gebhart/patrepeval huggingface dataset:
A Rational Comparison of the Optimal Promoter Edge Decoration of HDT NiMoS vs CoMoS Catalysts (2009)

In order to gain a better understanding of the morphology and promoter edge content of the active phase of industrial HDT NiMoP catalysts in working conditions, a multi-technique study has been undertaken on a series of NiMoP catalysts with various Ni/Mo ratios. The combination of X-ray Photoelectron Spectroscopy (XPS), Transition Electron Microscopy (TEM), Density Functional Theory (DFT) modeling and catalytic testing (toluene hydrogenation) provided data to build a morphological model of NiMoS nanocrystallites. A parallel has been established with their CoMoS counterparts obtained in our previous work in order to emphasize differences arising from the promoter atom. This study confirms the importance of the presence of mixed Ni-Mo sites on the edges of the NiMoS nanocrystallites, and especially on the M-edge for reactions involving hydrogenation. These results provide new guidelines for future and ever more active catalysts.
Surface Wrinkles Induced on Oriented Chitosan Films via Horseradish Peroxidase-catalyzed Reaction and Drying (2020)

Abstract Oriented chitosan films, prepared by elongation, are applied to a surface wrinkling system via a horseradish peroxidase-catalyzed surface reaction of ferulic acid and drying. The wrinkle morphologies of the obtained films are strongly affected by drying compression stress inverse to the elongation direction, probably caused by an entropic spring. The most oriented chitosan film elongated until a fracture strain showed a herringbone-like pattern produced by parallel and orthogonal compression stresses to the orientation direction.
Ascl2 and 11p15.5 amplification in colorectal cancer (2010)

We read with interest the recent article by Stange et al 1 describing gain of 11p or 11p15.5 in approximately one-quarter of colorectal cancer liver metastases compared with matched primary adenocarcinomas. Stange et al speculated that this event may be targeting several putative oncogenes and focused on achaete scute-like (Ascl)2 in particular.1 However, on examining our own published2 3 and unpublished data, we reached different conclusions regarding the role of Ascl2 in colorectal cancer.

We queried two series of primary colorectal cancers with both expression microarray and array comparative genomic hybridisation data. The first dataset relates to 37 cases (experiments conducted at Genentech; 100 k single nucleotide polymorphism array and HG-U133B GeneChip expression microarray (Affymetrix, Santa Clara, California, USA)). The second dataset relates to 30 cases from the commercial GeneLogic (Gaithersburg, Maryland, USA) database available at …
Profiles of Intraocular Pressure in Human Donor Eyes during Femtosecond Laser Procedures—A Comparative Study (2012)

Based on previous findings of visual field defects after LASIK, and as a consequence of the present study, it seems feasible to design patient interfaces in a more physiologic manner to prevent high IOPs during refractive procedures.
A Flexible and Robust Solution for Automated 384-well HDAC Profiling (2011)

Histone deacetylases (HDACs) remove acetyl groups from e-N-acetyl lysine residues on histones and other proteins. Acetyl group removal serves to increase the positive charge of histone tails, thus encouraging binding between histones and the DNA backbone and preventing transcription. HDACs are implicated in many human diseases, including cancer; making them an increasingly popular drug discovery research target. Here we monitor the deacetylation activity of multiple Class I and II HDAC enzymes in an automated fashion. Validation and pharmacology results demonstrate how the fluorescent assay technology and automated instrumentation may be used together to assess enzyme kinetics and inhibition.
Activation of the Anaerobic Ribonucleotide Reductase fromEscherichia coli (1997)

