gebhart/patrepeval huggingface dataset:
Fabrication and Characterization of Amorphous Cobalt-Doped Molybdenum Sulfide for Hydrogen Evolution Reaction (2015)

In the present study, hydrogen evolution reaction (HER) by alkaline water electrolysis was conducted without using a precious metal catalyst. We synthesized an amorphous cobalt-doped molybdenum sulfide by electrodeposition using different cobalt loadings. The amorphous Co-MoSx produced was characterized by scanning electron microscopy, transmission electron microscopy, and X-ray photoelectron spectroscopy. The cobalt doping and sulfidation procedure resulted in the successful fabrication of a candidate catalyst for the catalytic hydrogen evolution in alkaline solution with high intrinsic activity. Cobalt incorporated amorphous MoSx exhibited 3 times higher HER activity than non-promoted MoSx.
Laboratory-Scale Burning of Composite Solid Propellant UsingIn-SituSynthesized Iron Oxide (2016)

The focus of this study was to demonstrate the ability to synthesize in-situ iron oxide. The in-situ synthesis process to grow nano-particles in the propellant binder has been shown in previous studies to enhance the catalytic effect of titania in composition propellants. Upon the success of synthesizing the in-situ titania in the HTPB binder, now the authors have applied that same process to iron oxide. Results indicate the 15-to-20-nm-sized iron oxide particles grown in-situ indeed increase the burning rate on both aluminized and non-aluminized AP/HTPB-based propellants. SEM imaging was used to view the in-situ iron oxide in the HTPB binder, and it appeared to be well distributed within the binder. As this work represents the first iteration on the iron oxide synthesis process, additional iterations may be needed to unlock the full potential of iron oxide as a catalyst.
Fluides supercritiques et développement durable : de l’élaboration au recyclage des matériaux (2018)

International audience
Abnormal α to γ Transformation Behavior of Steels with a Martensite and Bainite Microstructure at a Slow Reheating Rate (2009)

The same coarse austenite (γ) grains as those before austenitizing emerge when a martensite or bainite steel with coarse grains is reheated to an austenite region at a slow reheating rate. This is called abnormal ferrite (α) to austenite (γ) transformation or γ grain memory. In this paper, α to γ transformation behavior is investigated in order to clarify the mechanism of abnormal α to γ transformation from the viewpoint of the roles of cementite and retained γ. (1) Coarse γ grains and fine globular γ grains that nucleate along the coarse γ grain boundaries are formed when bainite or martensite steel is reheated above the AC3 temperature. The size distribution of γ grain is the same as that before reheating. (2) Coarse γ grains are formed by the growth, impingement, and coalescence of acicular γ grains that corresponds to retained γ between laths. (3) Abnormal α to γ transformation is suppressed by decreasing the amount of retained γ and by increasing the amount of cementite before reheating. These results suggest that α to γ transformation behavior is governed by competition between the nucleation and growth of newly formed γ from the dissolution of cementite and the growth and coalescence of retained γ. Abnormal α to γ transformation occurs when the growth and coalescence of retained γ dominates rather than the nucleation and growth of globular γ grains.
Bacterial virulence against an oceanic bloom-forming phytoplankter is mediated by algal DMSP (2018)

