gebhart/patrepeval huggingface dataset:
Determination of relaxation time of a Josephson junction qubit (2004)

When a Josephson junction in the zero-voltage state is current-biased below its critical current, the rate that it escapes to the finite-voltage state depends on the quantum state of the junction. By employing a slow current sweep, it is possible to observe experimentally the emptying of the thermally populated first excited level as a well-defined feature in the escape rate. This feature provides a simple method of determining the junction's energy relaxation time ${T}_{1}$, a key parameter for evaluating its utility for quantum computation. We discuss the temperature regime where this effect is readily observable and describe how the emptying depends directly on the relaxation time. Our model of the junction dynamics agrees well with the measured escape rate of a $10\phantom{\rule{0.3em}{0ex}}\ensuremath{\mu}\mathrm{m}\ifmmode\times\else\texttimes\fi{}10\phantom{\rule{0.3em}{0ex}}\ensuremath{\mu}\mathrm{m}$ $\mathrm{Nb}\text{\ensuremath{-}}\mathrm{AlOx}\text{\ensuremath{-}}\mathrm{Nb}$ device in the 25 to $300\phantom{\rule{0.3em}{0ex}}\mathrm{mK}$ temperature range, yielding ${T}_{1}\ensuremath{\approx}4\phantom{\rule{0.3em}{0ex}}\mathrm{ns}$.
Beneficial effect of hydrogen in aluminum oxide deposited through the atomic layer deposition method on the electrical properties of an indium–gallium–zinc oxide thin-film transistor (2016)

Described herein is the role of hydrogen in aluminum oxide (Al2O3) gate dielectrics in amorphous indium–gallium–zinc oxide (a-InGaZnO or a-IGZO) thin-film transistors (TFTs). Compared to a-IGZO TFTs with a low-temperature (150°C) Al2O3 gate dielectric, a-IGZO devices with a high-temperature (250–300°C) Al2O3 gate dielectric exhibit poor transistor characteristics, such as low mobility, a high subthreshold slope, and huge hysteresis. Through DC and short-pulsed current–voltage (I–V) measurements, it was revealed that the degradation of the transistor performance stems from the charging and discharging phenomenon at the interface traps located in the interface between the a-IGZO semiconductor and the Al2O3 gate insulator. It was found that the low-temperature Al2O3 atomic layer deposition processed film contains a higher density of hydrogen atoms compared to high-deposition-temperature films. The study results show that a high concentration of hydrogen atoms can passivate the defect sites in the interface and bulk, which produces excellent transistor characteristics. This study demonstrated that hydrogen has a beneficial effect on the defect passivation for oxide TFTs.
A fully-automated method discovers loss of mouse-lethal and human-monogenic disease genes in 58 mammals (2020)

Gene losses provide an insightful route for studying the morphological and physiological adaptations of species, but their discovery is challenging. Existing genome annotation tools focus on annotating intact genes and do not attempt to distinguish nonfunctional genes from genes missing annotation due to sequencing and assembly artifacts. Previous attempts to annotate gene losses have required significant manual curation, which hampers their scalability for the ever-increasing deluge of newly sequenced genomes. Using extreme sequence erosion (amino acid deletions and substitutions) and sister species support as an unambiguous signature of loss, we developed an automated approach for detecting high-confidence gene loss events across a species tree. Our approach relies solely on gene annotation in a single reference genome, raw assemblies for the remaining species to analyze, and the associated phylogenetic tree for all organisms involved. Using human as reference, we discovered over 400 unique human ortholog erosion events across 58 mammals. This includes dozens of clade-specific losses of genes that result in early mouse lethality or are associated with severe human congenital diseases. Our discoveries yield intriguing potential for translational medical genetics and evolutionary biology, and our approach is readily applicable to large-scale genome sequencing efforts across the tree of life.
Myeloid differentiation of FdCP1 cells is dependent on Stat5 processing (2000)