The anaerobic ribonucleotide reductase of Escherichia coli catalyzes the synthesis of the deoxyribonucleotides required for anaerobic DNA synthesis. The enzyme is an alpha2beta2 heterotetramer. In its active form, the large alpha2 subunit contains an oxygen-sensitive glycyl radical, whereas the beta2 small protein harbors a [4Fe-4S] cluster that joins its two polypeptide chains. Formation of the glycyl radical in the inactive enzyme requires S-adenosylmethionine (AdoMet), dithiothreitol, K+, and either an enzymatic (reduced flavodoxin) or chemical (dithionite or 5-deazaflavin plus light) reducing system. Here, we demonstrate that AdoMet is directly reduced by the Fe-S center of beta2 during the activation of the enzyme, resulting in methionine and glycyl radical formation. Direct binding experiments showed that AdoMet binds to beta2 with a Kd of 10 microM and a 1:1 stoichiometry. Binding was confirmed by EPR spectroscopy that demonstrated the formation of a complex between AdoMet and the [4Fe-4S] center of beta2. Dithiothreitol triggered the cleavage of AdoMet, leading to an EPR-silent form of beta2 and, in the case of alpha2beta2, to glycyl radical formation. In both instances, 3 methionines were formed per mol of protein. Our results indicate that the Fe-S center of beta2 is directly involved in the reductive cleavage of AdoMet and suggest a new biological function for an iron-sulfur center, i.e redox catalysis, as recently proposed by others (Staples, R. C., Ameyibor, E., Fu, W., Gardet-Salvi, L., Stritt-Etter, A. L., Schürmann, P., Knaff, D. B., and Johnson, M. K. (1996) Biochemistry 35, 11425-11434).
Getting to Zero—and Beyond: California’s aspiration to become the first carbon-negative state appears to be achievable and affordable. (2023)

As a response to mounting concerns about the consequences of unabated climate change, California established in 2018 an aspirational goal of achieving a completely carbon-neutral economy by 2045, and becoming carbon negative after that. The state has long championed climate-friendly policies such as using energy more efficiently, generating power from renewable sources, and putting cleaner cars on the road, among other emissions-reduction strategies. Unfortunately, California’s own evaluations indicate that even when these are successful—after intensive electrification of the economy and a drastic shift away from fossil fuels—there will remain substantial greenhouse gas emissions. The residuals come from widespread small sources that are hard to control, and from larger sources that cannot be controlled in time.
Resonance Fiber Bragg Grating Sensor system based on Fourier Domain Mode-locking Laser (2012)

본 논문은 분광 영역 모드록킹(Fourier domain mode-locking: FDML) 레이저를 기반으로 공진형 광섬유 격자 센서를 구현한 결과를 보고한다. FDML 레이저는 파브리-페롯 가변 필터를 이용하여 링 형태로 구성하며, 레이저 공진기 안에 광섬유 격자 2개를 한 쌍으로 하여 센서부 2개를 삽입한 구조이다. 광섬유 격자는 반사 거울 역할을 하며, 광섬유 격자의 위치에 따라 독립된 FDML 레이저 공진기를 구성한다. 각각 센서부의 공진 주파수는 46.687 kHz 와 44.340 kHz이다. FBG 센서 시스템에 정적 및 동적 스트레인을 가하였으며, 정적 스트레인에 대해 파장 영역과 시간 영역에서 측정된 스트레인에 대한 변화율은 각각 <TEX>$0.61pm/{\mu}{\epsilon}$</TEX>, <TEX>$0.8ns/{\mu}{\epsilon}$</TEX> 이다. We report a resonance fiber Bragg sensor interrogation based on a Fourier domain mode-locking (FDML) laser. The FDML laser is constructed based on a conventional ring laser cavity configuration with fiber Fabry-Perot tunable filter (FFP-TF). There are two sensor parts which are composed with two FBGs inside the laser cavity. Each sensor part provides a separate laser cavity for the FDML laser. The resonance frequencies of the laser cavities are 46.687 kHz and 44.340 kHz, respectively. We applied a static and a dynamic strain on the FBG sensor system. The slope coefficients of the measured relative wavelength shift and relative time interval from the static strain are found to be <TEX>$0.61pm/{\mu}{\epsilon}$</TEX> and <TEX>$0.8ns/{\mu}{\epsilon}$</TEX>, respectively.
Subcritical-voltage magnetron RF power source (2023)

A system and method of operating a magnetron power source can achieve a broad range of output power control by operating a magnetron with its cathode voltage lower than that needed for free running oscillations (e.g., below the Kapitsa critical voltage or equivalently below the Hartree voltage) A sufficiently strong injection-locking signal enables the output power to be coherently generated and to be controlled over a broad power range by small changes in the cathode voltage. In one embodiment, the present system and method is used for a practical, single, frequency-locked 2-magnetron system design.
Resistance to HIV-1 infection among HIV-exposed seronegative partners in HIV-discordant couples is associated with higher frequency of CD8+ T cells expressing CD107a and b molecules (2014)

