gebhart/patrepeval huggingface dataset:
Synthesis of N3′-P5′-linked Phosphoramidate DNA by Nonenzymatic Template-Directed Primer Extension (2012)

A fast and accurate pathway for nonenzymatic RNA replication would simplify models for the emergence of the RNA world from the prebiotic chemistry of the early earth. However, numerous difficulties stand in the way of an experimental demonstration of effective nonenzymatic RNA replication. To gain insight into the necessary properties of potentially self-replicating informational polymers, we have studied several model systems based on amino-sugar nucleotides. Here we describe the synthesis of N3'-P5'-linked phosphoramidate DNA (3'-NP-DNA) by the template-directed polymerization of activated 3'-amino-2',3'-dideoxyribonucleotides. 3'-NP-DNA is an interesting model because of its very RNA-like A-type duplex conformation and because activated 3'-amino-2',3'-dideoxyribonucleotides are much more reactive than the corresponding activated ribonucleotides. In contrast to our previous studies with 2'-amino-2',3'-dideoxyribonucleotides (for which G and C but not A and T exhibit efficient template copying), we have found that all four canonical 3'-amino-2',3'-dideoxyribonucleotides (G, C, A, and T) polymerize efficiently on RNA templates. RNA templates are generally superior to DNA templates, and oligo-ribo-T templates are superior to oligo-ribo-U templates, which are the least efficient of the RNA homopolymer templates. We have also found that activation of 3'-aminonucleotides with 2-methylimidazole results in a ca. 10-fold higher polymerization rate relative to activation with imidazole, an observation that parallels earlier findings with ribonucleotides. We discuss the implications of our experiments for the possibility of self-replication in the 3'-NP-DNA and RNA systems.
Efficient Recruitment of Layer 2/3 Interneurons by Layer 4 Input in Single Columns of Rat Somatosensory Cortex (2008)

Interneurons in layers 2/3 are excited by pyramidal cells within the same layer (Reyes et al., 1998; Gupta et al., 2000), but little is known about translaminar innervation of these interneurons by spiny neurons in the main cortical input layer 4 (L4). Here, we investigated (1) how efficiently L4 spiny neurons excite L2/3 interneurons via monosynaptic connections, (2) whether glutamate release from axon terminals of L4 spiny neurons depends on the identity of the postsynaptic interneuron, and (3) how L4-to-L2/3 interneuron connections compare with L4-to-L2/3 pyramidal neuron connections. We recorded from pairs of L4 spiny neurons and L2/3 interneurons in acute slices of rat barrel cortex of postnatal day 20 (P20) to P29 rats. The L4-to-L2/3 interneuron connections had an average unitary EPSP of 1.2 +/- 1.1 mV. We found an average of 2.3 +/- 0.8 contacts per connection, and the L4-to-L2/3 interneuron innervation domains were mostly column restricted. Unitary EPSP amplitudes and paired-pulse ratios in the L4-to-L2/3 interneuron connections depended on the "group" of the postsynaptic interneuron. Averaged over all L4-to-L2/3 interneuron connections, unitary EPSP amplitudes were 1.8-fold higher than in the translaminar L4-to-L2/3 pyramidal cell connections. Our results suggest that L4 spiny neurons may more efficiently recruit L2/3 interneurons than L2/3 pyramidal neurons, and that glutamate release from translaminar boutons of L4 spiny neuron axons is target cell specific.
Serum Endostatin Is a Genetically Determined Predictor of Survival in Pulmonary Arterial Hypertension (2014)

Our data link increased expression of ES to disease severity in PAH and demonstrate a significant relationship with adverse outcomes. Circulating ES levels can be genetically influenced, implicating ES as a genetically determined modifier of disease severity impacting on survival. These observations support serum ES as a potential biomarker in PAH with the capacity to predict poor outcomes. More importantly, this study implicates Col18a1/ES as a potential new therapeutic target in PAH.
Quantitative microanalysis of carbide/carbide interfaces in WC–Co-base cemented carbides (1986)

