gebhart/patrepeval huggingface dataset:
Characterization of Viral and Human RNAs Smaller than Canonical MicroRNAs (2009)

Recently identified small (20 to 40 bases) RNAs, such as microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs) participate in important cellular pathways. In this report, we systematically characterized several novel features of human and viral RNA products smaller than miRNAs. We found that Kaposi sarcoma-associated herpesvirus K12-1 miRNA (23 bases) associates with a distinct, unusually small (17-base) RNA (usRNA) that can effectively downregulate a K12-1 miRNA target, human RAD21, suggesting that stable degradation-like products may also contribute to gene regulation. High-throughput sequencing reveals a diverse set of human miRNA-derived usRNAs and other non-miRNA-derived usRNAs. Human miRNA-derived usRNAs preferentially match to 5' ends of miRNAs and are also more likely to associate with the siRNA effector protein Ago2 than with Ago1. Many non-miRNA-derived usRNAs associate with Ago proteins and also frequently contain C-rich 3'-specific motifs that are overrepresented in comparison to Piwi-interacting RNAs and transcription start site-associated RNAs. We postulate that approximately 30% of usRNAs could have evolved to participate in biological processes, including gene silencing.
Comparison of similarity search algortihms over inverted indexes Project for MS&E239 Autum 2009 (2009)

In this project you will examine the performance of two inverted indexing similarity search algorithms. The similarity search is between two textual documents and is therefore performed in a high dimensional space (approximately millions of dimensions). An example is content match, where the query is composed of the content of a web page and the objects that we are searching for are ads mapped into the same space. Here, each unique word represents a separate dimension. The similarity search function in this project will be a simple dot product. The task is to examine and compare two different algorithms: term-at-the-time (TAAT) and document-at-the-time (DAAT). Both algorithms implement a top-k ranked retrieval, i.e. given a query, retrieve the k closest ads sorted by their similarity score. In our case the documents are ads and we will use these two terms interchangeably in the following. Each document is also assigned a document ID (DID). Each document has multiple features with their associated weights. The query is also a set of features with associated weights. The similarity between document and the query is defined using a dot product:
An approach to a selection system for adenosine‐deaminase‐positive (ADA+) cells and detection of rat ADA+ “revertants” (1985)

We have substituted deoxyadenosine or adenosine for hypoxanthine in the standard HAT selection system in an attempt to select for ADA-normal (ADA+) cells. ADA- human lymphoid line cells could not utilize deoxyadenosine as an alternative to hypoxanthine as a purine source (DAT) and failed to grow but were only somewhat inhibited in growth when adenosine was substituted for hypoxanthine (AAT). In contrast, ADA+ cells utilized adenosine or deoxyadenosine as efficiently as hypoxanthine as a purine source. Growth in DAT, but not in HAT, of an artificial mixture of one ADA+ human lymphoid cells in 1,000 ADA- cells resulted in enrichment of ADA+ cells to 25-86% of total cells. When we grew a rat ADA- cell line in two variations of the DAT system, we detected at least three electrophoretically different ADA+ patterns, one of which corresponded to normal rat ADA. These could represent "revertants."
Locally rigid, vessel-based registration for laparoscopic liver surgery (2015)

In this paper we propose a practical image-guided surgery system based on locally rigid registration of a CT-derived model to vascular structures located with LUS. In a physical phantom and during porcine laparoscopic liver resection, we demonstrate accuracy of target location commensurate with surgical requirements. We conclude that locally rigid registration could be sufficient for practically useful image guidance in the near future.
Cardiac-specific leptin receptor deletion exacerbates ischaemic heart failure in mice (2010)

these data indicate that leptin signalling mitigates cardiac injury in the post-MI failing heart by acting directly on cardiomyocytes to increase STAT3 and AMPK activation, to decrease cardiac hypertrophy, apoptosis, and inflammation, and to limit deleterious changes in cardiac structure, function, and glycolytic metabolism.
The Turing Test as Interactive Proof (2007)

Abstract In 1950, Alan Turing proposed his eponymous test based on indistinguishability of verbal behavior as a replacement for the question “Can machines think?” Since then, two mutually contradictory but well‐founded attitudes towards the Turing Test have arisen in the philosophical literature. On the one hand is the attitude that has become philosophical conventional wisdom, viz., that the Turing Test is hopelessly flawed as a sufficient condition for intelligence, while on the other hand is the overwhelming sense that were a machine to pass a real live full‐fledged Turing Test, it would be a sign of nothing but our orneriness to deny it the attribution of intelligence. The arguments against the sufficiency of the Turing Test for determining intelligence rely on showing that some extra conditions are logically necessary for intelligence beyond the behavioral properties exhibited by an agent under a Turing Test. Therefore, it cannot follow logically from passing a Turing Test that the agent is intelligent. I argue that these extra conditions can be revealed by the Turing Test, so long as we allow a very slight weakening of the criterion from one of logical proof to one of statistical proof under weak realizability assumptions. The argument depends on the notion of interactive proof developed in theoretical computer science, along with some simple physical facts that constrain the information capacity of agents. Crucially, the weakening is so slight as to make no conceivable difference from a practical standpoint. Thus, the Gordian knot between the two opposing views of the sufficiency of the Turing Test can be cut.
Ultrahigh-resolution optical coherence tomography for enhanced visualization of retinal pathology (2003)

