gebhart/patrepeval huggingface dataset:
Genome‐wide association study of INDELs identified four novel susceptibility loci associated with lung cancer risk (2019)

Genome-wide association studies (GWAS) have identified 45 susceptibility loci associated with lung cancer. Only less than SNPs, small insertions and deletions (INDELs) are the second most abundant genetic polymorphisms in the human genome. INDELs are highly associated with multiple human diseases, including lung cancer. However, limited studies with large-scale samples have been available to systematically evaluate the effects of INDELs on lung cancer risk. Here, we performed a large-scale meta-analysis to evaluate INDELs and their risk for lung cancer in 23,202 cases and 19,048 controls. Functional annotations were performed to further explore the potential function of lung cancer risk INDELs. Conditional analysis was used to clarify the relationship between INDELs and SNPs. Four new risk loci were identified in genome-wide INDEL analysis (1p13.2: rs5777156, Insertion, OR = 0.92, p = 9.10 × 10<sup>-8</sup> ; 4q28.2: rs58404727, Deletion, OR = 1.19, p = 5.25 × 10<sup>-7</sup> ; 12p13.31: rs71450133, Deletion, OR = 1.09, p = 8.83 × 10<sup>-7</sup> ; and 14q22.3: rs34057993, Deletion, OR = 0.90, p = 7.64 × 10<sup>-8</sup> ). The eQTL analysis and functional annotation suggested that INDELs might affect lung cancer susceptibility by regulating the expression of target genes. After conducting conditional analysis on potential causal SNPs, the INDELs in the new loci were still nominally significant. Our findings indicate that INDELs could be potentially functional genetic variants for lung cancer risk. Further functional experiments are needed to better understand INDEL mechanisms in carcinogenesis.
Evaluation of rosette infrasonic noise-reducing spatial filters (2003)

This paper presents results from recent tests of rosette infrasonic noise-reducing spatial filters at the Pinon Flat Observatory in southern California. Data from 18- and 70-m aperture rosette filters and a reference port are used to gauge the reduction in atmospheric wind-generated noise levels provided by the filters and to examine the effect of these spatial filters on spatially coherent acoustic signals in the 0.02- to 10-Hz band. At wind speeds up to 5.5 m/s, the 18-m rosette filter reduces wind noise levels above 0.2 Hz by 15 to 20 dB. Under the same conditions, the 70-m rosette filter provides noise reduction of up to 15 to 20 dB between 0.02 and 0.7 Hz. Standing wave resonance inside the 70-m filter degrades the reception of acoustic signals above 0.7 Hz. The fundamental mode of the resonance, 15 dB above background, is centered at 2.65-Hz and the first odd harmonic is observed at 7.95 Hz in data from the large filter. Analytical simulations accurately reproduce the noise reduction and resonance observed in the 70-m filter at all wind speeds above 1.25 m/s. Resonance theory indicates that internal reflections that give rise to the resonance observed in the passband are occurring at the summing manifolds, and not at the inlets. Rosette filters are designed for acoustic arrivals with infinite phase velocity. The plane-wave response of the 70-m rosette filter has a strong dependence on frequency above 3.5 Hz at grazing angles of less than 15 degrees from the horizontal. At grazing angles, complete cancellation of the signal occurs at 5 Hz. Theoretical predictions of the phase and amplitude response of 18- and 70-m rosette filters, that take into account internal resonance and time delays between the inlets, compare favorably with observations derived from a cross-spectral analysis of signals from the explosion of a large bolide.
Differential expression of the homeobox gene Hox-1.3 in F9 embryonal carcinoma cells. (1988)

The Hox-1.3 gene is located on mouse chromosome 6 and has been previously shown to be expressed in mouse embryos and adults. In this study, we have examined the steady-state levels of the Hox-1.3 transcripts in undifferentiated and differentiated F9 embryonal carcinoma cells. We find that there is a rapid increase of Hox-1.3 transcripts after differentiation induction of F9 cells. The level of the major 1.85-kilobase (kb) transcript peaks at 16-24 hr after differentiation induction of F9 cells. By using primer extension techniques the 5' ends of the major 1.85-kb transcript have been mapped to two sites in induced F9 cells. Cellular fractionation of RNA and transfer blot gel analysis has localized one minor transcript to the nucleus, whereas the major transcript and two additional minor transcripts appear in the nucleus and the cytoplasm of induced F9 cells. The results of nuclear run-off experiments with uninduced and induced F9 cell nuclei indicate that there is a substantial increase in the rate of Hox-1.3 transcription upon induction of F9 cells with retinoic acid.
Supplementary Figure S1 from EZH2 Inhibition Blocks Multiple Myeloma Cell Growth through Upregulation of Epithelial Tumor Suppressor Genes (2023)

