gebhart/patrepeval huggingface dataset:
On the Nature and Origin of DNA Strand Breaks in Elongating Spermatids1 (2005)

Transient DNA strand breaks are generated in the whole population of elongating spermatids and are perfectly coincident with histone H4 hyperacetylation at chromatin-remodeling steps. Given the limited DNA repair capacity of elongating spermatids, chromatin remodeling may present a threat to genetic integrity of the male gamete. The nature of the DNA strand breakage, the enzymes involved, and the role of H4 hyperacetylation in the process must be determined to further investigate the potential mutagenic consequences of this important transition. We used the metachromatic dye acridine orange in combination with fluorescence-activated cell sorting to achieve separation of spermatids according to their condensation state. Using single-cell electrophoresis (comet assay), in both alkaline and neutral conditions, we demonstrated that double-stranded breaks account for most of the DNA fragmentation observed in purified elongating spermatids. DNA strand breaks were generated in round spermatids as a result of de novo histone hyperacetylation induced by trichostatin A, whereas an increase in endogenous DNA strand breaks was observed in elongating spermatids. Using a short-term culture of testicular cells, we demonstrated that DNA strand breaks in spermatids were abolished on incubation with two functionally different topoisomerase II inhibitors. Hence, topoisomerase II appears as the unique enzyme responsible for the transient double-stranded breaks in elongating spermatids but depends on histone hyperacetylation for its activity.
Reconstituted synaptotagmin I mediates vesicle docking, priming, and fusion (2011)

The synaptic vesicle protein synaptotagmin I (syt) promotes exocytosis via its ability to penetrate membranes in response to binding Ca(2+) and through direct interactions with SNARE proteins. However, studies using full-length (FL) membrane-embedded syt in reconstituted fusion assays have yielded conflicting results, including a lack of effect, or even inhibition of fusion, by Ca(2+). In this paper, we show that reconstituted FL syt promoted rapid docking of vesicles (<1 min) followed by a priming step (3-9 min) that was required for subsequent Ca(2+)-triggered fusion between v- and t-SNARE liposomes. Moreover, fusion occurred only when phosphatidylinositol 4,5-bisphosphate was included in the target membrane. This system also recapitulates some of the effects of syt mutations that alter synaptic transmission in neurons. Finally, we demonstrate that the cytoplasmic domain of syt exhibited mixed agonist/antagonist activity during regulated membrane fusion in vitro and in cells. Together, these findings reveal further convergence of reconstituted and cell-based systems.
Protecting ownership rights of a lossless image coder through hierarchical watermarking (2002)

Current market forces make it necessary for designers to protect their work against illicit use. Digital watermarks can be used to sign a design and thus establish ownership. We present a hierarchical set of techniques for intellectual property protection of a linear predictive image coder. Watermarking techniques employed include switching entries in the Huffman coding table, applying zero cost hardware transformations, embedding a signature in the scheduling of shared hardware resources, and applying a watermark to the physical layout. Using these methods, it is possible to watermark complete ASIC or FPGA designs with little overhead in performance or achieved compression rates.
From technology assessment to responsible research and innovation (RRI) (2016)

How can technology assessment methodologies be developed to move ethical questions to the forefront of enquiry? This methodological question was one of the key factors in an exercise in Responsible Research and Innovation carried out as part of SNIFFPHONE, a project on medical diagnostics. This paper discusses the methods used to apply Responsible Research and Innovation (RRI) in SNIFFPHONE, one of the European Commission's H2020 projects. In addition we will describe shortly implementation plan and first activities of RRI in another H2020 project, called BODEGA. The aim of the project is to build an expertise at the European level about human factors in future smart borders (e.g. ABC gates, video based risk analysis) in a way to enhance its efficiency without negative side effects.
Adaptive and big data scale parallel execution in oracle (2013)

This paper showcases some of the newly introduced parallel execution methods in Oracle RDBMS. These methods provide highly scalable and adaptive evaluation for the most commonly used SQL operations - joins, group-by, rollup/cube, grouping sets, and window functions. The novelty of these techniques is their use of multi-stage parallelization models, accommodation of optimizer mistakes, and the runtime parallelization and data distribution decisions. These parallel plans adapt based on the statistics gathered on the real data at query execution time. We realized enormous performance gains from these adaptive parallelization techniques. The paper also discusses our approach to parallelize queries with operations that are inherently serial. We believe all these techniques will make their way into big data analytics and other massively parallel database systems.
Dissociation of the phenanthroimidazole dimer A highly delocalized radical Gomberg revisited (2005)