An ultrahigh resolution ophthalmic optical coherence tomography (OCT) system has been developed. Using a femtosecond Ti:sapphire laser light source, which generates bandwidths of ~150 nm at 800 nm, real-time, cross-sectional imaging of the retina with ~3 &mu;m axial resolution is possible. Ultrahigh resolution OCT images of retinal morphology were obtained in normal subjects and patients with retinal disease. Intraretinal architectural morphology associated with macular diseases such as macular edema, epiretinal membranes, and macular holes can be visualized with unprecedented resolution. Ultrahigh resolution ophthalmic OCT promises to improve the early diagnosis of retinal diseases as well as enable monitoring of disease progression and the efficacy of therapeutic intervention.
Correcting ESL errors using phrasal SMT techniques (2006)

This paper presents a pilot study of the use of phrasal Statistical Machine Translation (SMT) techniques to identify and correct writing errors made by learners of English as a Second Language (ESL). Using examples of mass noun errors found in the Chinese Learner Error Corpus (CLEC) to guide creation of an engineered training set, we show that application of the SMT paradigm can capture errors not well addressed by widely-used proofing tools designed for native speakers. Our system was able to correct 61.81% of mistakes in a set of naturally-occurring examples of mass noun errors found on the World Wide Web, suggesting that efforts to collect alignable corpora of pre- and post-editing ESL writing samples offer can enable the development of SMT-based writing assistance tools capable of repairing many of the complex syntactic and lexical problems found in the writing of ESL learners.
Data driven discovery of conjugated polyelectrolytes for optoelectronic and photocatalytic applications (2021)

Abstract Conjugated polyelectrolytes (CPEs), comprised of conjugated backbones and pendant ionic functionalities, are versatile organic materials with diverse applications. However, the myriad of possible molecular structures of CPEs render traditional, trial-and-error materials discovery strategy impractical. Here, we tackle this problem using a data-centric approach by incorporating machine learning with high-throughput first-principles calculations. We systematically examine how key materials properties depend on individual structural components of CPEs and from which the structure–property relationships are established. By means of machine learning, we uncover structural features crucial to the CPE properties, and these features are then used as descriptors in the machine learning to predict the properties of unknown CPEs. Lastly, we discover promising CPEs as hole transport materials in halide perovskite-based optoelectronic devices and as photocatalysts for water splitting. Our work could accelerate the discovery of CPEs for optoelectronic and photocatalytic applications.
Supplementary Methods and Figure Legend from Genetically Defined Subsets of Human Pancreatic Cancer Show Unique <i>In Vitro</i> Chemosensitivity (2023)

&lt;p&gt;PDF file, 76K.&lt;/p&gt;
LED 패키지 솔더 접합부의 기계적 신뢰성에 미치는 열처리의 영향 (2012)

We studied the effect of heat treatment on the microstructures and mechanical strength of the solder joints in the Light Emitting Diode (LED) packages. The commercial LED packages were mounted on the a flame resistance-4 (FR4) Printed Circuit Board (PCB) in the reflow process, and then the joints were aged at 125℃ for 100, 200, 300, 500 and 1000 hours, respectively. After the heat treatment, we measured the shear strength of the solder joints between the PCB and the LED packages to evaluate their mechanical property. We used Pb-free Sn-3.0Ag-0.5Cu solder to bond between the LED packages and the PCBs using two different surface finishes, Electroless Nickel-Immersion Gold (ENIG) and Electroless Nickel-Electroless Palladium-Immersion Gold (ENEPIG). The microstructure of the solder joints was observed by a scanning electron microscope (SEM). (Cu,Ni)6Sn5 intermetallic compounds (IMCs) formed between the solder and the PCB, and the thickness of the IMCs was increased with increasing aging time. The shear strength for the ENIG finished LED package increased until aging for 300 h and then decreased with increasing aging time. On the other hand, in the case of an ENEPIG finished LED package, the shear strength decreased after aging for 500 h.
Matrix-isolation study of the pyrolysis of bromochloromethyl-substituted organomercury compounds. Infrared spectra of the bromochlorocarbene andree radicals CCl2Br and CClBr2 (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMatrix-isolation study of the pyrolysis of bromochloromethyl-substituted organomercury compounds. Infrared spectra of the bromochlorocarbene andree radicals CCl2Br and CClBr2A. K. Maltsev, O. M. Nefedov, R. H. Hauge, J. L. Margrave, and D. SeyferthCite this: J. Phys. Chem. 1971, 75, 26, 3984–3988Publication Date (Print):December 1, 1971Publication History Published online1 May 2002Published inissue 1 December 1971https://pubs.acs.org/doi/10.1021/j100695a013https://doi.org/10.1021/j100695a013research-articleACS PublicationsRequest reuse permissionsArticle Views28Altmetric-Citations20LEARN 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 optionsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Supplementary Figure 5 from Activation of the <i>NOTCH</i> Pathway in Head and Neck Cancer (2023)