&lt;p&gt;MMSET expression analysis in MM cell lines&lt;/p&gt;
Self-Sensitized Photooxidation of Naphthols to Naphthoquinones and the Use of Naphthoquinones as Visible Light Photocatalysts in Batch and Continuous Flow Reactors (2023)

Visible light photooxidation of naphthols to produce naphthoquinones, such as the natural product juglone, has been known for decades and has been widely utilized to benchmark the performances of a variety of photocatalytic systems. We discovered that these transformations can occur without the help of a photocatalyst and, even more intriguingly, that the photocatatyst-free process provides higher yields compared to control experiments utilizing state-of-the-art photocatalysts. In addition, we demonstrate that naphthoquinones and their corresponding naphthol precursors can act as alternatives to commonly used organic and organometallic photocatalysts with applications to challenging targets, such as the antimalarial drug artemisinin. This approach was finally transposed in continuous flow reactors where high photocatalyst stability and process efficiency are demonstrated with a 23× improvement in the space-time yield.
Geographic Disparities in Access to Simultaneous Pancreas and Kidney Transplant in the Pre- and Post-Pancreas Allocation System Eras (2019)

Geographic disparities in access to SPK declined slightly but persisted post-PAS. With new allocation change proposals and elimination of listing criteria for T2DM, further monitoring is warranted.
Co-implantation of Al+, P+, and S+ with Si+ implants into In0.53Ga0.47As (2015)

Elevated temperature, nonamorphizing implants of Si+, and a second co-implant of either Al+, P+, or S+ at varying doses were performed into In0.53Ga0.47As to observe the effect that individual co-implant species had on the activation and diffusion of Si doping after postimplantation annealing. It was found that Al, P, and S co-implantation all resulted in a common activation limit of 1.7 × 1019 cm−3 for annealing treatments that resulted in Si profile motion. This is the same activation level observed for Si+ implants alone. The results of this work indicate that co-implantation of group V or VI species is an ineffective means for increasing donor activation of n-type dopants above 1.7 × 1019 cm−3 in InGaAs. The S+ co-implants did not show an additive effect in the total doping despite exhibiting significant activation when implanted alone. The observed n-type active carrier concentration limits appear to be the result of a crystalline thermodynamic limit rather than dopant specific limits.
Morphological work function dependence of rare-earth disilicide metal nanostructures (2008)

The work functions of various DySi(2-x) nanostructures epitaxially grown on a Si(001) surface were correlated with the structure using high-resolution Kelvin probe force microscopy and scanning tunneling microscopy in ultrahigh vacuum. Dy adatoms induce a surface dipole on Si(001) that increases the surface potential from 0.26 to 0.42 eV with respect to 2 x 1 reconstructed Si(001). DySi(2-x) nanowires showed a 0.2-0.23 eV lower work function than DySi(2-x) nanoislands, which can be attributed to confinement of electrons along the surface normal that induces a surface dipole when the film thickness approaches the Fermi wavelength. The ability to tune the work function of metal nanostructures should be useful for understanding how electronic structure affects catalytic activity.
Assessment of bacterial and viral gut communities in healthy and tumoral colorectal tissue using RNA and DNA deep-sequencing (2023)

Abstract Human gut microbiome studies typically focus on 16S RNA analyses and bacterial identification at the genus level. We analyzed bacterial and viral communities in colorectal tissue using both DNA and RNA sequencing and improved taxonomy resolution to species level. Specimens from 10 colorectal cancer patients and 10 matched control patients were DNA and RNA sequenced using Illumina Novaseq. Following taxonomy classification using Kraken 2, alpha and beta diversities (different metrics) as well as relative and differential abundance were calculated. There were no viral differences, but P. nesessarius had a highly increased presence in tumors (p=0.001). RNA analyses showed that A. massiliensis had a highly decreased transcription in tumors (p=0.002) while F. nucleatum transcription was highly increased in tumors (p=0.002). In conclusion, joint assessment of the metagenome (DNA) and the metatranscriptome (RNA) at the species level identifies specific bacterial species as tumor-associated.
Synthesis of LiAl2(OH)6+ intercalated montmorillonite by a hydrothermal soft chemical reaction (2000)

