gebhart/patrepeval huggingface dataset:
A high-throughput screen of inactive X chromosome reactivation identifies the enhancement of DNA demethylation by 5-aza-2′-dC upon inhibition of ribonucleotide reductase (2015)

Taken together, our study identifies a drug combination that enhances DNA demethylation by altering nucleotide metabolism. This demonstrates that Xi-reactivation assays can be used to optimize the epigenetic activity of drug combinations.
The development of the quartz crystal oscillator industry of World War II (2005)

This paper offers a history of a critical episode in military and electronics history-the difficult creation of quartz crystal frequency control units for radio communications during World War II. As a means of controlling the frequencies of radio transmitters and receivers, amateur radio hobbyists quickly accepted the quartz crystal oscillator after its initial development in the late 1920s. The military, however, declined to adopt this technology until just prior to World War II. Due to the small market for crystal oscillators, no mass production industry had ever developed to produce this extremely high precision electronic component. As war engulfed the nation, the U.S. Army Signal Corps found itself in the dangerous position of having gambled the integrity of its communications equipment on a component that could not possibly be produced in the quantities immediately needed. This paper looks at the challenges the United States faced in building a crystal manufacturing capability and in supplying this industry with sufficient supplies of raw quartz. A fairly specialized component of communications technology emerged from spare beginnings in prewar amateur radio to become the very foundation of a wide range of electronic devices today.
Recombinant human erythropoietin. (1989)

The characteristics and uses of epoetin alfa (recombinant human erythropoietin) are described, and the issues associated with its use are discussed. The use of epoetin alfa was recently approved by FDA for the treatment of anemia associated with end-stage renal disease. Epoetin alfa acts on burst-forming and colony-stimulating units in the blood to raise hemoglobin and hematocrit levels, thus correcting the patient's anemia. It has a relatively short half-life and may be given either i.v. or s.c. Doses vary and must be adjusted according to the individual patient response. Clinical trials have involved doses ranging from 15 to 500 units/kg three times per week. Treatment causes a dose-related rise in the hematocrit, with subsequent improvement in the quality of life of dialysis patients. Adverse effects include hypertension, iron deficiency, and thrombocytosis. Additional research indicates that epoetin alfa may be effective in the correction of other uncomplicated anemias, such as those related to antineoplastic therapy. Issues facing hospital pharmacists and other health-care professionals include cost (the estimated cost of therapy is $4000 to $8000 per patient per year), appropriate use and potential misuse, use and reimbursement for indications not included in FDA-approved labeling, and restriction to particular prescribers. Because epoetin alfa does not produce therapeutic effects for at least 7 to 14 days, it is an ideal agent for formulary restriction. Epoetin alfa, like other products of biotechnology, will have substantial impact, both therapeutic and economic, on the practice of pharmacy. Hospital pharmacists need to be aware of these new therapies so that they may act quickly and decisively when issues associated with their use arise.
The thermodynamics and kinetics of electron transfer in the cytochrome P450<sub>cam</sub> enzyme system (1999)

In anaerobic environments the first electron transfer in substrate-free P450cam is known to be thermodynamically unfavourable, but in the presence of dioxygen the reduction potential for the reaction shifts positively to make electron transfer thermodynamically favourable. Nevertheless a slower rate of electron transfer is observed in the substrate-free P450cam compared to substrate-bound P450cam. The ferric haem centre in substrate-free P450cam changes from six co-ordinate to five co-ordinate when reduced whereas in substrate-bound P450cam the iron centre remains five co-ordinate in both oxidation states. The slower rate of electron transfer in the substrate-free P450cam is therefore attributed to a larger reorganisation energy as predicted by Marcus theory.
Transcriptional and posttranscriptional regulation of β<sub>2</sub>-adrenergic receptor gene in rat liver during sepsis (1999)

Changes in beta(2)-adrenergic receptor (beta(2)-AR) gene expression in the rat liver during different phases of sepsis were studied. Sepsis was induced by cecal ligation and puncture (CLP). Septic rats exhibit two metabolically distinct phases: an initial hyperglycemic (9 h after CLP; early sepsis) followed by a hypoglycemic phase (18 h after CLP; late sepsis). The [(3)H]dihydroalprenolol binding studies show that the density of beta(2)-AR was decreased by 12 and 35% during the early and late phases of sepsis, respectively. Western blot analyses depict that the beta(2)-AR protein level was reduced by 37 and 72% during early and late sepsis, respectively. The reverse transcription polymerase chain reaction and Southern blot analyses reveal that the steady-state level of beta(2)-AR mRNA was decreased by 37% during early phase and 77% during late phase of sepsis. Nuclear run-off assays show that the rate of transcription of beta(2)-AR mRNA was reduced by 36% during early sepsis and 64% during late sepsis. The stability assays indicate that the half-life of beta(2)-AR mRNA was shortened by 21 and 50% during the early and late phases of sepsis, respectively, indicating that the rate of degradation of beta(2)-AR mRNA was progressively enhanced during sepsis. These findings demonstrate that the beta(2)-AR gene was underexpressed in the liver during the progression of sepsis, and, furthermore, the underexpression of the beta(2)-AR gene was the result of a reduction in the rate of transcription coupled with an enhancement in the rate of degradation of beta(2)-AR gene transcripts. Thus our findings that the transcriptional and posttranscriptional regulation of beta(2)-AR gene associated with decreases in beta(2)-AR number and its protein expression may provide a molecular mechanistic explanation for the development of hypoglycemia during the late stage of sepsis.
Analysis of structural changes in plasma-deposited fluorinated silicon dioxide films caused by fluorine incorporation using ring-statistics based mechanism (1999)