Abstract Emiliania huxleyi is a bloom forming microalga that impacts the global sulfur cycle by producing large amounts of dimethylsulfoniopropionate (DMSP) and its volatile metabolic product dimethyl sulfide (DMS). Top-down regulation of E. huxleyi blooms is attributed to viruses and grazers, however, the possible involvement of algicidal bacteria in bloom demise is still elusive. We isolated from a North Atlantic E. huxleyi bloom a Roseobacter strain, Sulfitobacter D7, which exhibited algicidal effects against E. huxleyi upon co-culturing. Both the alga and the bacterium were found to co-occur during a natural E. huxleyi bloom, therefore establishing this host-pathogen system as an attractive, ecologically relevant model for studying alga-bacterium interaction in the oceans. During interaction, Sulfitobacter D7 consumed and metabolized algal DMSP to produce high amounts of methanethiol, an alternative product of DMSP catabolism. We revealed a unique strain-specific response, in which E. huxleyi strains that exuded higher amounts of DMSP were more susceptible to Sulfitobacter D7 infection. Intriguingly, exogenous application of DMSP enhanced bacterial virulence and induced susceptibility in a resistant algal strain to the bacterial pathogen. This DMSP-dependent pathogenicity was highly specific as compared to supplementation of propionate and glycerol. We propose a novel function for DMSP, in addition to its central role in mutualistic interactions, as a mediator of bacterial virulence that may regulate E. huxleyi blooms.
X-ray crystallographic analysis of the hydration of A- and B-form DNA at atomic resolution (1998)

We have determined single crystal structures of an A-DNA decamer and a B-DNA dodecamer at 0.83 and 0.95 A, respectively. The resolution of the former is the highest reported thus far for any right-handed nucleic acid duplex and the quality of the diffraction data allowed determination of the structure with direct methods. The structures reveal unprecedented details of DNA fine structure and hydration; in particular, we have reexamined the overall hydration of A- and B-form DNA, the distribution of water around phosphate groups, and features of the water structure that may underlie the B to A transition.
Supplementary Figures from Distinct Mechanisms of Mismatch-Repair Deficiency Delineate Two Modes of Response to Anti–PD-1 Immunotherapy in Endometrial Carcinoma (2023)

&lt;p&gt;Supplementary Figure S1: Additional characterization of the clinical trial cohort.Supplementary Figure S2: Additional characterization of exome profiles and defining MLH1 methylation status.Supplementary Figure S3: JAK1 alterations are most frequent in endometrial cancer.Supplementary Figure S4: Final cell counts in each scRNA-seq sample.Supplementary Figure S5: Longitudinal transcriptional profiling of circulating immune cells before and after PD-1 blockade.Supplementary Figure S6: Differential abundance of cell neighborhoods after PD-1 immunotherapy.Supplementary Figure S7: Differential abundance of cell neighborhoods in JAK1-mutant tumors.Supplementary Figure S8: Transcriptional profiles of T and NK cells in responders vs non-responders.Supplementary Figure S9: Gene expression changes in T and NK cells following PD-1 immunotherapy.Supplementary Figure S10: Additional transcriptional characterization of CD16+ NK cells in epiR patients.&lt;/p&gt;
MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions (2018)

Abstract Motivation Long non-coding RNAs (lncRNAs) are defined as transcripts longer than 200 nucleotides that do not get translated into proteins. Often these transcripts are processed (spliced, capped, polyadenylated) and some are known to have important biological functions. However, most lncRNAs have unknown or poorly understood functions. Nevertheless, because of their potential role in cancer, lncRNAs are receiving a lot of attention, and the need for computational tools to predict their possible mechanisms of action is more than ever. Fundamentally, most of the known lncRNA mechanisms involve RNA-RNA and/or RNA-protein interactions. Through accurate predictions of each kind of interaction and integration of these predictions, it is possible to elucidate potential mechanisms for a given lncRNA. Approach Here we introduce MechRNA, a pipeline for corroborating RNA-RNA interaction prediction and protein binding prediction for identifying possible lncRNA mechanisms involving specific targets or on a transcriptome-wide scale. The first stage uses a version of IntaRNA2 with added functionality for efficient prediction of RNA-RNA interactions with very long input sequences, allowing for large-scale analysis of lncRNA interactions with little or no loss of optimality. The second stage integrates protein binding information pre-computed by GraphProt, for both the lncRNA and the target. The final stage involves inferring the most likely mechanism for each lncRNA/target pair. This is achieved by generating candidate mechanisms from the predicted interactions, the relative locations of these interactions and correlation data, followed by selection of the most likely mechanistic explanation using a combined p-value. Results We applied MechRNA on a number of recently identified cancer-related lncRNAs (PCAT1, PCAT29, ARLnc1) and also on two well-studied lncRNAs (PCA3 and 7SL). This led to the identification of hundreds of high confidence potential targets for each lncRNA and corresponding mechanisms. These predictions include the known competitive mechanism of 7SL with HuR for binding on the tumor suppressor TP53, as well as mechanisms expanding what is known about PCAT1 and ARLn1 and their targets BRCA2 and AR, respectively. For PCAT1-BRCA2, the mechanism involves competitive binding with HuR, which we confirmed using HuR immunoprecipitation assays. Availability MechRNA is available for download at https://bitbucket.org/compbio/mechrna Contact backofen@informatik.uni-freiburg.de , cenksahi@indiana.edu Supplementary information Supplementary data are available at Bioinformatics online.
Metabolic disturbances in synovial fluid are involved in the onset of synovitis in heifers with acute ruminal acidosis (2019)