Carbide/carbide boundaries in WC–Co-base cemented carbides containing 6–20 wt-%Co were studied with two high resolution microanalytical techniques: atom probe field ion microscopy and analytical transmission electron microscopy. All boundaries studied, i.e. WC/WC boundaries and, in materials containing cubic carbides (γ-phase), WC/γ and γ/γ boundaries, were found to contain about half a monolayer of cobalt, localized to a zone of monolayer thickness. The carbide/carbide boundaries may thus be described as grain (phase) boundaries to which cobalt has segregated. The carbide skeleton model for WC–Co is thereby confirmed. In WC–Co materials which contain Cr3C2 as a grain growth inhibitor, chromium segregates to WC grain boundaries.MST/354
<i>Drosophila</i> PIWI associates with chromatin and interacts directly with HP1a (2007)

The interface between cellular systems involving small noncoding RNAs and epigenetic change remains largely unexplored in metazoans. RNA-induced silencing systems have the potential to target particular regions of the genome for epigenetic change by locating specific sequences and recruiting chromatin modifiers. Noting that several genes encoding RNA silencing components have been implicated in epigenetic regulation in Drosophila, we sought a direct link between the RNA silencing system and heterochromatin components. Here we show that PIWI, an ARGONAUTE/PIWI protein family member that binds to Piwi-interacting RNAs (piRNAs), strongly and specifically interacts with heterochromatin protein 1a (HP1a), a central player in heterochromatic gene silencing. The HP1a dimer binds a PxVxL-type motif in the N-terminal domain of PIWI. This motif is required in fruit flies for normal silencing of transgenes embedded in heterochromatin. We also demonstrate that PIWI, like HP1a, is itself a chromatin-associated protein whose distribution in polytene chromosomes overlaps with HP1a and appears to be RNA dependent. These findings implicate a direct interaction between the PIWI-mediated small RNA mechanism and heterochromatin-forming pathways in determining the epigenetic state of the fly genome.
Efficient Non-Viral Transfection of Mouse and Human Embryonic Stem Cells. (2004)

Abstract BACKGROUND: Development of efficient non-viral gene transfer technologies for embryonic stem (ES) cells is urgently needed for various existing and new ES cell-based research strategies. In this study we investigated mRNA electroporation as a tool for short-term gene transfer in both mouse and human ES cells. METHODS: Culture and mRNA electroporation conditions for feeder-free cultured mouse and human ES cells were optimized on three mouse ES cell lines (E14, R1 and HM-1) and one human ES cell line (H9). After electroporation with EGFP mRNA, transfected ES cell populations were analyzed by FACS for EGFP expression, viability and phenotype. Also, stably-transfected mouse ES cell lines containing Lox-P or FRT-flanked reporter genes were electroporated with mRNA encoding Cre- or FLPe-recombinase proteins. Monitoring recombination efficiency was done based on the appearance and/or disappearance of fluorescent reporter genes, as determined by FACS analysis. ES cells that underwent recombination were further analyzed for potential to differentiate towards the neural lineage and differentiated cells were analyzed by FACS for expression of neural markers. RESULTS: (A) Electroporation of EGFP mRNA in mouse ES cells resulted in high level transgene expression (>90% EGFP positive cells) combined with low electroporation-induced cell mortality (>90% viable cells). Moreover, the electroporation procedure did not influence ES cell phenotype and further cell culture of undifferentiated ES cell populations. Electroporation of mRNA encoding Cre- or FLPe-recombinase proteins in stably-transfected mouse ES cell lines containing LoxP- or FRT-flanked reporter genes resulted in a recombination efficiency of respectively 75% and 90%. Moreover, these recombination events did not have influence on ES cell phenotype, viability, growth potential, and their ability to differentiate towards neural cell types upon retinoic acid stimulation. (B) Although human ES cells are much more sensitive as compared to mouse ES cells, we were able to develop improved culture and electroporation conditions for feeder-free maintained H9 human ES cells, which resulted in high level transgene expression (>90% EGFP+ cells) combined with high cell viability (>90% viable cells) after EGFP mRNA electroporation. CONCLUSIONS: RNA electroporation is a highly efficient method for short-term genetic loading of both mouse and human ES cells. Ongoing research now focuses on either short-term (via direct mRNA electroporation) or sustained (via mRNA-based FLPe-recombination) expression of transcription factors in ES cells and their influence on cell-fate within in vitro cultured embryoid bodies.
Analysis of SIP's applicability in Smart Grid environment (2011)

