gebhart/patrepeval huggingface dataset:
Biomarker Accessible and Chemically Addressable Mechanistic Subtypes of BRAF Melanoma (2017)

Genomic diversity among melanoma tumors limits durable control with conventional and targeted therapies. Nevertheless, pathologic activation of the ERK1/2 pathway is a linchpin tumorigenic mechanism associated with the majority of primary and recurrent disease. Therefore, we sought to identify therapeutic targets that are selectively required for tumorigenicity in the presence of pathologic ERK1/2 signaling. By integration of multigenome chemical and genetic screens, recurrent architectural variants in melanoma tumor genomes, and patient outcome data, we identified two mechanistic subtypes of BRAF<sup>V600</sup> melanoma that inform new cancer cell biology and offer new therapeutic opportunities. Subtype membership defines sensitivity to clinical MEK inhibitors versus TBK1/IKBKε inhibitors. Importantly, subtype membership can be predicted using a robust quantitative five-feature genetic biomarker. This biomarker, and the mechanistic relationships linked to it, can identify a cohort of best responders to clinical MEK inhibitors and identify a cohort of TBK1/IKBKε inhibitor-sensitive disease among nonresponders to current targeted therapy.<b>Significance:</b> This study identified two mechanistic subtypes of melanoma: (1) the best responders to clinical BRAF/MEK inhibitors (25%) and (2) nonresponders due to primary resistance mechanisms (9.9%). We identified robust biomarkers that can detect these subtypes in patient samples and predict clinical outcome. TBK1/IKBKε inhibitors were selectively toxic to drug-resistant melanoma. <i>Cancer Discov; 7(8); 832-51. ©2017 AACR.</i><i>See related commentary by Jenkins and Barbie, p. 799</i><i>This article is highlighted in the In This Issue feature, p. 783</i>.
ChemInform Abstract: Competing Reaction Pathways in Protonation Reactions of a Low‐Valent Tungsten Alkylidyne Isocyanide Complex: Formation of Nitrilium and Aminoalkyne Ligands. (1991)

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.
Factors determining the location of forest products firms (1991)

In the past decade there has been an increase in the number of intrastate, state and regional programs aimed at encouraging forest resource based economic development in northeastern USA. These programs were aimed at deriving economic benefits from the large volume of mature forest resources in the region. The improvement of rura1 communities by creating job opportunities was seen as one of the primary benefits of the development programs, and they therefore focused attention on attracting firms and new manufacturing facilities. Most of these programs set the location of forest products firms as their target and seem to operate on the hypothesis that all forest products firms have the same general requirement when choosing a new location. The purpose of this study was twofold: first to test the hypothesis that different types of forest products firms have the same location requirements and second to test the hypothesis that location determinants within communities are the same irrespective of their size.
Permian Basin processing and handling shallow anomalies and permit holes: A compressive seismic acquisition and reconstruction case study (2019)

Shallow gas hazards and acquisition permit holes are common challenges for the oil & gas explorations in the Permian Basin. Compressive seismic acquisition has been adopted to mitigate the issues due to permit holes comparing to conventional seismic acquisitions. Amplitude friendly compressive seismic data processing flows are designed and performed to preserve the gas pocket amplitude anomalies and to resolve the target reservoir interval imaging. Post-migration L1 Frequency Normalization has further improved the image resolution to assist in structural and amplitude interpretations. Presentation Date: Tuesday, September 17, 2019 Session Start Time: 1:50 PM Presentation Start Time: 2:15 PM Location: 303B Presentation Type: Oral
Simultaneous intensity, birefringence, and flow measurements using high-speed fiber-based optical coherence tomography (2002)