Fluorinated silicon dioxide (SiOF) films were prepared by remote plasma enhanced chemical vapor deposition using SiF4, O2, H2, and He reaction gases. Fourier transform infrared spectroscopy studies accompanied by molecular orbital (MO) modeling were used to explain structural changes in SiOF films caused by F incorporation. On the basis of the results of MO modeling, it was shown that F atoms incorporated into the SiOF network only slightly affect the geometry of ring units, the main building blocks of SiOF film network, and cannot cause strong changes in the value of the average Si–O–Si angle, 〈θ〉. Ring-statistics-based mechanism is proposed to explain the increase in 〈θ〉 in SiOF films with F content. It is supposed that interaction of highly reactive F species from the incoming flux with the growing SiOF network during deposition process induces the preferential conversion of the most strained small-order ring units into those of higher order characterized by larger 〈θ〉. As a result, the 〈θ〉 in SiOF film increases and film structural homogeneity improves with increasing the F content in the incoming flux. It is assumed that structural changes in SiOF films caused by F incorporation are not the abrupt transition from the ring-built SiOF network to the ring-free chain-like network, but a continuous shift of the ring distribution function towards the large-size high-order rings which causes the increase in 〈θ〉 within SiOF network, a reduction in the film density, and an enhancement of the film moisture absorptivity.
Therapeutic Potential of KELEA Activated Water (2015)

For over a century, the goal of therapeutic medicine has been to specifically correct the biochemical abnormalities identifiable in diseased cells by using pharmaceutical drugs. The amounts of drug prescribed are consistent with direct biochemical effects on the diseased cells. By contrast, homeopathy claims that sub-biochemical amounts of various drugs can also have specific beneficial effects. A different interpretation of homeopathy is offered in this article. It is that homeopathy does not have the specificity claimed by its proponents, yet can be therapeutic by enhancing the body’s alternative cellular energy (ACE) pathway. It is proposed that effective homeopathic liquid formulations are characterized by an enhanced kinetic activity resulting from the absorption of an environmental force termed KELEA (Kinetic Energy Limiting Electrostatic Attraction). Various diluted herbal tinctures are able to transfer KELEA into water; a process facilitated by succussion (repeated jolting). Once water is sufficiently activated it can then directly absorb KELEA from the environment leading to its further activation and to the potential energy transfer to added water. It can similarly be used to provide KELEA to the body’s fluids and, thereby, enhance the body’s ACE pathway.
Secretory expression of biologically active human Herpes virus interleukin-10 analogues in Escherichia colivia a modified Sec-dependent transporter construct (2013)

In this study, proof of principle is provided that E. coli cells are a suitable chassis for secretory expression of viral IL-10 cytokines encoded by codon-optimized synthetic genes fused to the E. coli ompF signal sequence. In vitro biological activity evidenced by activation of transcription factor STAT3 and suppression of TNF-α in mammalian cell lines was shown to be strictly dependent on export of viral IL-10 proteins into the periplasmic compartment. E. coli might serve as carrier system for in situ delivery of therapeutic molecules in the gut, thus representing a further step in the development of novel approaches for treatment of IBD.
Genetic Algorithms for Solving a Class of Constrained Nonlinear Integer Programs (2001)

We consider a class of constrained nonlinear integer programs, which arise in manufacturing batch‐sizing problems with multiple raw materials. In this paper, we investigate the use of genetic algorithms (GAs) for solving these models. Both binary and real coded genetic algorithms with six different penalty functions are developed. The real coded genetic algorithm works well for all six penalty functions compared to binary coding. A new method to calculate the penalty coefficient is also discussed. Numerical examples are provided and computational experiences are discussed.
Acoustically detectable cellular-level lung injury induced by fluid mechanical stresses in microfluidic airway systems (2007)