Results of a calculational study at the B3LYP/6-3/G* level concerning the dimerization of the phenanthroimidazole radical are reported herein. The optimized minimum energies of six dimer structures corresponding to CC, CN, and NN bonding have been obtained. The lowest energy dimer is found to be that resulting from NN bonding (12). However, this does not correspond to an X-ray structure study of the experimentally isolated dimer (13), which reveals CN bonding, as is also deduced from an NMR investigation. The variance between the experimental structure and the calculational lowest energy one is examined on the basis of steric interactions: virtually retained planarity, and hence, full conjugation in the two phenanthroimidazole halves in 12, vs. twisting and lack of coplanarity in the other dimer structures. Importantly, spin density calculations reveal a negligible spin density on the nitrogens, rendering dimer 12 formation through NN bonding highly improbable. A bond dissociation energy of 16.5 kcal/mol (1 cal = 4.184 J) is calculated for the experimental dimer 13, which is by far the lowest CN bond energy recorded so far in the literature. As well, this value is of the same order of magnitude as the calculated CC BDE in hexaphenylethane, which had been postulated by Gomberg in 1900 as the molecule formed on dimerization of the triphenymethyl radical, but so far not observed experimentally. Key words: delocalized radical dimerization, phenanthroimidazole dimer, Gomberg's dimer, X-ray structure, CN bond dissociation energy.
Micro/Nano Devices for Chemical Analysis (2016)

Since the concept of micro total analysis systems (µ-TAS) has been advocated, various kinds of micro/nano devices have been developed by researchers in many ﬁelds, such as in chemistry, chemical engineering, mechanical engineering, electric engineering, biology, and medicine, among others.[...].
Environmental and demographic risk factors for egg allergy in a population‐based study of infants (2012)

Exposure in the first year of life to siblings and dogs may decrease the risk of subsequent egg allergy. Infants with a family history of allergy and those with parents born in East Asia are at increased risk of egg allergy.
Discovery of a Novel Glucagon Receptor AntagonistN-[(4-{(1S)-1-[3-(3, 5-Dichlorophenyl)-5-(6-methoxynaphthalen-2-yl)-1H-pyrazol-1-yl]ethyl}phenyl)carbonyl]-β-alanine (MK-0893) for the Treatment of Type II Diabetes (2012)

A potent, selective glucagon receptor antagonist 9m, N-[(4-{(1S)-1-[3-(3,5-dichlorophenyl)-5-(6-methoxynaphthalen-2-yl)-1H-pyrazol-1-yl]ethyl}phenyl)carbonyl]-β-alanine, was discovered by optimization of a previously identified lead. Compound 9m is a reversible and competitive antagonist with high binding affinity (IC(50) of 6.6 nM) and functional cAMP activity (IC(50) of 15.7 nM). It is selective for glucagon receptor relative to other family B GPCRs, showing IC(50) values of 1020 nM for GIPR, 9200 nM for PAC1, and >10000 nM for GLP-1R, VPAC1, and VPAC2. Compound 9m blunted glucagon-induced glucose elevation in hGCGR mice and rhesus monkeys. It also lowered ambient glucose levels in both acute and chronic mouse models: in hGCGR ob/ob mice it reduced glucose (AUC 0-6 h) by 32% and 39% at 3 and 10 mpk single doses, respectively. In hGCGR mice on a high fat diet, compound 9m at 3, and 10 mpk po in feed lowered blood glucose levels by 89% and 94% at day 10, respectively, relative to the difference between the vehicle control and lean hGCGR mice. On the basis of its favorable biological and DMPK properties, compound 9m (MK-0893) was selected for further preclinical and clinical evaluations.
ChemInform Abstract: NUCLEOPHILER CHARAKTER VON ALKYLRADIKALEN 2. MITT. SELEKTIVE ALKYLIERUNG VON PYRIDIN, CHINOLIN UND ACRIDIN DURCH HYDROPEROXIDE UND OXAZIRANE (1970)

Abstract Das Peroxid (I) reagiert mit Chinolin (II) in Gegenwart von Fe(II)‐Sa1z über ein Radikal zum 2‐ und 4‐alkylierten Chinolin (IIIa).
Immunoprofiling toll-like receptor ligands: Comparison of immunostimulatory and proinflammatory profiles in ex vivo human blood models (2010)