&lt;p&gt;PDF file - 68K, Growth effects of HEY1 siRNA inhibition in HNSCC cells with wildtype NOTCH1 status. HEY1 was downregulated in UPCI-SCC090 and SCC61 by siRNA as described in methods. The effect of siHEY1 on the expression of HEY1 is shown on the left. The effect of HEY1 downregulation on cell proliferation for these two cell lines is shown on the right. Note, there is over 90% transfection efficiency of HEY1 downregulation for each cell line, however the strong growth inhibition effect was shown only for NOTCH1 wildtype 090 cell line.&lt;/p&gt;
Interleukin 10 production correlates with pathology in human Leishmania donovani infections. (1993)

We have found that an important Th2 cytokine, IL-10, is produced by tissues from patients acutely infected with Leishmania donovani. In all individuals tested, IL-10 mRNA production was increased in lymph nodes taken during acute disease over that observed in postacute samples. In contrast, both pre- and posttreatment lymph nodes had readily detected mRNA for IFN-gamma and IL-2. A down-regulating effect of IL-10 on leishmania-induced proliferative responses was demonstrated when Hu rIL-10 was added to cultures of PBMC from clinically cured individuals. PBMC from individuals with acute visceral leishmaniasis responded to stimulation with leishmania lysate by producing IL-10 mRNA. Simultaneously cultured PBMC collected from the same patients after successful chemotherapy produced no detectable IL-10 mRNA after leishmania antigen stimulation. Neutralizing anti-IL-10 mAb added to PBMC from patients with acute visceral leishmaniasis markedly increased the proliferative response to leishmania lysate. Finally, we observed mRNA for IL-10 and IFN-gamma concurrently in a lesion from a patient with post-kala-azar dermal leishmaniasis (PKDL). These results indicate the production of IL-10 during L. donovani infection, and suggest a role for this cytokine in the regulation of immune responsiveness during visceral leishmaniasis.
Introduction and expression of genes for metabolic engineering applications in Saccharomyces cerevisiae (2011)

Metabolic pathway engineering in the yeast Saccharomyces cerevisiae leads to improved production of a wide range of compounds, ranging from ethanol (from biomass) to natural products such as sesquiterpenes. The introduction of multienzyme pathways requires precise control over the level and timing of expression of the associated genes. Gene number and promoter strength/regulation are two critical control points, and multiple studies have focused on modulating these in yeast. This MiniReview focuses on methods for introducing genes and controlling their copy number and on the many promoters (both constitutive and inducible) that have been successfully employed. The advantages and disadvantages of the methods will be presented, and applications to pathway engineering will be highlighted.
Measurement of Harmonic Reflections - An X-Ray Method for Real Structure Analysis of Semiconducting Compounds (1992)

An X-ray scattering technique is developed for quantitative analysis of local deviation from stoichiometry in semiconducting compounds, i.e. native point defect concentrations as well as their correlations to strain-effective density fluctuations of microdefects. Because of the direct interaction with the crystal lattice by X-ray diffraction, there is an advantage of having no restrictions by the electronic parameters in the semiconductor. The measurement principle is a simultaneous intensity registration of quasi-forbidden as well as fundamental reflections with a high degree of accuracy. Specific information contents and influences of errors are discussed. Examples illustrate the potential of the diffraction technique. The full efficiency of the technique will be realized by amplying synchrotron radiation. Es wird eine Röntgenbeugungstechnik zur lokalen, quantiativen Analyse von Unstöchiometrien in Form atomarer Fehlstellen in Einkristallen halbleitender Verbindungen vorgestellt. Ebenso wird deren Korrelation zu verzerrungswirksamen Dichtefluktuationen von Mikrodefekten erfaßt. Aufgrund der bei Röntgenbeugung direkten Wechselwirkung mit dem Kristallgitter bestcht ein Vorteil des Verfahrens in der Unabhängigkeit von den elektrischen Parametern des Halbleiterkristalls. Das Meßprinzip beruht auf einer simultanen, hochgenauen Intensitätsdetektion eines quasiverbotenen und eines Fundamentalreflexes. Die jeweiligen, spezifischen Informationsgehalte und Fehlereinflüsse auf diese Reflexe werden diskutiert. Beispiele belegen die Leistungsfähigkeit dieser Beugungstechnik, die erst durch Anwendung einer Synchroton-Strahlungsquelle ausgeschöpft werden kann.
Analysis of three 2,3-dihydroxybiphenyl 1,2-dioxygenases found in Rhodococcus globerulus P6. Identification of a new family of extradiol dioxygenases. (1994)