The IL-3 family of cytokines transduces signals through Stat5 and regulates myeloid development. Previous studies have determined that a carboxy terminally truncated isoform of Stat5 is activated in immature myeloid cells. This isoform, which lacks a transcriptional activation domain, is generated by a protein-processing event. To determine whether Stat5 cleavage plays an important role in the growth and maturation of myeloid progenitors, the FdCP1 model of myeloid maturation was evaluated. FdCP1 cells are IL-3-dependent myeloid progenitors that differentiate into monocytes when cultured in granulocyte macrophage-colony-stimulating factor (GM-CSF). Consistent with their immature phenotype, when FdCP1 cells are cultured in IL-3 they exhibit robust protease activity and signal through truncated Stat5 isoforms. In contrast, maturation leads to a loss of protease activity and a switch to the expression to full-length Stat5 isoforms. Introduction of a noncleavable, full-length Stat5 mutant into undifferentiated FdCP1 cells leads to a partially differentiated phenotype and prevents further differentiation in response to GM-CSF. These results support our hypothesis that Stat5 processing is important for myeloid maturation. (Blood. 2000;96:1358-1365)
Purification of surcrose esters by selective adsorption (1976)

Abstract Long chain fatty acid esters of sucrose from the solvent‐free, soap‐catalyzed interesterification of molten sucrose and glycerides were acidulated to destroy the soaps, washed to remove unreacted sucrose, and freed of unreacted glycerides and free fatty acids by a procedure adaptable to large scale use. Separation of the glycerides and free fatty acids from the sucrose esters was accomplished by passing the product through selected adsorbents, up to a 1:2 ratio of product to adsorbent, and eluting with selected solvents. Effectiveness of the separations was monitored by thin layer chromatography. Neutral bleaching clay would be the adsorbent of choice for a large scale purification scheme employing benzene as the eluent for the removal of glycerides and free fatty acids followed with ethanol for removal of the sucrose esters.
Transcription of Ribosomal 5‐S RNA by RNA Polymerase C in Isolated Chromatin from HeLa Cells (1977)

The synthesis of ribosomal 5‐S RNA in vitro in isolated chromatin from HeLa cells was studied by hybridization of the product to a plasmid DNA probe which contained the 5‐S RNA genes from Xenopus mulleri . It was found that endogenous RNA polymerase C, contained in the chromatin, actively synthesizes RNA which hybridizes to the DNA for 5‐S RNA. The molecular weight of this RNA, judged by gel filtration and electrophoresis in formamide‐containing polyacrylamide gels, is of distinct 5‐S size. Hybridisation of the product synthesized in vitro to the DNA for 5‐S RNA can be competed quantitatively by the presence of unlabelled cytoplasmic 5‐S RNA. Presaturation of the DNA‐containing filters with cytoplasmic 5‐S RNA prevents hybridisation, indicating that antisense transcripts are not synthesized to a measurable extent in this system. The addition of Escherichia coli RNA polymerase to chromatin stimulates the synthesis of bulk RNA, and beyond certain concentrations also leads to enhanced formation of hybridizable sequences. These are, however, predominantly contained in molecules of high molecular weight, indicating abberent initiations and/or terminations of the bacterial polymerase at random sites. These data re‐emphasize the necessity of concurrent hybridization and size analyses for the assay of specific transcription. Homologous RNA polymerase C, added to chromatin either as a crude preparation in the presence of polymerase A or as purified enzyme, resulted in increased production of hybridizable 5‐S RNA sequences, the formation of which was suppressible by high concentrations of α‐aminitin. The RNA products synthesized under these conditions were predominantly asymmetric and hybridized in a discrete peak at the 5‐S position. This is in contrast to results found for the bacterial enzyme which synthesized a high proportion of antisense transcripts on isolated chromatin. These findings indicate strongly that a particular RNA polymerase species of homologous source should be used when analyzing the transcription of specific genes in vitro .
FULL-SCALE COLD CRUCIBLE TEST ON VITRIFICATION OF SAVANNAH RIVER SITE SB4 HLW SURROGATE (2008)