There is a pressing need for the development of novel, safe, and effective adjuvants. The recent discovery and characterization of pathogen-associated molecular pattern (PAMP)-recognizing elements such as the Toll-like, NOD-like, and RIG-like receptors, has brought into sharp focus the role of PAMPs in bridging the innate and adaptive immune responses, and a detailed understanding of the immunostimulatory vis-à-vis proinflammatory activities could lead to the development of effective adjuvants, monophosphoryl lipid A being an excellent example. We describe in this paper a series of hierarchical assays that were employed to characterize TLR agonists in vitro including primary TLR-reporter assays, secondary indices of immune activation, and tertiary screens characterizing transcriptomal activation patterns to identify optimal immunostimulatory chemotypes. The evaluation of representative members of known human TLR agonists demonstrate that TLR2, -4, -5, and -7 agonists were immunostimulatory. TLR7 agonists were extremely immunostimulatory, stimulating nearly all subsets of lymphocytes without inducing proinflammatory cytokine responses. The TLR5 agonist, flagellin, while immunostimulatory, was also highly proinflammatory. These results suggest that TLR agonists other than lipid A-like chemotypes could be developed into potential adjuvants, and that this series of hierarchical assays could be adapted to rapidly identify in large libraries, compounds with adjuvantic potential that lack proinflammatory responses.
D-amino acid-mediated translation arrest is modulated by the identity of the incoming aminoacyl-tRNA (2018)

Abstract A complete understanding of the determinants that restrict D-amino acid incorporation by the ribosome, which is of interest to both basic biologists as well as the protein engineering community, remains elusive. Previously, we demonstrated that D-amino acids are successfully incorporated into the C-terminus of the nascent polypeptide chain. Ribosomes carrying the resulting peptidyl-D-aminoacyl-tRNA (peptidyl-D-aa-tRNA) donor substrate, however, partition into subpopulations that either undergo translation arrest through inactivation of the ribosomal peptidyl-transferase center (PTC) or remain translationally competent. The proportion of each subpopulation is determined by the identity of the D-amino acid sidechain. Here, we demonstrate that the identity of the aminoacyl-tRNA (aa-tRNA) acceptor substrate that is delivered to ribosomes carrying a peptidyl-D-aa-tRNA donor further modulates this partitioning. Our discovery demonstrates that it is the pairing of the peptidyl-D-aa-tRNA donor and the aa-tRNA acceptor that determines the activity of the PTC. Moreover, we provide evidence that both the amino acid and tRNA components of the aa-tRNA donor contribute synergistically to the extent of arrest. The results of this work deepen our understanding of the mechanism of D-amino acid-mediated translation arrest and how cells avoid this precarious obstacle, reveal similarities to other translation arrest mechanisms involving the PTC, and provide a new route for improving the yields of engineered proteins containing D-amino acids.
MU-MIMO beamforming with full-duplex open-loop training (2015)

In this paper, full-duplex radios are used to continuously update the channel state information at the transmitter, which is required to compute the downlink precoding matrix in MIMO broadcast channels. The full-duplex operation allows leveraging channel reciprocity for open-loop uplink training to estimate the downlink channels. However, the uplink transmission of training creates interference at the downlink receiving mobile nodes. We characterize the optimal training resource allocation and its associated spectral efficiency, in the proposed open-loop training based full-duplex system. We also evaluate the performance of the half-duplex counterpart to derive the relative gains of full-duplex training. Despite the existence of the inter-node interference due to full-duplex, significant spectral efficiency improvement is attained over half-duplex operation.
Politiques urbaines et développement local (1993)

Analyse comparative des politiques de développement économique local dans les villes moyennes en France et en Grande-Bretagne, à travers l'étude des cas de Coventry et de Rennes. La 1ère partie est une analyse des politiques du gouvernement central, des tendances des politiques de développement économique local, des restructurations économiques et spatiales liées à la crise et du rôle des facteurs sociaux locaux. La 2ème partie met en évidence les facteurs qui déterminent la politique de développement économique dans les deux villes et montre l'importance du jeu des acteurs politiques et sociaux locaux. (Résumé éditeur)
A Combined Experimental and Theoretical Study of Anion–π Interactions in Bis(pyrimidine) Salts (2007)

Abstract We report the synthesis and X‐ray characterization of an N , N′ ‐tetramethylenebis(2‐aminopyrimidinium) tetrafluoroborate salt that exhibits anion–π interactions that are responsible for the crystal packing. The anion forms a sandwich complex with two pyrimidine rings. When the anion is nitrate, the crystal packing is governed by anion–π interactions and hydrogen bonds, and the sandwich complex is not formed. Finally, a theoretical study of the anion–π interactions in charged pyrimidine rings is in good agreement with the experimental findings. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2007)
Body mass index in HER2-negative metastatic breast cancer treated with first-line paclitaxel and bevacizumab (2018)