The polychlorobiphenyl-degrading bacterium Rhodococcus globerulus P6 contains three bphC genes encoding 2,3-dihydroxybiphenyl 1,2-dioxygenases. One of them, bphC1, is clustered with the bphB gene which encodes 2,3-dihydroxy-4-phenylhexa-4,6-diene dehydrogenase and constitutes part of the bph operon specifying the degradation of biphenyl. The nucleotide sequence of bphB and the three bphC genes has been determined. The protein products of the bphBC1 gene cluster were found to exhibit significant homology with the corresponding proteins of analogous degradative pathways in Gram-negative bacteria; the highest homology was in those of the toluene degradation pathway of Pseudomonas putida strain F1. No homology was found between bphC2 and bphC3 and any other sequence in the database. At least two of the three meta cleavage enzymes are inducible by biphenyl. 2,3-Dihydroxybiphenyl 1,2-dioxygenase II, encoded by the bphC2 gene, was purified to apparent homogeneity from a recombinant Escherichia coli strain. The enzyme differed from other extradiol dioxygenases in having a subunit molecular mass of 21 kDa and a hexameric structure. The enzyme contains one tightly bound iron per subunit. These characteristics demonstrate that the 2,3-dihydroxybiphenyl 1,2-dioxygenases encoded by bphC2 and bphC3 belong to a new class of extradiol dioxygenases.
Demonstration of universal time-reversal for qubit processes (2022)

In quantum mechanics, the unitary nature of time evolution makes it intrinsically reversible, given control over the system in question. Remarkably, there have been several recent demonstrations of protocols for reverting unknown unitaries in scenarios where even the interactions with the target system are unknown. These protocols are limited by their probabilistic nature, raising the fundamental question of whether time-reversal could be performed deterministically. Here we show that quantum physics indeed allows for this by exploiting the non-commuting nature of quantum operators, and demonstrate a recursive protocol for two-level quantum systems with an arbitrarily high probability of success. Using a photonic platform, we achieve an average rewinding fidelity of over 95%. Our protocol, requiring no knowledge of the quantum process to be rewound, is optimal in its running time, and brings quantum rewinding into a regime of practical relevance.
High Efficieny, High Speed Optical Modulation at a Telecom Wavelength Using the Quantum Zeno Effect in a Ladder Transition in Rb Atoms (2011)

We show, theoretically and experimentally, how a high efficiency, high speed optical modulator can be realized at a telecommunication wavelength using the quantum zeno effect in a ladder transition in Rb atoms at room temperature.
Gas-phase nuclear magnetic resonance investigation of chemical exchange in N,N-dimethylacetamide. Medium effects on kinetic parameters (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTGas-phase nuclear magnetic resonance investigation of chemical exchange in N,N-dimethylacetamide. Medium effects on kinetic parametersBrian D. Ross, Nancy S. True, and Gerald B. MatsonCite this: J. Phys. Chem. 1984, 88, 12, 2675–2678Publication Date (Print):June 1, 1984Publication History Published online1 May 2002Published inissue 1 June 1984https://pubs.acs.org/doi/10.1021/j150656a049https://doi.org/10.1021/j150656a049research-articleACS PublicationsRequest reuse permissionsArticle Views284Altmetric-Citations46LEARN 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 options Get e-Alerts
Mitochondrial Injury and Protection in Ischemic Pre- and Postconditioning (2010)

Mitochondrial damage is a determining factor in causing loss of cardiomyocyte function and viability, yet a mild degree of mitochondrial dysfunction appears to underlie cardioprotection against injury caused by postischemic reperfusion. This review is focused on two major mechanisms of mitochondrial dysfunction, namely, oxidative stress and opening of the mitochondrial permeability transition pore. The formation of reactive oxygen species in mitochondria will be analyzed with regard to factors controlling mitochondrial permeability transition pore opening. Finally, these mitochondrial processes are analyzed with respect to cardioprotection afforded by ischemic pre- and postconditioning.
Identification of Vulnerable Coronary Plaque With Intravascular OCT (2002)

Intravascular OCT was performed in patients following myocardial infarction. Atherosclerotic plaque type and structure were compared for disrupted and non-disrupted locations. Our results suggest that intravascular OCT provides an accurate method for identifying vulnerable plaques.