The full-scale cold crucible test on vitrification of sludge batch 4 (SB4) Savannah River Site HLW surrogate using a 418 mm inner diameter stainless steel crucible was carried-out for 66 hrs. Commercially available Frit 503-R4 (8 wt.% Li{sub 2}O, 16 wt.% B{sub 2}O{sub 3}, 76 wt.% SiO{sub 2}) was used as a glass forming additive at a calcine to frit ratio of 1:1 (50 wt.% calcine, 50 wt.% frit). Two portions of slurry prepared from frit and mixture of chemicals simulating waste in amount of {approx}750 kg and from frit and waste surrogate prepared by the SRT-MST-2007-00070 procedure in amount of {approx}1,300 kg with water content of {approx}27 and {approx}50 wt.%, respectively, was processed and {approx}875 kg of the vitrified product in total ({approx}415 + 460 kg) was obtained. Average parameters were as follows: vibration power - 121.6 to 134.1 kW, feed rate (capacity) - 25.1 to 39.8 kg/hr, glass pour rate (productivity) - 14.0 kg/hr specific energy expenses for feed processing - 4.8 to 3.4 kW x hr/kg, specific energy expenses for glass production (melting ratio) - 8.7 to 9.6 kW x hr/kg, specific glass productivity - 2453 kg/(m{sup 2} x d). The product was composed of major vitreous and minor spinel structure phases. No nepheline phase was found. Average degree of crystallinity was estimated to be {approx}12 vol.%. Cesium was found to be the most volatile component (up to {approx}60 wt.% of total). Lithium, sodium and boron are less volatile. Other major feed constituents (Al, Si, Mg, Fe, Mn) were not volatile but their carry-over with gas-vapor flow occurred.
Identification of Putative Biosynthetic Gene Clusters for Tolyporphins in Multiple Filamentous Cyanobacteria (2021)

Tolyporphins A-R are unusual tetrapyrrole macrocycles produced by the non-axenic filamentous cyanobacterium HT-58-2. A putative biosynthetic gene cluster for biosynthesis of tolyporphins (here termed BGC-1) was previously identified in the genome of HT-58-2. Here, homology searching of BGC-1 in HT-58-2 led to identification of similar BGCs in seven other filamentous cyanobacteria, including strains <i>Nostoc</i> sp. 106C, <i>Nostoc</i> sp. RF31YmG, <i>Nostoc</i> sp. FACHB-892, <i>Brasilonema octagenarum</i> UFV-OR1, <i>Brasilonema octagenarum</i> UFV-E1, <i>Brasilonema sennae</i> CENA114 and <i>Oculatella</i> sp. LEGE 06141, suggesting their potential for tolyporphins production. A similar gene cluster (BGC-2) also was identified unexpectedly in HT-58-2. Tolyporphins BGCs were not identified in unicellular cyanobacteria. Phylogenetic analysis based on 16S rRNA and a common component of the BGCs, TolD, points to a close evolutionary history between each strain and their respective tolyporphins BGC. Though identified with putative tolyporphins BGCs, examination of pigments extracted from three cyanobacteria has not revealed the presence of tolyporphins. Overall, the identification of BGCs and potential producers of tolyporphins presents a collection of candidate cyanobacteria for genetic and biochemical analysis pertaining to these unusual tetrapyrrole macrocycles.
Antimicrobial Activity and Bacterial-Membrane Interaction of Ovine-Derived Cathelicidins (2004)

Three ovine-derived cathelicidins, SMAP29, OaBac5mini, and OaBac7.5mini, were compared with respect to their antibacterial activities and interactions with membranes. SMAP29 was confirmed to be alpha-helical, broad spectrum, and able to disrupt both the outer and the cytoplasmic membranes at relatively low concentrations. In contrast, the two proline- and arginine-rich OaBac peptides had more-modest antibacterial activities, reduced levels of lipopolysaccharide binding, and a lesser ability to depolarize the cytoplasmic membrane, consistent with a cytoplasmic target.
Some extensions of nyquist's telegraph transmission theory (1965)

The conditions necessary to achieve undistorted transmission of a pulse signal over a channel of finite bandwidth have been set down by Nyquist. These conditions are extended in this paper to eliminate the bandwidth restrictions. Conditions on the real and imaginary parts of the overall system characteristic which lead to the elimination of intersymbol amplitude and pulse width distortion are found. These generalized constraints do not depend on any sharp band limitation and permit one to find ideal conditions for band pass and gradual cutoff systems. The application of Nyquist's conditions usually amounts to equalizing the transmission characteristics in order to approximate an overall linear phase and some sort of symmetrical amplitude roll-off. This paper shows that the principles of channel shaping for distortionless transmission are a good deal more flexible than this. The application of this more general interpretation of Nyquist's theory is illustrated by several examples.
Mining Characteristic Relations Bind to RNA Secondary Structures (2009)