The evidence emerged from the TOURANDOT trial encourages evaluating the role of anthropometric determinants on treatment outcomes in HER2-negative metastatic breast cancer patients treated with bevacizumab-including regimens. We thus analyzed data from a subgroup of these patients from a larger cohort previously assessed for treatment outcomes. Patients were included in the present analysis if body mass index values had been recorded at baseline. Clinical benefit rates, progression free survival and overall survival were assessed for the overall study population and subgroups defined upon molecular subtype. One hundred ninety six patients were included (N:196). Body mass index showed no impact on clinical benefit rates in the overall study sample and in the luminal cancer subset (p = 0.12 and p = 0.79, respectively), but did so in the triple negative subgroup, with higher rates in patients with body mass index ≥25 (p = 0.03). In the overall study sample, body mass index did no impact progression free or overall survival (p = 0.33 and p = 0.67, respectively). Conversely, in triple negative patients, progression free survival was significantly longer with body mass index ≥25 (6 vs 14 months, p = 0.04). In this subset, overall survival was more favorable (25 vs 19 months, p = 0.02). The impact of the molecular subtype was confirmed in multivariate models including the length of progression free survival, and number of metastatic sites (p < 0.0001). Further studies are warranted to confirm our findings in more adequately sized, ad hoc, prospective studies.
Search for the lepton-flavour violating decays B0 → K*0τ±μ∓ (2023)

A bstract A first search for the lepton-flavour violating decays B 0 → K *0 τ ± μ ∓ is presented. The analysis is performed using a sample of proton-proton collision data, collected with the LHCb detector at centre-of-mass energies of 7, 8 and 13 TeV between 2011 and 2018, corresponding to an integrated luminosity of 9 fb − 1 . No significant signal is observed, and upper limits on the branching fractions are determined to be $$ \mathcal{B}\left({B}^0\to {K}^{\ast 0}{\tau}^{+}{\mu}^{-}\right)&lt;1.0(1.2)\times {10}^{-5} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mi>B</mml:mi> <mml:mfenced> <mml:mrow> <mml:msup> <mml:mi>B</mml:mi> <mml:mn>0</mml:mn> </mml:msup> <mml:mo>→</mml:mo> <mml:msup> <mml:mi>K</mml:mi> <mml:mrow> <mml:mo>∗</mml:mo> <mml:mn>0</mml:mn> </mml:mrow> </mml:msup> <mml:msup> <mml:mi>τ</mml:mi> <mml:mo>+</mml:mo> </mml:msup> <mml:msup> <mml:mi>μ</mml:mi> <mml:mo>−</mml:mo> </mml:msup> </mml:mrow> </mml:mfenced> <mml:mo>&lt;</mml:mo> <mml:mn>1.0</mml:mn> <mml:mfenced> <mml:mn>1.2</mml:mn> </mml:mfenced> <mml:mo>×</mml:mo> <mml:msup> <mml:mn>10</mml:mn> <mml:mrow> <mml:mo>−</mml:mo> <mml:mn>5</mml:mn> </mml:mrow> </mml:msup> </mml:math> and $$ \mathcal{B}\left({B}^0\to {K}^{\ast 0}{\tau}^{-}{\mu}^{+}\right)&lt;8.2(9.8)\times {10}^{-6} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mi>B</mml:mi> <mml:mfenced> <mml:mrow> <mml:msup> <mml:mi>B</mml:mi> <mml:mn>0</mml:mn> </mml:msup> <mml:mo>→</mml:mo> <mml:msup> <mml:mi>K</mml:mi> <mml:mrow> <mml:mo>∗</mml:mo> <mml:mn>0</mml:mn> </mml:mrow> </mml:msup> <mml:msup> <mml:mi>τ</mml:mi> <mml:mo>−</mml:mo> </mml:msup> <mml:msup> <mml:mi>μ</mml:mi> <mml:mo>+</mml:mo> </mml:msup> </mml:mrow> </mml:mfenced> <mml:mo>&lt;</mml:mo> <mml:mn>8.2</mml:mn> <mml:mfenced> <mml:mn>9.8</mml:mn> </mml:mfenced> <mml:mo>×</mml:mo> <mml:msup> <mml:mn>10</mml:mn> <mml:mrow> <mml:mo>−</mml:mo> <mml:mn>6</mml:mn> </mml:mrow> </mml:msup> </mml:math> at the 90% (95%) confidence level.
Imaging obliquely illuminated skin lesions for skin cancer detection (2000)

This study was designed to distinguish between benign and pre-cancerous pigmented skin lesions using obliquely incident light combined with statistical image analysis. Preliminary results indicate that skin lesions can be characterized using appropriate texture features.
Serum Concentrations of Antigen-Specific IgG4 in Patients with Japanese Cedar Pollinosis (2021)