We describe a microfabricated airway system integrated with computerized air-liquid two-phase microfluidics that enables on-chip engineering of human airway epithelia and precise reproduction of physiologic or pathologic liquid plug flows found in the respiratory system. Using this device, we demonstrate cellular-level lung injury under flow conditions that cause symptoms characteristic of a wide range of pulmonary diseases. Specifically, propagation and rupture of liquid plugs that simulate surfactant-deficient reopening of closed airways lead to significant injury of small airway epithelial cells by generating deleterious fluid mechanical stresses. We also show that the explosive pressure waves produced by plug rupture enable detection of the mechanical cellular injury as crackling sounds.
Electromagnetic navigation in medicine – basic issues, advantages and shortcomings, prospects of improvement (2010)

This paper presents most essential problems related to electromagnetic navigation (EM) systems employed in medicine. The principle of operation of the EM navigation system, advantages of the method, requirements imposed and disadvantages of commercially available solutions have been presented. Possibilities of improvement of metrological and usable properties of such systems have been shown. The most important part of the paper is a proposal for modifications allowing significant improvement of the system operation and its capabilities. The effectiveness of these improvements has been investigated using a computer model and, partially, also the physical model of the system. The problem of distortions of magnetic field distribution caused by the presence of conducting and magnetic objects is also discussed.
Endogenous human stem cell-associated retroviruses (2015)

Abstract Recent discoveries of endogenous human stem cell-associated retroviruses (SCARs) revealed consistent activation of specific endogenous retroviral elements in human preimplantation embryos and documented the essential role of the sustained retroviral activities in the maintenance of pluripotency, functional identity and integrity of naïve-state embryonic stem cells, and anti-viral resistance of the early-stage human embryos. SCARs activity have been implicated in seeding thousands’ human-specific regulatory sequences in the hESC genome. Activation of specific SCARs, namely LTR7/HERVH and LTR5_Hs/HERVK, has been demonstrated in patients diagnosed with multiple types of cancer, autoimmune diseases, neurodegenerative disorders and it is likely associated with the emergence of clinically lethal therapy resistant death-from-cancer phenotypes in a sub-set of cancer patients diagnosed with different types of malignant tumors.
Time-lapse (4-D) seismic monitoring of primary production of turbidite reservoirs at South Timbalier Block 295, offshore Louisiana, Gulf of Mexico (2000)

Abstract Two seismic surveys acquired over South Timbalier Block 295 field (offshore Louisiana) record significant differences in amplitude that are correlated to hydrocarbon production at multiple reservoir levels. The K8 sand, a solution-gas-drive reservoir, shows increases in seismic amplitude associated with gas exsolution. The K40 sand, a water-drive reservoir, shows decreases in seismic amplitude associated with increases in water saturation. A methodology is presented to optimize the correlation between two seismic surveys after they have been individually processed (poststack). This methodology includes rebinning, crosscorrelation, band-pass filtering, and cross-equalization. A statistical approach is developed to characterize the correlation between the seismic surveys. This statistical analysis is used to discriminate seismic amplitude differences that record change in rock and fluid properties from those that could be the result of miscorrelation of the seismic data. Time-lapse seismic analysis provides an important new approach to imaging hydrocarbon production; it may be used to improve reservoir characterization and guide production decisions.
<b>Target genes and regulatory domains of the GAMYB transcriptional activator in cereal aleurone</b> (1999)

GAMYB is an MYB transcription factor which is expressed in cereal aleurone cells in response to gibberellin (GA). HvGAMYB binds to the TAACAAA box of a high-pl alpha-amylase gene promoter and transcriptionally activates its expression. In this study, we examined the role of HvGAMYB in activating expression of other GA-regulated genes encoding hydrolytic enzymes. In transient expression experiments, HvGAMYB transactivated expression of reporter genes fused to a low-pl alpha-amylase gene promoter, an EII (1-3, 1-4)-beta-glucanase gene promoter and a cathepsin B-like protease promoter. HvGAMYB DNA binding specificity was determined using a PCR-based random site selection using HvGAMYB fusion protein isolated from E. coli. The deduced consensus closely resembled gibberellin response elements in alpha-amylase promoters. Functional analysis of HvGAMYB by transient expression of C terminal HvGAMYB deletions in barley aleurone cells identified two transcriptional activation domains (TADs) which function in transcriptional regulation of both high- and low-pl alpha-amylase promoters. The same TADs were identified using a heterologous yeast expression system. Together, these results indicate that HvGAMYB has two TADs. These domains are C-terminal to its DNA-binding domain.
Semantic Interoperability Between Relational Database Systems (2007)