A LiAl2(OH)6+ intercalated montmorillonite was prepared from a montmorillonite by using a hydrothermal soft chemical process. As a first step, lithium aluminium hydroxide complex ions (LixAln(OH)mz+) were inserted into the interlayer space of the montmorillonite by an ion-exchange reaction. In the second step, the ion-exchanged montmorillonite was hydrothermally treated to polymerize the complex ions in the interlayer space, forming a sandwich-like layered compound. The mechanism of formation of the sandwich layered structure was investigated by XRD, TG–DTA, chemical analyses and FTIR spectroscopy. Na+ and Ca2+ ions in the interlayer space of the montmorillonite were first exchanged with LixAln(OH)mz+ complex ions, and during this process the basal spacing of the montmorillonite increased from 1.6 to 2.0 nm after the ion-exchange. Two types of reactions of the ion-exchanged montmorillonite were observed under the hydrothermal conditions. In the temperature range 100–150 °C, the basal spacing changed from 2.0 to 1.7 nm, corresponding to polymerization of LixAln(OH)mz+ complex ions to LiAl2(OH)6+ layers between the silicate layers. At temperatures over 200 °C, Li+ ions of LiAl2(OH)6+ layers probably migrated into the octahedral sheets of silicate layers, accompanied by a decrease of the basal spacing from 1.7 to 1.4 nm. The LixAln(OH)mz+ complex ion was also used for pillaring montmorillonite, and a pillared montmorillonite with a basal spacing of 1.5 nm was obtained by heat treatment of this LixAln(OH)mz+ ion-exchanged montmorillonite in air at 500 °C.
Comparison of Ensemble and Single Molecule Methods for Particle Characterization and Binding Analysis of a PEGylated Single Domain Antibody (2018)

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Cerebral toxoplasmosis in AIDS: a simple laboratory technique for diagnosis (1984)

Journal Article Cerebral toxoplasmosis in AIDS: a simple laboratory technique for diagnosis Get access A. Datry, A. Datry Dept. of Parasitology and Tropical Medicine, Groupe Hospitalier Pitié-Salpêtrière, 47 Boulevard de l'Hôpital, 75651 Paris Cedex 13, France Search for other works by this author on: Oxford Academic PubMed Google Scholar G. Lecso, G. Lecso Dept. of Parasitology and Tropical Medicine, Groupe Hospitalier Pitié-Salpêtrière, 47 Boulevard de l'Hôpital, 75651 Paris Cedex 13, France Search for other works by this author on: Oxford Academic PubMed Google Scholar W. Rozenbaum, W. Rozenbaum Dept. of Parasitology and Tropical Medicine, Groupe Hospitalier Pitié-Salpêtrière, 47 Boulevard de l'Hôpital, 75651 Paris Cedex 13, France Search for other works by this author on: Oxford Academic PubMed Google Scholar M. Danis, M. Danis Dept. of Parasitology and Tropical Medicine, Groupe Hospitalier Pitié-Salpêtrière, 47 Boulevard de l'Hôpital, 75651 Paris Cedex 13, France Search for other works by this author on: Oxford Academic PubMed Google Scholar M. Gentilini M. Gentilini Dept. of Parasitology and Tropical Medicine, Groupe Hospitalier Pitié-Salpêtrière, 47 Boulevard de l'Hôpital, 75651 Paris Cedex 13, France Search for other works by this author on: Oxford Academic PubMed Google Scholar Transactions of The Royal Society of Tropical Medicine and Hygiene, Volume 78, Issue 5, 1984, Pages 679–680, https://doi.org/10.1016/0035-9203(84)90239-6 Published: 01 January 1984 Article history Published: 01 January 1984 Accepted: 25 April 1984
Vascular complications following coronary intervention correlate with long‐term cardiac events (2004)

We aimed to study the consequences and late outcomes of patients who experienced peripheral vascular complications (PVCs) following percutaneous coronary interventions (PCI). A retrospective analysis of the medical records of 10,669 patients who underwent PCI and experienced PVC between 1995 and 2002 was conducted. One thousand ninety-six patients (10.27% of the study cohort) had PVC post-PCI. After PCI, patients with PVC had higher rates of in-hospital complications (P < 0.001) when compared to patients without PVC, including Q-wave myocardial infarction (MI; 1.2% vs. 0.3%), coronary artery bypass grafting (CABG; 3.8% vs. 0.6%), and death (4.0% vs. 1.0%). At 1-year follow-up, late complications of MI (37.4% vs. 25.4%), non-Q-wave MI (34.9% vs. 22.7%), death (12.9% vs. 5.9%), and CABG (5.7% vs. 4.5%) were higher (< 0.001) in patients with PVC compared to those without. Multivariate analysis identified PVC as a significant predictor of 1-year mortality (P = 0.045). This study underscores the need to make diligent efforts to minimize PVC and follow up these patients for future coronary events.
Cebulantin, a Cryptic Lanthipeptide Antibiotic Uncovered Using Bioactivity‐Coupled HiTES (2019)