Acute ruminal acidosis (ARA) is the result of increased intake of highly fermentable carbohydrates, which frequently occurs in dairy cattle and is associated with aseptic polysynovitis. To characterise the metabolic changes in the joints of animals with ARA, we performed an untargeted gas chromatography-mass spectrometry (GC-MS)-based metabolomic analysis of synovial fluid. Seven heifers were challenged with an intraruminal oligofructose overload (13 g/kg of body weight [BW]) dissolved in water. Synovial fluid samples were collected at 0, 9 and 24 h post-overload. Metabolome analysis revealed the presence of 67 metabolites. At 9 h post-overload, glyceric acid, cellobiose, fructose and lactic acid were all increased, whereas at 24 h, sorbitol, lactic acid and fructose levels were all increased >10-fold. At 24 h, citric acid and threonine levels were significantly reduced. We detected increased L- and D-lactate, and the presence of interleukin-6 (IL-6) in synovial fluid. Furthermore, using bovine fibroblast-like synoviocytes, we observed that D-lactate induces IL-6 synthesis. Our results suggest that ARA produces severe metabolomic changes in synovial fluid, including disturbances in starch and sucrose metabolism, and increased lactate levels. These changes were observed prior to the appearance of synovitis, suggesting a potential role in the onset of polysynovitis.
Active species in the anionic ring-opening polymerization of cyclic carbonates (1989)

Anionic ring opening polymerization of 5,5-dimethyl-1,3-dioxan-2-one (2,2-dimethyltrimethylene carbonate) (1) initiated by sec-butyllithium, sodium methoxide or potassium dihydronaphthylide was found to proceed via alcoholate anions. This finding is based on 31P NMR spectroscopic studies of the polymer end groups, which result from the reaction of the living polymer with diphenyl chlorophosphate.
Biosensor libraries harness large classes of binding domains for allosteric transcription regulators (2017)

Bacteria’s ability to specifically sense small molecules in their environment and trigger metabolic responses in accordance is an invaluable biotechnological resource. While many transcription factors (TFs) mediating these processes have been studied, only a handful has been leveraged for molecular biology applications. To expand this panel of biotechnologically important sensors here we present a strategy for the construction and testing of chimeric TF libraries, based on the fusion of highly soluble periplasmic binding proteins (PBPs) with DNA-binding domains (DBDs). We validated this strategy by constructing and functionally testing two unique sense-and-response regulators for benzoate, an environmentally and industrially relevant metabolite. This work will enable the development of tailored biosensors for synthetic regulatory circuits.
The Stability of Free Fermi Hamiltonians (2017)

Recent results have shown the stability of frustration-free Hamiltonians to weak local perturbations, assuming several conditions. In this paper, we prove the stability of free fermion Hamiltonians which are gapped and local. These free fermion Hamiltonians are not necessarily frustration-free, but we are able to adapt previous work to prove stability. The key idea is to add an additional copy of the system to cancel topological obstructions. We comment on applications to quantization of Hall conductance in such systems.
Positive tone oxide nanoparticle EUV (ONE) photoresists (2016)