Purpose: To elucidate the usefulness of Japanese cedar pollen (JCP)-specific antigen-specific immunoglobulin (IgG) 4 as a biomarker for predicting the efficacy of sublingual immunotherapy for cedar pollen-induced allergic rhinitis. Methods: We divided a total of 105 cases with Japanese cedar pollinosis into three groups: “SLIT Successful,” SLIT Unsatisfactory,” and “SCIT” groups. The SLIT group patients were treated with JCP Droplet (Torii Pharmaceutical Co. Ltd., Tokyo, Japan) for one year from 2015 and were divided into two groups, the SLIT Successful group or the SLIT Unsatisfactory group. The SLIT Successful group (n = 16) were subjects treated by SLIT only, who were able to experience control of their naso-ocular symptoms without the need for antiallergic rescue agents during the peak season of atmospheric pollen. The SLIT Unsatisfactory group (n = 76) comprised subjects treated with SLIT only, who did not respond successfully, and were administered with rescue agents to control their naso-ocular symptoms. The SCIT group had been treated with standardized JCP extract (Torii Pharmaceutical Co., Ltd., Tokyo, Japan) for three years from 2012, and were also able to experience control of their symptoms during the peak pollen season without the need for antiallergic rescue agents. We determined the serum level of JCP-specific immunoglobulin E (IgE), IgG, and IgG4 used in the 3gAllergy-specific IgE assay (3gAllergy). The serum levels of periostin and SCCA2 were measured using established ELISA procedures (clones SS18A and SS17B; Shino-Test, Japan) following the manufacturer’s instructions. We then made ROC curves for each group and assessed which index was best able to predict the efficacy of sublingual immunotherapy. Results: Serum JCP-specific IgE was significantly lower in the SCIT group than in the SLIT Successful group and the SLIT Unsatisfactory group (p &lt; 0.05). Serum JCP-specific IgG was significantly higher in the SCIT group and the SLIT Successful group than in the SLIT Unsatisfactory group (p &lt; 0.05). Serum JCP-specific IgG4 was also significantly higher in the SCIT group and the SLIT Successful group than in the SLIT Unsatisfactory group (p &lt; 0.05). There was no significant difference among serum levels of periostin in the SCIT group, the SLIT Successful group, or the SLIT Unsatisfactory group. There was also no significant difference in SCCA2 among the three groups. In terms of ROC curves, a serum JCP-specific IgG4 value greater than 989.5 UA/mL showed the best sensitivity (93.3%) and specificity (94.7%) (p &lt; 0.05) among other parameters. Conclusions: The serum JCP-specific IgG4 level is significantly correlated with the clinical efficacy of SLIT. Serum JCP-specific IgG4 cutoff levels greater than 989.5 UA/mL were correlated with an effective clinical response to SLIT, with a sensitivity of 93.3% and a specificity of 94.7%.
Genetic stability of rotaviruses recovered from asymptomatic neonatal infections (1988)

The sequence of the VP7 gene from 19 rotavirus strains recovered from asymptomatically infected newborn infants was determined by direct analysis of transcript RNAs synthesized from virus present in the stool. For five viruses the entire VP7 gene was sequenced, whereas in the remaining instances only a portion of the gene could be sequenced. In 19 specimens collected over a 4-year period, only five nucleotide substitutions were detected. None of them resulted in an amino acid substitution. Examination of a 306-nucleotide segment of gene 4 in 11 specimens yielded similar results. These results suggest that the mutation rate of rotaviruses in nature is lower than that of single-stranded RNA viruses such as poliovirus and influenza virus.
Is there any exposure from a mobile phone in stand-by mode? (2012)

Several studies have been using a GSM mobile phone in stand-by mode as the source for exposure, and they claimed that this caused effects on for instance sleep and testicular function. In stand-by mode the phone is only active in periodic location updates, and this occurs with a frequency set by the net operator. Typical updates occur with 2-5 h in between, and between these updates the phone is to be considered as a passive radio receiver with no microwave emission. Thus, the exposure in stand-by mode can be considered negligible.
Stereoselective Total Synthesisof (+)-Valienamine and (+)-4-epi-Valienamine viaa Ring-Closing Enyne Metathesis Protocol (2009)

Stereoselective total synthesis of (+)-valienamine is reported utilizing Sharpless asymmetric dihydroxylation, diastereoselective Carreira alkynylation, and ring-closing enyne metathesis (RCEYM) as key steps from l-serine. A similar strategy is also reported for the first total synthesis of (+)-4-epi-valienamine.