Abstract The majority of natural product biosynthetic gene clusters in bacteria are silent under standard laboratory growth conditions, making it challenging to uncover any antibiotics that they may encode. Herein, bioactivity assays are combined with high‐throughput elicitor screening (HiTES) to access cryptic, bioactive metabolites. Application of this strategy in Saccharopolyspora cebuensis , with inhibition of Escherichia coli growth as a read‐out, led to the identification of a novel lanthipeptide, cebulantin. Extensive NMR spectroscopic analysis allowed the elucidation of the structure of cebulantin. Subsequent bioactivity assays revealed it to be an antibiotic selective for Gram‐negative bacteria, especially against Vibrio species. This approach, referred to as bioactivity‐HiTES, has the potential to uncover cryptic metabolites with desired biological activities that are hidden in microbial genomes.
Internal Strain Monitoring of Composite Materials with Microstructed Optical Fiber Bragg Grating Sensors (2015)

We present a sensing system based on a combination of 2 optical fibers sensors which are integrated in a composite laminate and that allows three dimensional internal strain measurement in the material. The fiber sensor consists in fiber Bragg gratings fabricated in a dedicated microstructured optical fiber which features enhanced response to transverse strain. We developed a numerical model of the sensor and benchmarked it with experiments performed on laminated composite coupons equipped with this sensor. With this technique, we can measure the strain along the three principal mechanical directions of the coupon with a theoretical strain resolution of 5 μe in the transverse directions which is a 6-fold improvement over results reported in literature. doi: 10.12783/SHM2015/14
Synthesis of Nitro Esters of Prednisolone, New Compounds Combining Pharmacological Properties of Both Glucocorticoids and Nitric Oxide (2003)

Glucocorticoids (GC) are widely used in therapy for their many pharmacological properties including antiinflammatory and immunosuppressive actions. However, their use over long periods is hampered by a number of severe side effects. Given the biological properties of nitric oxide (NO) and previous experience with nonsteroidal antiinflammatory agents, we synthesized new chemical entities combining both NO and GC properties. Here we report the synthesis of nitro esters of prednisolone obtained through the esterification, with different linkers, on the hydroxy group at C-21 position of the corticosteroid structure. The alkyl chain, as of the nitrooxy derivative (2), or aromatic linkers, as of o-, m-, and p-nitrooxymethylbenzoate derivatives (3-5), respectively, furnish stable compounds that release NO and inhibit the GC receptors in biological assays. To improve solubility we introduced a more water-soluble linker such as the nitrooxyalkylpiperidine or -piperazine group (6-9). Also these compounds retained properties of both NO and prednisolone. Compound 5 (NCX 1015) was selected for its better profile: enhanced antiinflammatory properties and reduced side effects compared with prednisolone. NCX 1015 is currently under preclinical development.
In Situ Characterization of Ceria Oxidation States in High-Temperature Electrochemical Cells with Ambient Pressure XPS (2010)

Ambient pressure X-ray photoelectron spectroscopy (XPS) is used to measure near-surface oxidation states and local electric potentials of thin-film ceria electrodes operating in solid oxide electrochemical cells for H2O electrolysis and H2 oxidation. Ceria electrodes which are 300 nm thick are deposited on YSZ electrolyte supports with porous Pt counter electrodes for single-chamber tests in H2/H2O mixtures. Between 635 and 740 °C, equilibrium (zero-bias) near-surface oxidation states between 70 and 85% Ce3+ confirm increased surface reducibility relative to bulk ceria. Positive cell biases drive H2O electrolysis on ceria and further increase the percentage of Ce3+ on the surface over 100 μm from an Au current collector, signifying broad regions of electrochemical activity due to mixed ionic-electronic conductivity of ceria. Negative biases to drive H2 oxidation decrease the percentage of Ce3+ from equilibrium values but with higher electrode impedances relative to H2O electrolysis. Additional tests indicate that increasing H2-to-H2O ratios enhances ceria activity for electrolysis.
Surfactant-free syntheses and pair distribution function analysis of osmium nanoparticles (2021)