Nanoparticles with a variety of organic/inorganic combinations have been investigated and the negative tone patterning was demonstrated using EUV radiation. Zirconium methacrylate (ZrMAA) nanoparticles had sensitivity with EUV exposure as high as 4.2 mJ/cm<sup>2</sup> with a resolution up to 22 nm, and an LER of 5.6 nm. Meanwhile, the dual-tone behavior of ZrMAA photoresists using e-beam and deep UV exposures is another attractive feature of the nanoparticle photoresists, which may be further applied with EUV lithography. The current study investigates the positive tone patterning of ZrMAA and the process-dependent image reversal. Our proposed patterning mechanism is further illustrated and optimized based in a positive tone behavior study.
ChemInform Abstract: A Modified Bischler‐Napieralski Procedure for the Synthesis of 3‐Aryl‐ 3,4‐dihydroisoquinolines. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Supplementary Figure S3 from YAP Orchestrates Heterotypic Endothelial Cell Communication via HGF/c-MET Signaling in Liver Tumorigenesis (2023)

&lt;p&gt;Analysis of scRNA-seq data derived from healthy liver tissues&lt;/p&gt;
Chemical Vapor Deposition of Molybdenum Silicide (1988)

A cold‐wall reactor has been used to deposit molybdenum silicide films from a mixture of and . The composition of the resulting films can be controlled by the deposition temperature, and stoichiometry is obtained with a substrate temperature of 200°C. The film composition is independent of reactant gas ratios in the range of 1–10. The as‐deposited films are generally amorphous as determined by x‐ray analysis. Annealing at 950°C in argon converts the films to tetragonal polycrystalline .
Guest Editors’ Introduction: Special Issue on Advances in Management of Softwarized Networks (2017)

Softwarization of networks is an important trend, enabled by the NV (Network Virtualization), SDN (Software-Defined Networking), and NFV (Network Function Virtualization) paradigms and offers many advantages for network operators, service providers and datacenter providers. Given the strong interest in both industry and academia in the softwarization of telecommunication networks and cloud computing infrastructures, a series of special issues was established in IEEE Transactions on Network and Service Management, which aims at the timely publication of recent innovative research results on management of softwarized networks.
Specific Detection of Antibiotics by Silicon-on-Chip Photonic Crystal Biosensor Arrays (2017)

Photonic crystal (PC) microcavities formed by 2-D air holes on silicon-on-insulator substrates were utilized as biosensors to detect antibiotics with high specificity. The antibiotic, gentamicin, with molecular weight of only 478 g/mol, was successfully detected via its binding to corresponding antibody pre-immobilized on the sensor surface. Detection range (in concentration) was extended by combining different types of PC biosensors on a single silicon chip, covering from 0.1 nM to 1 μM . Specificity of detection was also verified on the studied antibiotic.
Cover Picture: On the Origin of the “Giant” Electroclinic Effect in a “De Vries”‐Type Ferroelectric Liquid Crystal Material for Chirality Sensing Applications (ChemPhysChem 6/2009) (2009)

Abstract The cover picture shows characteristics of a new ‘de Vries’‐type ferroelectric liquid crystal in which the ferroelectric transition is an order–disorder transition where the directions of molecular tilt inside a smectic layer order into a certain direction. Since the rod‐like molecules (drawn as cylinders) are tilted in the paraelectric SmA* (with random tilt directions) as well as in the ferroelectric SmC* phase, the ferroelectric transition is connected with a rather weak contraction of the smectic layer thickness (even though the optical tilt θ reaches values of about 25°). On page 890, F. Giesselmann et al. show that this new ferroelectric material exhibits a remarkably weak temperature dependence of its giant electroclinic effect (the coupling between tilt and elelctric field) in the SmA* phase. The origin of this striking electroclinic effect is the co‐occurrence of a ‘de Vries’‐type ordering with a weak first‐order tilting transition. magnified image
Supplementary Figure 2 from Complete Regression of Metastatic Renal Cell Carcinoma by Multiple Injections of Engineered Mesenchymal Stem Cells Expressing Dodecameric TRAIL and HSV-TK (2023)