Smart Grid is the modernization of the existing power grid, which utilizes the digital technology for the two-way exchange of information and electricity between the utilities and consumers.It requires a communication overlay' network, which facilitates intelligent communication between various nodes of the heterogeneous Smart Grid network.SIP is widely used in similar communication overlay' networks for the IP telephony as an established de-facto protocol for session management'.This project discusses the use of SIP in the Smart Grid environment.This project gives a detailed analysis on the appropriateness of using SIP (Session Initiation Protocol) in the Smart Grid environment.The project mainly investigates the role of SIP in HAN (Home Area Network) and Demand Response System.In HAN, one of the network segments of the Smart Grid network, the interaction of the residential or commercial devices (such as TV, washing machine, surveillance camera, etc.) with the smart meter/energy management system and vice-versa is analyzed.An observation of the proposed SIP-Zigbee interworking architecture involving the SIP presence framework is done.The Event-service model of SIP is analyzed which makes it an effective protocol and architecture to realize open automated demand response system in the smart grid.
Evaluation of New Online Automated Embolic Signal Detection Algorithm, Including Comparison With Panel of International Experts (2000)

By using the frequency specificity of the intensity increase occurring with embolic signals, we have developed an automated detection system with a much improved sensitivity. Its performance was equal to that of some human experts and only slightly below the mean performance of a panel of human experts
Clinical Experience with Intravesical Prostaglandin E <sub>2</sub> | A Prospective Study of 36 Patients (1980)

In a prospective study, intravesical prostaglandins were given to 36 patients who had urinary symptoms associated with a poorly functioning detrusor; 67% of these patients were found to be in chronic retention. Using standard urodynamic techniques, 72% showed objective evidence of an immediate improvement in detrusor function and there was prolonged therapeutic benefit in 39%. A prolonged response occurred only in patients who had an intact sacral reflex arc and urodynamic evidence of a pathologically enlarged bladder, and who did not have radiologically demonstrable outflow obstruction. The use of intravesical prostaglandin to stimulate the detrusor was also found to be of value as a urodynamic technique for the investigation of the lower urinary tract.
Albright's hereditary osteodystrophy with extensive heterotopic ossification of the oral and maxillofacial region: how fetuin research may help a seemingly impossible condition. (2007)

Albright"s hereditary osteodystrophy (AHO) is a complex genetic disorder characterized by brachydactyly, gonadotropin resistance, hypothyroidism, pseudohypoparathyroid syndrome and heterotopic ossification. Heterotopic ossification rarely occurs in the maxillofacial region. In this article, we present such a case, describe the etiology, characteristics and treatment of AHO and suggest a potential role of an inhibitor of bone formation such as fetuin in preventing recurrence of aberrant ossification.
<i>In Situ</i> Growth of Cellular Two-Dimensional Silicon Oxide on Metal Substrates (2013)

Crystalline hexagonally ordered silicon oxide layers with a thickness of less than a nanometer are grown on transition metal surfaces in an in situ electron microscopy experiment. The nucleation and growth of silica bilayers and monolayers, which represent the thinnest possible ordered structures of silicon oxide, are monitored in real time. The emerging layers show structural defects reminiscent of those in graphene and can also be vitreous. First-principles calculations provide atomistic insight into the energetics of the growth process. The interplay between the gain in silica-metal interaction energy due to their epitaxial match and energy loss associated with the mechanical strain of the silica network is addressed. The results of calculations indicate that both ordered and vitreous mono/bilayer structures are possible, so that the actual morphology of the layer is defined by the kinetics of the growth process.
A Ball‐Milling‐Enabled Reformatsky Reaction (2019)