A surfactant-free synthesis of precious metal nanoparticles performed in low boiling point solvents and in alkaline conditions has been reported recently. This strategy presents several advantages over alternative colloidal syntheses. The resulting nanoparticles are readily relevant for applications like catalysis and the synthetic process is compatible with large scale production. Alkaline mono-alcohols are here investigated as solvent and reducing agents to obtain colloidal Os nanoparticles by this low temperature (&lt; 100 °C) surfactant-free synthesis. The effect of precursor (OsCl3 or H2OsCl6), precursor concentration (up to 100 mM), solvent (methanol or ethanol), presence or absence of base (NaOH) and addition of water (0 to 100 v.%) on the resulting nanomaterials is discussed. It is fond that no base is required to obtain Os nanoparticles as opposed to the case of Pt NPs for instance. The robustness of the synthesis for concentration of precursor up to 100 mM allows to perform X-ray total scattering with pair distribution function (PDF) analysis that shows that the 1-2 nm hcp NPs forms from chain-like [OsOxCly]-complexes.
Subarachnoid catheter placement after wet tap for analgesia in labor: influence on the risk of headache in obstetric patients (2003)

Subarachnoid catheter placement after wet tap in obstetric patients reduces the PDPH rate and does so to a greater extent if left in place for 24 hours after delivery.
Neubewertung des Schutzes von In-vitro-Embryonen in Deutschland (2021)

Wie entwickelt sich menschliches Leben, wodurch lässt sich die Fortpflanzungsmedizin verbessern und in welcher Weise können Stammzellen bei der Entwicklung neuer Therapien gegen Volkskrankheiten wie Diabetes oder Herzinfarkt helfen? Zur Beantwortung dieser Fragen dürfen Wissenschaftlerinnen und Wissenschaftler in Deutschland bislang nur wenig beitragen, da dafür erforderliche Studien an menschlichen Embryonen außerhalb des Körpers durch das Embryonenschutzgesetz (ESchG) verboten sind. In ihrer gemeinsamen Stellungnahme „Neubewertung des Schutzes von In-vitro-Embryonen in Deutschland“ empfehlen Leopoldina und Akademienunion, Embryonenforschung für hochrangige Forschungsziele im Einklang mit internationalen ethischen Standards künftig zu ermöglichen und den dafür erforderlichen Rechtsrahmen neu zu diskutieren.
Conditional Graphical Models for Protein Structural Motif Recognition (2009)

Determining protein structures is crucial to understanding the mechanisms of infection and designing drugs. However, the elucidation of protein folds by crystallographic experiments can be a bottleneck in the development process. In this article, we present a probabilistic graphical model framework, conditional graphical models, for predicting protein structural motifs. It represents the structure characteristics of a structural motif using a graph, where the nodes denote the secondary structure elements, and the edges indicate the side-chain interactions between the components either within one protein chain or between chains. Then the model defines the optimal segmentation of a protein sequence against the graph by maximizing its "conditional" probability so that it can take advantages of the discriminative training approach. Efficient approximate inference algorithms using reversible jump Markov Chain Monte Carlo (MCMC) algorithm are developed to handle the resulting complex graphical models. We test our algorithm on four important structural motifs, and our method outperforms other state-of-art algorithms for motif recognition. We also hypothesize potential membership proteins of target folds from Swiss-Prot, which further supports the evolutionary hypothesis about viral folds.
Chemical Synthesis of Oligosaccharides: Efficiency and Selectivity. (1998)

Due to high demand to access biologically important oligosaccharide structures, efficient and stereoselective synthetic methods are required. This article addresses these two issues from our recent studies. The first part deals with β-mannosylation and α-sialylation known as the two most difficult glycosylation reactions which were now made possible by means of an “intramolecular aglycon delivery” system and control by “auxiliary”, respectively. In the second part, the remarkably efficient “orthogonal glycosylation strategy” which was developed based on tactical analysis of oligosaccharide synthesis is described.
The DNA Binding Arm of λ Repressor: Critical Contacts from a Flexible Region (1991)

Segments of protein that do not adopt a well-ordered conformation in the absence of DNA can still contribute to site-specific recognition of DNA. The first six residues (NH2-Ser1-Thr2-Lys3-Lys4-Lys5-Pro6-) of phage lambda repressor are flexible but are important for site-specific binding. Low-temperature x-ray crystallography and codondirected saturation mutagenesis were used to study the role of this segment. All of the functional sequences have the form [X]1-[X]2-[Lys or Arg]3-[Lys]4-[Lys or Arg]5-[X]6. A high-resolution (1.8 angstrom) crystal structure shows that Lys3 and Lys4 each make multiple hydrogen bonds with guanines and that Lys5 interacts with the phosphate backbone. The symmetry of the complex breaks down near the center of the site, and these results suggest a revision in the traditional alignment of the six lambda operator sites.