydecanoate, a mitochondrial KATP-channel blocker, was ineffective, as were sulpiride, a D2-receptor antagonist, and tertiapin, a G protein-coupled K+-channel inhibitor. Diazoxide, a sulfonylurea receptor 1 (SUR1)selective KATP-channel opener, prevented DA modulation by H2O2, glutamate, and GABA, whereas cromakalim, a SUR2-selective opener, did not. Thus, endogenous H2O2 activates SUR1-containing KATP channels in the plasma membrane to inhibit DA release. These data not only demonstrate that KATP channels can modulate CNS transmitter release in response to fast-synaptic transmission but also introduce H2O2 as a KATP-channel regulator.
Immune complex–FcγR interaction modulates monocyte/macrophage molecules involved in inflammation and immune response (2003)

The interaction between receptors for the Fc portion of IgG (FcgammaRs) from monocytes/macrophages and immune complexes (IC) triggers regulatory and effector functions. Recently, we have demonstrated that IC exert a drastic inhibition of basal and IFN-gamma-induced expression of MHC class II on human monocytes. Taking into account that the regulation of MHC class II molecules is a crucial event in the immune response, in this report we extend our previous studies analysing the effect of STAT-1 phosphorylation in the down-regulatory process, the fate of the intracellular pool of MHC class II molecules and the effect of complement on MHC class II down-regulation induced by IC. We also studied the effect of IC on the expression of MHC class II (I-A(d)) in macrophages using a mouse model of chronic inflammation. We demonstrate that IC induce a depletion not only on surface expressed but also on intracellular MHC class II content and that IC-induced down-regulation of MHC class II is not mediated by the inhibition of STAT-1 phosphorylation. On the other hand, the effect of IC is not specific for the down-regulation of MHC class II, for it could be restricted to other molecules involved in inflammatory processes. Our experiments also show that the activation of the complement system could be a crucial step on the regulation of the effect of IC on MHC class II expression. In agreement with our in vitro experiments using human monocytes, IC treatment reduces the expression of MHC class II in a mouse model of chronic inflammation.
Isolation, purification, and alteration of some functional groups of major milk proteins: A review (1997)

This review covers selected methods of isolation and purification of mainly alpha s-casein, beta-casein, kappa-casein, beta-lactoglobulin, and alpha-lactalbumin. Selected methods of alteration of some functional groups of these proteins also were reviewed. Isolation and purification of milk proteins per se are methods of modifying the individual milk proteins. Gram quantities of these proteins can now be purified in a relatively short time using ion-exchange resins. Due to the prominent use of non-food-grade reagents in the procedures for preparation of these milk proteins, individual proteins are not maximally utilized for the manufacture of food/feed and pharmaceutical products. Therefore, intensive research efforts are needed to obviate the problems associated with underutilization of milk proteins.
Systematic classification of vertebrate chemokines based on conserved synteny and evolutionary history (2012)

The genes involved in host defences are known to undergo rapid evolution. Therefore, it is often difficult to assign orthologs in multigene families among various vertebrate species. Chemokines are a large family of small cytokines that orchestrate cell migration in health and disease. Herein, we have surveyed the genomes of 18 representative vertebrate species for chemokine genes and identified a total of 553 genes. We have determined their orthologous relationships and classified them in accordance with the current systematic chemokine nomenclature system. Our study reveals an interesting evolutionary history that gave origin and diversification to the vertebrate chemokine superfamily.
The endophytic fungus Piriformospora indica reprograms barley to salt-stress tolerance, disease resistance, and higher yield (2005)

Disease resistance strategies are powerful approaches to sustainable agriculture because they reduce chemical input into the environment. Recently, Piriformospora indica, a plant-root-colonizing basidiomycete fungus, has been discovered in the Indian Thar desert and was shown to provide strong growth-promoting activity during its symbiosis with a broad spectrum of plants. Here, we report on the potential of P. indica to induce resistance to fungal diseases and tolerance to salt stress in the monocotyledonous plant barley. The beneficial effect on the defense status is detected in distal leaves, demonstrating a systemic induction of resistance by a root-endophytic fungus. The systemically altered "defense readiness" is associated with an elevated antioxidative capacity due to an activation of the glutathione-ascorbate cycle and results in an overall increase in grain yield. Because P. indica can be easily propagated in the absence of a host plant, we conclude that the fungus could be exploited to increase disease resistance and yield in crop plants.