An operationally simple one-jar one-step mechanochemical Reformatsky reaction using in situ generated organozinc intermediates under neat grinding conditions has been developed. Notable features of this reaction protocol are that it requires no solvent, no inert gases, and no pre-activation of the bulk zinc source. The developed process is demonstrated to have good substrate scope (39-82 % yield) and is effective irrespective of the initial morphology of the zinc source.
Antiproliferative and apoptotic effects of two new gold(III) methylsarcosinedithiocarbamate derivatives on human acute myeloid leukemia cells in vitro (2007)

[Au(MSDT)Cl2] (dichloro[methyl N-(dithiocarboxy-kS,kS')-N-methylglicinato]gold(III)) and [Au(MSDT)Br2] (dibromo[methyl N-(dithiocarboxy-kS,kS')-N-methylglicinato]gold(III)) gold(III) dithiocarbamate derivatives are two newly synthesized gold(III) derivatives of methylsarcosinedithiocarbamate, containing a sulfur chelating ligand that is able to bind the metal center strongly, so preventing interactions with sulfur-containing enzymes; in fact these reactions are believed to be responsible for the nephrotoxicity induced by the platinum(II)-based drugs. Their activity has been compared with the well-known platinum-based anticancer agent cisplatin on a panel of acute myelogenous leukemia cell lines representing different French-American-British subtypes and in the Philadelphia-positive cell line K562. Both compounds suppressed, in a dose-dependent manner, colony formation in methylcellulose with ID50 values of about 10-fold lower than that of the reference drug. After a short exposure (18 h), our compounds, but not cisplatin, were able to: downregulate the antiapoptotic molecule Bcl-2, upregulate the proapoptotic molecule Bax and induce apoptosis, as determined by a strong induction of APO2.7 and phosphatidylserine exposure. Finally, after a 72-h exposure, both gold(III) dithiocarbamate derivatives determined modest cell cycle modifications, but induced DNA fragmentation in all myeloid cell lines tested. Altogether, our results indicate that these new gold(III) dithiocarbamate derivatives might represent novel potentially active drugs for the management of myeloid leukemia, able to combine cytostatic and apoptotic activity with reduced nephrotoxicity.
Robust design of rail-to-rail CMOS operational amplifiers for a low power supply voltage (1996)

New bias circuits which provide currents to n- and p-channel differential pairs placed in parallel are introduced. The bias currents are a function of the input common mode voltage in such a way that the total transconductance, g/sub mT/, of the differential pairs is constant over the entire common mode range. The bias circuits, together with the differential pairs, are used to design input stages of low-voltage (/spl les/3.3 V) complementary metal-oxide-semiconductor (CMOS) operational amplifiers (op amps). The new circuits are robust in that they do not require transconductance parameter matching of n- and p-channel transistors for proper operation. A simple rail-to-rail common source output stage with class AB control is also developed and used in the design of two-stage op amps. Experimental results of MOSIS test chips containing a family of low-voltage op amps fabricated in 2 /spl mu/m p-well process are provided. The results demonstrate the effectiveness and robustness of the proposed constant transconductance input stages in achieving constant opamp unity gain frequency with very low levels of total harmonic distortion (THD) and with 3.3 V and 2.5 V power supply voltage.
After Twenty-Five Years of User Modeling and Adaptation...What Makes us UMAP? (2017)

ACM UMAP 2017 is the 25th conference on User Modeling, on Adaptive Hypermedia, or on both together (since 2009). The research has actually been going on for more than 25 years as initially there was a conference only every two years. This keynote offers both reflection on the past and outlook into the future, with the burning question: What makes us UMAP? We perform research on modeling users (individuals as well as groups), not just for fun but to use these models for recommendations and for adaptation. That's not unique to us. In recommender systems analyzing user behavior is needed in order to give better and better recommendations, and likewise an area like educational data mining analyzes how learners study in order to best guide them to new learning material or followup courses. With analysis of social networks and website adaptation we step into the same research area that is covered by the hypertext community. If all of this is "us" but "not just us", where is our identity?
Sequence requirements for function of the<i>Drosophila</i>chorion gene locus ACE3 replicator and ori-β origin elements (2004)