Relational database systems (RDBSs) are well-known and widely used in many organizations, however, semantic conflicts between the participating RDBSs must be resolved before data can be exchanged between them. Semantic resolution between the RDBSs is extremely difficult to address mainly because participating RDBSs are designed and built independently. Furthermore, individual RDBSs are likely to evolve over time and the changes must be reconciled dynamically. In this paper, we describe an approach to resolve the semantic conflicts between RDBSs automatically while allowing the individual RDBSs to evolve. Relational database ontology (RDBO) is created and used to ensure the semantic descriptions of the individual RDBSs are conformed to a set of vocabularies, structures, and restrictions. We show how a modified reasoning engine is used to validate and infer additional semantic relationships from the existing relationships. We also show how terms defined in different database ontologies are compared to each other semantically using semantic weights and our modified reasoning engine. As a result, RDBSs can intemperate with each other seamlessly and at the correct level of semantics defined in their ontologies.
Fabrication of Thermoresponsive Nanofibers for Cell Sorting and Aligned Cell Sheet Engineering (2016)

Poly(N-isopropylacrylamide-co-N-hydroxysuccinimide ester) was synthesized by free radical polymerization followed by gelatin grafting to obtain biocompatible thermosensitive poly(N-isopropylacrylamide-co-N-hydroxysuccinimide ester)-g-gelatin. Electrospinning was then applied to fabricate aligned thermoresponsive poly(N-isopropylacrylamide-co-N-hydroxysuccinimide ester)-g-gelatin nanofiber mats. Cell coculture study showed that this kind of nanofiber mats performed different surface adhesion to rat fibroblast cells and phoenix cells at 37 degrees C, phoenix cells can then be sorted out firstly by gradient cooling treatment. The fibroblast cells that had attached on the nanofiber mats were allowed to proliferate to reach confluence. These fibroblast cells tended to elongate along with the oriented direction of the nanofibers during culture and finally formed oriented cell sheets. This kind of aligned cell sheet could easily detach from nanofiber mats by low temperature treatment. This technique is simple and can easily harvest target cells and aligned cell sheets with minimum invasion, which has the potential to be applied in tissue engineering and regenerative medicine.
Top requirements on the SD-WAN security checklist (2017)

Any significant network upgrade presents a challenge for CIOs and CISOs. So much can go wrong – from delays due to transition downtime and user retraining, to potential loss of data. But often, the single biggest concern will be security. This is especially true when contemplating a fundamental change in networking architecture, such as a migration to software-defined networking (SDN). Any significant network upgrade presents a challenge. So much can go wrong – from delays due to transition downtime and user retraining, to potential loss of data. But often, the single biggest concern will be security. This is especially true when contemplating a fundamental change in networking architecture, such as a migration to software-defined networking (SDN). Michael Wood of VeloCloud explains how it is possible to reap the benefits of new technology while maintaining and even improving security through the correct implementation of SD-WAN.
IBR-based compression for remote visualization (2003)

The standard way of remotely visualizing virtual worlds is downloading the virtual world to the user's computer, then rendering it. This approach is plagued by many problems which can be overcome by moving the rendering at server's side and by essentially turning interactive visualization into an image transmission problem. How to effectively compress the rendered views which need to be transmitted to the client is a fundamental issue within this remote visualization scenario. This work presents an original compression scheme for remote visualization based on image based rendering. A remote visualization system incorporating this compression method was implemented and its experimental performance is discussed.
Correction to Screening of Selective Inhibitors of 1α,25-Dihydroxyvitamin D<sub>3</sub> 24-Hydroxylase Using Recombinant Human Enzyme Expressed in <i>Escherichia coli</i> (2011)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionORIGINAL ARTICLEThis notice is a correctionCorrection to Screening of Selective Inhibitors of 1α,25-Dihydroxyvitamin D3 24-Hydroxylase Using Recombinant Human Enzyme Expressed in Escherichia coliJinge Zhu, Rafal Barycki, Grazia Chiellini, and Hector F. DeLuca*Cite this: Biochemistry 2011, 50, 30, 6606Publication Date (Web):July 11, 2011Publication History Received28 June 2011Published online11 July 2011Published inissue 2 August 2011https://doi.org/10.1021/bi200997nCopyright © 2011 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views284Altmetric-Citations-LEARN 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 (656 KB) Get e-Alertsclose Get e-Alerts
On Context-Dependent Clustering of Bandits (2016)

We investigate a novel cluster-of-bandit algorithm CAB for collaborative recommendation tasks that implements the underlying feedback sharing mechanism by estimating the neighborhood of users in a context-dependent manner. CAB makes sharp departures from the state of the art by incorporating collaborative effects into inference as well as learning processes in a manner that seamlessly interleaving explore-exploit tradeoffs and collaborative steps. We prove regret bounds under various assumptions on the data, which exhibit a crisp dependence on the expected number of clusters over the users, a natural measure of the statistical difficulty of the learning task. Experiments on production and real-world datasets show that CAB offers significantly increased prediction performance against a representative pool of state-of-the-art methods.