The identification of RNA secondary structures has been among the most exciting recent developments in biology and medical science. It has been recognized that there is an abundance of functional structures with frameshifting, regulation of translation, and splicing functions. However, the inherent signal for secondary structures is weak and generally not straightforward due to complex interleaving substrings. This makes it difficult to explore their potential functions from various structure data. Our approach, based on a collection of predicted RNA secondary structures, allows us to efficiently capture interesting characteristic relations in RNA and bring out the top-ranked rules for specified association groups. Our results not only point to a number of interesting associations and include a brief biological interpretation to them. It assists biologists in sorting out the most significant characteristic structure patterns and predicting structure-function relationships in RNA.
Retinoblastoma Protein Prevents Staurosporine-Induced Cell Death in a Retinoblastoma-Defective Human Glioma Cell Line (2007)

These results imply that enforced Rb expression protects cells from genomic instability induced by staurosporine regardless of its upstream molecular effects.
ACTR-52. CLINICAL IMPACT OF TERT PROMOTER DETECTION IN CIRCULATING CELL-FREE DNA OF PATIENTS WITH GLIOBLASTOMA – A PILOT STUDY (2017)

Detection of circulating cell-free tumor-derived DNA (cfDNA) has been shown to be of clinical value in monitoring cancer treatment. Having in mind that somatic TERT promoter (TERTp) mutations are clonal and frequent in IDH-wild-type glioblastoma (GBM), we conducted a pilot study to assess the clinical impact of TERTp-mutant cfDNA detection in CSF and plasma in GBM patient. A total of 30 GBM patients were prospectively enrolled. Matched plasma and CSF samples were collected before tumor resection in all patients. Using the IonTorrent PGM semiconductor sequencing platform, we analyzed the collected cfDNA and matched tumor DNA samples for hotspot mutations in the promoter region of TERT (C228 and C250). Logistic regression analysis was performed to evaluate the clinical impact of the variant allele frequency (VAF) of TERTp-mutant cfDNA in predicting patients’ overall (OS) and progression-free (PFS) survival. 25 patients had a TERTp-mutant GBM. The matched TERTp-CSF-derived cfDNA was successfully detected with 100% specificity and 92% sensitivity (23 patients). The median VAF of the CSF-cfDNA was 20.3% (0.08%-70.3%). In the plasma, the sensitivity of TERTp-mutant cfDNA detection was far lower (12%). There was a statistically significant linear relationship between the CSF-VAFs and PFS (R2 = 0.1615; p=0.0418). Strikingly, in the multivariate analysis, the median VAF for CSF-cfDNA was the best predictor for PFS (p=0.007, HR=4.1, 95% CI: 1.4–11.3) and OS (p=0.013, HR=4.7, 95% CI: 1.3–15.8). In contrast, all other included clinical parameters (age, tumor volume, extent of resection, MGMT promoter methylation status) did not appear as an independent prognostic factor. We propose that the detection and accurate quantification of TERTp-mutant CSF-cfDNA in GBM patients is feasible with a high sensitivity and specificity. Additionally, although generated on a small cohort, our findings indicate that pre-resection CSF-derived cfDNA might be a suitable marker to predict survival in TERTp-mutant GBM patients.
Metal-catalyzed rearrangements of 3-allenyl 3-hydroxyindolin-2-ones in the presence of halogenated reagents (2012)

The reactions of 3-allenyl 3-hydroxyoxindoles with a variety of halogenated reagents in the presence of catalytic amounts of precious metal salts were explored. Both, rearrangement and oxycyclization reactions to give 4-(1-halovinyl)-quinolinediones or spirocyclic halooxindoles, respectively, are competitive pathways. The kind of functionalization is substrate and reaction conditions dependent.
A model parameter and MAD prediction scheme for h.264 macroblock layer rate control (2008)