Methods Ten HIV-1 ESN in HIV-discordant couples were enrolled at the Fann University hospital, Dakar, Senegal. Thirty HIV-1 infected patients (10 HIV-1 non transmitted partners in discordant coupes and 20 HIV-1 infected partners in HIV-concordant couples) and 10 HIV-negative unexposed subjects were included as controls. Levels of CD107a and b, and CD107a/b+IFN-g+ in CD8+ T cells sub-set were measured in fresh PBMC by flow cytometry, in the presence or absence of stimulation with SEB.
Analysis of current sampling errors in PWM, VSI drives (2013)

Current measurement and pulse-width modulation (PWM) are critical components of modern current controlled voltage source inverters (VSI). Current measurement enables accurate and robust closed-loop control of current, while PWM enables the efficient, high bandwidth regulation of the voltage. These two components do not operate independently, however. The synthesized voltage from PWM, a sequential series of discrete voltage levels, from a predefined finite set of possible levels, is only equivalent to the desired voltage on an average basis. As a result, the response of the electrical current to this synthesized voltage deviates from the response to the desired voltage. This deviation from the desired response, when combined with the standard synchronous sampling method, results in current measurement errors. This paper will present an analytical derivation of this current response deviation. This can be used to model the current measurement errors. A better understanding of this phenomenon will result in better design and control of power converter systems. The analytical work will be evaluated and verified using simulations and experimental measurements.
Asymmetry by Electrophilic Rearrangement of Symmetric 2-Pyridone Photodimers (2005)

[reaction: see text] Halogenation of achiral trans-2-pyridone photodimers results in 1,3-migration of an amide nitrogen and formation of a chiral structure with six stereogenic centers and well-differentiated functionality. The reactivity of this product toward nucleophiles, including the allylic halide, is dominated by participation by the amide nitrogen.
Chemical characteristics and microbial degradation of humate (1993)

Abstract Humates are often used in agriculture as a source of organic matter. This study was conducted to characterize a commercial humate and to evaluate its chemical and decomposition characteristics. Characterization methods included fractionization of humic and fulvic acids of the humate, based on their alkali/acid insolubility; elemental analysis; acidic functional group analysis; and E4/E6 ratio determinations. The humate consisted of the following: 58% organic matter, 32% ash, and 10% moisture. Humic fraction was mostly humic acid (76%), with some fulvic acid (18%). Organic elemental composition [59% carbon (C), 5% hydrogen (H), and 36% oxygen (O)] also suggests a humic‐acid nature. Inorganic elemental content of this humate, which was primarily aluminum (Al) [4.9%] and iron (Fe) [0.46%], reflects its spodic origin. Much of the Al present, however, results from the flocculant (alum) used at the mining site to precipitate the humate. The relatively low total acidity of this humate (250 cmol/kg) suggests the blockage of some of its functional groups by Al, Fe, and associated clay minerals. After purification, total acidity increased to 510 cmol/kg and acidity associated with carboxyl groups increased to 280 cmol/kg. Results of E4/E6 determinations for the humate (2.5) and the humic‐acid fraction (4.8) also suggested that the organic fraction was predominately humic acid. Decomposition of the humate was estimated by measuring the quantity of carbon dioxide (CO2) evolved during a four‐week incubation. Results suggested a relative resistance to microbial degradation. However, results also suggested the presence of some readily decomposable C compounds associated with humate. Agricultural use of this humate reguires some modifications to produce a more reactive material. This may include a change of flocculant and a lowering of its ash content.
Isolation and Structure Elucidation of Two New Antibacterial Compounds Produced by Chrysosporium queenslandicum. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
SIM2l attenuates resistance to hypoxia and tumor growth by transcriptional suppression of HIF1A in uterine cervical squamous cell carcinoma (2017)

Despite chemoradiotherapy being one of the most important modalities in advanced cervical cancer, there is a lack of both usable biomarkers to predict treatment outcome and of knowledge about the mechanism of refractoriness to the therapy. Here we identified a transcriptional factor Single-minded homolog 2 (SIM2) as an independent predictive biomarker for uterine cervical squamous cell carcinoma (CvSCC). The retrospective study showed that high expression level of SIM2 was correlated to good survival in CvSCC patients. SIM2 knockdown in CvSCC cell lines showed resistance to hypoxia with increased expression of HIF1A and its target genes. Loss of SIM2 also caused growth promotion, resistance to ROS, and radiation in 3D culture. Furthermore, SIM2 knockdown suppressed tumor growth with increased HIF-1α expression and angiogenesis in vivo. On the other hand, SIM2 long isoform (SIM2l)-overexpressed cells had contrary results, indicating the long isoform plays a key role for maintenance of these phenotypes. These data indicated that SIM2l has a potential to be precision medicine for CvSCC patients and that anti-angiogenesis therapy might be usable for SIM2l<sup>Low</sup> poor survivors.
Low sample volume origami-paper-based graphene-modified aptasensors for label-free electrochemical detection of cancer biomarker-EGFR (2020)