The developmentally regulated amplification of the Drosophila third chromosome chorion gene locus requires multiple chromosomal elements. Amplification control element third chromosome (ACE3) appears to function as a replicator, in that it is required in cis for the activity of nearby DNA replication origin(s). Ori-beta is the major origin in the locus, and is a sequence-specific element that is sufficient for high-level amplification in combination with ACE3. Sequence requirements for amplification were examined using a transgenic construct that was buffered from chromosomal position effects by flanking insulator elements. The parent construct supported 18- to 20-fold amplification, and contained the 320 bp ACE3, the approximately 1.2 kb S18 chorion gene and the 840 bp ori-beta. Deletion mapping of ACE3 revealed that an evolutionarily conserved 142 bp core sequence functions in amplification in this context. Several deletions had quantitative effects, suggesting that multiple, partially redundant elements comprise ACE3. S. cerevisiae ARS1 origin sequences could not substitute for ori-beta, thereby confirming the sequence specificity of ori-beta. Deletion mapping of ori-beta identified two required components: a 140 bp 5' element and a 226 bp A/T-rich 3' element called the beta-region that has significant homology to ACE3. Antibody to the origin recognition complex subunit 2 (ORC2) recognizes large foci that localize to the endogenous chorion gene loci and to active transgenic constructs at the beginning of amplification. Mutations in Orc2 itself, or the amplification trans regulator satin eliminated the ORC2 foci. By contrast, with a null mutation of chiffon (dbf4-like) that eliminates amplification, diffuse ORC2 staining was still present, but failed to localize into foci. The data suggest a novel function for the Dbf4-like chiffon protein in ORC localization. Chromosomal position effects that eliminated amplification of transgenic constructs also eliminated foci formation. However, use of the buffered vector allowed amplification of transgenic constructs to occur in the absence of detectable foci formation. Taken together, the data suggest a model in which ACE3 and ori-beta nucleate the formation of a ORC2-containing chromatin structure that spreads along the chromosome in a mechanism dependent upon chiffon.
New human myelodysplastic cell line, TER‐3: G‐CSF specific downregulation of Ca<sup>2+</sup>/calmodulin‐dependent protein kinase IV (2002)

We have established a new hematopoietic cell line from a patient with myelodysplastic syndrome (MDS), which was refractory anemia with excess blasts (RAEB). This cell line, designated TER-3, depends on several cytokines for long-term survival and growth, and requires interleukin-3 (IL-3) for continuous growth. Cytochemical analysis revealed that TER-3 cells are weakly dianisidine positive and nonspecific esterase positive, but peroxidase negative. The surface marker profile shows that the TER-3 cells are strongly positive for myeloid, lymphoid, and megakaryocytic antigens such as CD15, CD19, and CD61, and negative for some common multilineage antigens such as CD13, CD33, and CD34. Thus, this cell line has a multilineage phenotype, suggesting that the transformation event occurred in multipotent stem cells. Dianisidine- and nonspecific esterase-positive TER-3 cells increase with granulocyte-colony stimulating factor (G-CSF) rather than with IL-3. These results suggest that the cell line is useful for understanding the mechanism underlying G-CSF-associated hematopoietic cell differentiation and activation in the patient with MDS.
JACOB: just a content-based query system for video databases (2002)

The increasing development of advanced multimedia applications requires new technologies for organizing and retrieving by content databases of still digital images or digital video sequences. The authors describe JACOB, a prototypal system allowing content-based browsing and querying in video databases. The JACOB system automatically splits a video into a sequence of shots, extracts a few representative frames (said r-frames) from each shot and computes r-frame descriptors based on features like color and texture. No user action is required during the database population step. Queries exploit this image content description and may be direct or by example.
Discovery of hyper protein-producing bacteria and their utilization to the production of useful proteins. (1987)

, B.
Coping with latency in SOC design (2002)

Latency-insensitive design is the foundation of a correct-by-construction methodology for SOC design. This approach can handle latency's increasing impact on deep-submicron technologies and facilitate the reuse of intellectual-property cores for building complex systems on chips, reducing the number of costly iterations in the design process.