&lt;p&gt;PDF file - 58K, Dose-dependent induction of apoptosis by dodecameric TRAIL expressing MSCs&lt;/p&gt;
New optical magnetic field sensor with optional white light source (abstract) (1991)

A new type of magnetic field sensor which measures ac electric current utilizing Faraday rotation is proposed. On a Faraday element a stabilized dc bias magnetic field Hb is applied. Output signal is given by the ratio R = I2ω/Iω, where Iω and I2ω are fundamental and second harmonic signals generated by the field Hx which the ac current induces. Since R is calculated as R = Hx/4Hb, we can measure Hx independent not only of light intensity but also of the Verdet constant (and therefore its temperature dependence) of the Faraday element. This was supported by experiments performed at 20–100 °C for HeNe laser (λ=0.633 and 1.15 μm) light on Faraday elements of FR-5 paramagnetic glass and Bi-substituted YIG crystal. The bias field Hb was generated by a stabilized dc current in a coil and using a SmGdCo plastic magnet with very weak temperature dependence of remanent magnetization (&amp;lt;1% at T=20–120 °C). According to theory the equation holds even when broad spectrum polychromatic light is used. This was confirmed by experiments performed with a halogen-lamp white light transmitted through an optical fiber. Calculated signal-to-noise ratio of the sensor with a polychromatic light agreed with experiments.
Comments and additions to recent papers on new convolutional codes (2001)

Recent publications on new improved convolutional codes claim different codes to be optimum under the optimum distance spectrum (ODS) criterion. This correspondence presents results from a study independent of the previous works, and seeks to clarify some inconsistencies. In addition, some new improved feed-forward convolutional encoders are presented.
Dosage Thresholds for AAV2 and AAV8 Photoreceptor Gene Therapy in Monkey (2011)

Gene therapy is emerging as a therapeutic modality for treating disorders of the retina. Photoreceptor cells are the primary cell type affected in many inherited diseases of retinal degeneration. Successfully treating these diseases with gene therapy requires the identification of efficient and safe targeting vectors that can transduce photoreceptor cells. One serotype of adeno-associated virus, AAV2, has been used successfully in clinical trials to treat a form of congenital blindness that requires transduction of the supporting cells of the retina in the retinal pigment epithelium (RPE). Here, we determined the dose required to achieve targeting of AAV2 and AAV8 vectors to photoreceptors in nonhuman primates. Transgene expression in animals injected subretinally with various doses of AAV2 or AAV8 vectors carrying a green fluorescent protein transgene was correlated with surgical, clinical, and immunological observations. Both AAV2 and AAV8 demonstrated efficient transduction of RPE, but AAV8 was markedly better at targeting photoreceptor cells. These preclinical results provide guidance for optimal vector and dose selection in future human gene therapy trials to treat retinal diseases caused by loss of photoreceptors.
A diacridine derivative that binds by bisintercalation at two contiguous sites on DNA (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA diacridine derivative that binds by bisintercalation at two contiguous sites on DNAGraham J. Atwell, Georgina M. Stewart, Werner Leupin, and William A. DennyCite this: J. Am. Chem. Soc. 1985, 107, 14, 4335–4337Publication Date (Print):July 1, 1985Publication History Published online1 May 2002Published inissue 1 July 1985https://pubs.acs.org/doi/10.1021/ja00300a046https://doi.org/10.1021/ja00300a046research-articleACS PublicationsRequest reuse permissionsArticle Views90Altmetric-Citations26LEARN 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 Get e-Alerts