In this work, an electrochemical paper-based aptasensor was fabricated for label-free and ultrasensitive detection of epidermal growth factor receptor (EGFR) by employing anti-EGFR aptamers as the bio-recognition element. The device used the concept of paper-folding, or origami, to serve as a valve between sample introduction and detection, so reducing sampling volumes and improving operation convenience. Amino-functionalized graphene (NH<sub>2</sub>-GO)/thionine (THI)/gold particle (AuNP) nanocomposites were used to modify the working electrode not only to generate the electrochemical signals, but also to provide an environment conducive to aptamer immobilization. Electrochemical characterization revealed that the formation of an insulating aptamer-antigen immunocomplex would hinder electron transfer from the sample medium to the working electrode, thus resulting in a lower signal. The experimental results showed that the proposed aptasensor exhibited a linear range from 0.05 to 200 ngmL<sup>-1</sup> (<i>R</i> <sup>2</sup> = 0.989) and a detection limit of 5 pgmL<sup>-1</sup> for EGFR. The analytical reliability of the proposed paper-based aptasensor was further investigated by analyzing serum samples, showing good agreement with the gold-standard enzyme-linked immunosorbent assay.
Improving method of real-time offset tuning for arterial signal coordination using probe trajectory data (2017)

In the environment of intelligent transportation systems, traffic condition data would have higher resolution in time and space, which is especially valuable for managing the interrupted traffic at signalized intersections. There exist a lot of algorithms for offset tuning, but few of them take the advantage of modern traffic detection methods such as probe vehicle data. This study proposes a method using probe trajectory data to optimize and adjust offsets in real time. The critical point, representing the changing vehicle dynamics, is first defined as the basis of this approach. Using the critical points related to different states of traffic conditions, such as free flow, queue formation, and dissipation, various traffic status parameters can be estimated, including actual travel speed, queue dissipation rate, and standing queue length. The offset can then be adjusted on a cycle-by-cycle basis. The performance of this approach is evaluated using a simulation network. The results show that the trajectory-based approach can reduce travel time of the coordinated traffic flow when compared with using well-defined offline offset.
Supplementary Table 1 from A MicroRNA Expression Signature for Cervical Cancer Prognosis (2023)

Supplementary Table 1 from A MicroRNA Expression Signature for Cervical Cancer Prognosis
Use of Parallel Synthesis To Probe Structure−Activity Relationships among 12-Helical β-Peptides:  Evidence of a Limit on Antimicrobial Activity (2005)

We report structure-activity trends among helix-forming beta-amino acid oligomers that are intended to mimic alpha-helical host-defense peptides. Parallel synthesis of two small, focused beta-peptide libraries allowed us to identify relatively short (11-residue) beta-peptides that display antimicrobial activity. These beta-peptides exhibit selectivity for bacteria relative to human red blood cells. A large hydrophobic helical surface is necessary for antimicrobial activity. Longer analogues (16 residues) of the most active library members were prepared and evaluated. Some of these longer beta-peptides showed very good antimicrobial activity, but none was more active than a previously reported beta-peptide [Porter, E. A.; Wang, X.; Lee, H.-S.; Weisblum, B.; Gellman, S. H. Nature 2000, 404, 565]. The extensive literature on alpha-helical host-defense peptides and related alpha-peptides indicates that such molecules are seldom active at concentrations below 1 microg/mL, and our results suggest that amphiphilic helical beta-peptides are subject to a comparable limit.
Amplitude analysis of the Λc+→pK−π+ decay and Λc+ baryon polarization measurement in semileptonic beauty hadron decays (2023)