In this paper, we show that inaccurate model parameters degrade performance of R-Q model based rate control, and oscillations of estimated model parameters often occur in the classic quadratic R-Q model based macroblock (MB) layer rate control. To resolve the parameter oscillation problem, we thus propose to use a linear R-Q model rather than the quadratic R-Q model for MB layer rate control and a novel context-adaptive scheme for estimating mean absolute difference (MAD) and parameters for the linear R-Q model. The proposed context is adaptively computed according to local video signal characteristics using a Manhattan distance metric and an improved 2D sliding window method. Extensive experiments show that compared to the H.264 reference JM software, MB layer rate control algorithm using our proposed scheme significantly improves the MAD and model parameters prediction accuracy and bit achievement accuracy, and hence obtains much better rate distortion performance.
Antibiotics as Signal Molecules (2011)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTAntibiotics as Signal MoleculesDiego Romero, Matthew F. Traxler, Daniel López, and Roberto Kolter*View Author Information Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, United StatesE-mail: [email protected]. Address: 200 Longwood Avenue, Armenise Building, Room 219, Boston, MA 02115. Telephone: (+1) 617-432-1776. Fax: (+1) 617-738-7664.Cite this: Chem. Rev. 2011, 111, 9, 5492–5505Publication Date (Web):July 25, 2011Publication History Received10 February 2011Published online25 July 2011Published inissue 14 September 2011https://pubs.acs.org/doi/10.1021/cr2000509https://doi.org/10.1021/cr2000509review-articleACS PublicationsCopyright © 2011 American Chemical SocietyRequest reuse permissionsArticle Views6768Altmetric-Citations289LEARN 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:Antimicrobial agents,Bacteria,Biofilms,Genetics,Molecules Get e-Alerts
F1F0 ATP Synthase–Cyclophilin D Interaction Contributes to Diabetes-Induced Synaptic Dysfunction and Cognitive Decline (2016)

Mitochondrial abnormalities are well known to cause cognitive decline. However, the underlying molecular basis of mitochondria-associated neuronal and synaptic dysfunction in the diabetic brain remains unclear. Here, using a mitochondrial single-channel patch clamp and cyclophilin D (CypD)-deficient mice (Ppif <sup>-/-</sup>) with streptozotocin-induced diabetes, we observed an increase in the probability of Ca<sup>2+</sup>-induced mitochondrial permeability transition pore (mPTP) opening in brain mitochondria of diabetic mice, which was further confirmed by mitochondrial swelling and cytochrome c release induced by Ca<sup>2+</sup> overload. Diabetes-induced elevation of CypD triggers enhancement of F<sub>1</sub>F<sub>0</sub> ATP synthase-CypD interaction, which in turn leads to mPTP opening. Indeed, in patients with diabetes, brain cypD protein levels were increased. Notably, blockade of the F<sub>1</sub>F<sub>0</sub> ATP synthase-CypD interaction by CypD ablation protected against diabetes-induced mPTP opening, ATP synthesis deficits, oxidative stress, and mitochondria dysfunction. Furthermore, the absence of CypD alleviated deficits in synaptic plasticity, learning, and memory in diabetic mice. Thus, blockade of ATP synthase interaction with CypD provides a promising new target for therapeutic intervention in diabetic encephalopathy.
Authors' response to ‘Aspirin dose for treatment of Kawasaki disease’ (2014)

We read with interest the letter by Dr Krasseman1 regarding anti-inflammatory doses of aspirin used in the acute phase of Kawasaki disease (KD). Indeed, higher doses of aspirin are currently used in the USA (80–100 mg/kg/day), while in Japan a lower dose of 30–50 mg/kg/day is advocated.2–6 Similarly, in the UK, the latter modest dose has been recommended since 20027 ,8 for the acute phase of KD as a number of previous studies have suggested this lower dose is equally as effective, and may be associated with less toxicity.2 ,4 …
TRIPS competition flexibilities (2010)

International trade legislation and TRIPS in particulate contain elements of a competition law system. Flexibilities in the system leave substantial discretion to developing countries, which can apply these rules to counterbalance demands imposed on them by the IPR obligations contained in the Agreement. To create a reasonable balance, precise standards regarding competition law interpretation and enforcement is required. In spite of the mishaps with the Singapore issues in the Doha round, the WTO still provides the right forum for such discussions. Post-Doha it must be possible to re-establish the discussion. The way forward may well be a new Fair Trade Agreement under the WTO “umbrella”.
Lattice dynamics and vibrational spectra of polythiophene. I. Oligomers and polymer (1991)

The vibrational dynamics of oligomers of thiophene is treated theoretically and the experimental infrared and Raman spectra are studied with the main purpose to derive information for the interpretation of the spectra of polythiophene. The optimized geometries and the vibrational force field are calculated for the oligomers Thn (n=1, 2, 3, 4, and 6) and the parameters are used for PTh. For PTh and two isotopic derivatives dispersion curves and k=0 phonons frequencies are calculated and a vibrational assignment is proposed.