An amplitude analysis of ${\mathrm{\ensuremath{\Lambda}}}_{c}^{+}\ensuremath{\rightarrow}p{K}^{\ensuremath{-}}{\ensuremath{\pi}}^{+}$ decays together with a measurement of the ${\mathrm{\ensuremath{\Lambda}}}_{c}^{+}$ polarization vector in semi\ifmmode \bar{o}\else \={o}\fi{}leptonic beauty hadron decays is presented. A sample of 400 000 candidates is selected from proton-proton collisions recorded by the LHCb detector at a center-of-mass energy of 13 TeV. An amplitude model is developed and the resonance fractions as well as two- and three-body decay parameters are reported. The mass and width of the $\mathrm{\ensuremath{\Lambda}}(2000)$ state are also determined. A significant ${\mathrm{\ensuremath{\Lambda}}}_{c}^{+}$ polarization is found. A large sensitivity of the ${\mathrm{\ensuremath{\Lambda}}}_{c}^{+}\ensuremath{\rightarrow}p{K}^{\ensuremath{-}}{\ensuremath{\pi}}^{+}$ decay to the polarization is seen, making the amplitude model suitable for ${\mathrm{\ensuremath{\Lambda}}}_{c}^{+}$ polarization measurements in other systems.
Fiber Nonlinearity Compensation: Practical Use Cases and Complexity Analysis (2015)

We review the applications of fiber nonlinearity compensation (NLC) in homogeneous and heterogeneous networks, (non)dispersion-managed links, and terabit transmission systems. Practically viable intra-channel NLC is shown to allow ~3.7dB gains, well beyond conventionally acknowledged bounds.
General Catalysts for the Suzuki—Miyaura and Sonogashira Coupling Reactions of Aryl Chlorides and for the Coupling of Challenging Substrate Combinations in Water. (2006)

Abstract For Abstract see ChemInform Abstract in Full Text.
A Hardware Prototype of Sub-Nyquist Radar With Distorted Pulse Shape (2020)

Sub-Nyquist radar systems operate at lower sampling rates compared to the Nyquist rate and hence reduce the hardware cost and complexity. Sub-Nyquist systems uses the knowledge of the transmit pulse and the receive signal model to estimate the targets from lowrate samples. However, in practice, the pulse shape is often distorted and unknown at the receiver. Recently, a multiple-receiver based sub-Nyquist radar was proposed that estimates the targets without knowledge of the pulse shape. In this demo, we build a hardware prototype to demonstrate the proposed sub-Nyquist radar. We show that while operating at 10 times below the Nyquist rate the proposed two-receiver system with unknown pulse has comparable performance to a single-receiver sub-Nyquist system with a known pulse.
Periodicities in data observed during the minimum and the rising phase of solar cycle23; years 1996-1999 (2001)

Three types of observations: the daily values of the solar radio flux at 7 frequencies, the daily international sunspot number and the daily Stanford mean solar magnetic field were processed in order to find all the periodicities hidden in the data. Using a new approach to the radio data, two time series were obtained for each frequency examined, one more sensitive to spot magnetic fields, the other to large magnetic structures not connected with sunspots. Power spectrum analysis of the data was carried out separately for the minimum (540 days from 1 March 1996 to 22 August 1997) and for the rising phase (708 days from 23 August 1997 to 31 July 1999) of the solar cycle 23. The Scargle periodograms obtained, normalized for the effect of autocorrelation, show the majority of known periods and reveal a clear difference between the periodicities found in the minimum and the rising phase. We determined the rotation rate of the "active longitudes" in the rising phase as equal to 444.4 ± 4 nHz ($26\fd0 \pm 0\fd3$). The results indicate that appropriate and careful analysis of daily radio data at several frequencies allows the investigation of solar periodicities generated in different layers of the solar atmosphere by various phenomena related to the periodic emergence of diverse magnetic structures.
Crystal structure of a pentamidine-oligonucleotide complex: implications for DNA-binding properties (1992)

The crystal structure of the complex formed between the dodecanucleotide d(CGCGAATTCGCG)2 and the drug pentamidine, which is active against the Pneumocystis carinii pathogen in AIDS patients, has been determined to a resolution of 2.1 A and an R-factor of 19.4%. Analysis of the structure has shown the drug to be bound in the 5'-AATT minor groove region of the duplex, with the amidinium groups H-bonded to adenine N3 atoms in an interstrand manner. The drug molecule adopts an extended conformation, and the immediate binding site spans four base pairs. Structural details of the drug-DNA interactions are discussed, and comparison is made with the dodecamer complex of the structurally similar berenil ligand.
Prognostic Impact of Diabetes and Prediabetes on Survival Outcomes in Patients With Chronic Heart Failure: A Post‐Hoc Analysis of the GISSI‐HF (Gruppo Italiano per lo Studio della Sopravvivenza nella Insufficienza Cardiaca‐Heart Failure) Trial (2017)

URL: http://www.clinicaltrials.gov. Unique identifier: NCT00336336.