Recent extensions to conventional OCT imaging include polarization-sensitive optical coherence tomography (PS-OCT) and optical Doppler tomography (ODT), enabling further information to be acquired in addition to tissue structure. We demonstrate here that structure, birefringence and blood flow measurements may be carried out simultaneously, using both techniques of polarization-sensitive OT and phase- resolved ODT. Images of in vivo human skin acquired with a high-speed fiber-based system are presented. The concurrent processing of data is performed with no penalty to signal- to-noise ratio, and without degradation of either the individual structure, birefringence or flow images.
Activation of thermomechanical pulp by laccases as studied by UV-Vis, UV resonance Raman and FTIR spectroscopy 10th EWLP, Stockholm, Sweden, August 25–28, 2008 (2009)

Abstract The changes in lignin structure of spruce thermomechanical pulp (TMP), induced by treatment with laccase of Trametes hirsuta (ThL) and laccase of Melanocarpus albomyces (MaL), has been investigated by UV-Vis, UV resonance Raman (UVRR), and Fourier transform infrared (FTIR) spectroscopy. The spectroscopic results showed that the structural changes were small; however, the changes were slightly more pronounced in the case of MaL. Nevertheless, the brightness of the pulps remained higher after treatment with MaL than after treatment with ThL. Accordingly, MaL is a promising enzyme for fiber activation and functionalization.
Energy transformations early in the bacteriorhodopsin photocycle revealed by DNP-enhanced solid-state NMR (2008)

By exploiting dynamic nuclear polarization (DNP) at 90 K, we observe the first NMR spectrum of the K intermediate in the ion-motive photocycle of bacteriorhodopsin. The intermediate is identified by its reversion to the resting state of the protein in red light and by its thermal decay to the L intermediate. The (15)N chemical shift of the Schiff base in K indicates that contact has been lost with its counterion. Under these circumstances, the visible absorption of K is expected to be more red-shifted than is observed and this suggests torsion around single bonds of the retinylidene chromophore. This is in contrast to the development of a strong counterion interaction and double bond torsion in L. Thus, photon energy is stored in electrostatic modes in K and is transferred to torsional modes in L. This transfer is facilitated by the reduction in bond alternation that occurs with the initial loss of the counterion interaction, and is driven by the attraction of the Schiff base to a new counterion. Nevertheless, the process appears to be difficult, as judged by the multiple L substates, with weaker counterion interactions, that are trapped at lower temperatures. The double-bond torsion ultimately developed in the first half of the photocycle is probably responsible for enforcing vectoriality in the pump by causing a decisive switch in the connectivity of the active site once the Schiff base and its counterion are neutralized by proton transfer.
Automated System for Measuring the Constants of Low-Q Piezoelectric Materials (1985)

We have implemented a new system for extracting the relevant constants of unloaded piezoelectric resonators from impedance measurements. This system utilizes the facility of computer controlled acquisition systems to obtain large quantities of data, and a least-squares fitting procedure to interpret the data in an optimal way. This method is especially valuable for low-Q piezoelectric materials which are not treated accurately by many standard measurement techniques. It also facilitates the collection of data from a large number of identical disks, for studying their piece-to-piece variations, or for quality control in transducer production.
Halato-telechelic polymers. 11. Viscoelastic behavior of .alpha.,.omega.-dicarboxylatopolybutadiene based on group 4 metal ions (1985)

peer reviewed
High-Resolution Ion Implantation from keV to MeV (2012)

With the trend in miniaturisation of electronic, optoelectronic or photonic devices, it becomes necessary to control, at the highest level, the number and positioning of dopant atoms which are introduced in the devices by ion implantation. As well, new promissing fields of research like quantum information processing in the solid-state also require an exact placement of implanted atoms which could be operated as the quantum bits of a future quantum computer In these purposes, an ideal ion implantation setup would provide deterministic single ions and nanometer spatial resolution.
Comparing pathways for electricity-based production of dimethoxymethane as a sustainable fuel (2021)

A hierarchical methodology for process design and evaluation reveals how the remarkable achievements in catalyst development for dimethoxymethane (DMM) synthesis can make DMM a sustainable future e-fuel.
Substitution Effects in Highly Syndioselective Styrene Polymerization Catalysts Based on Single-Component Allyl ansa-Lanthanidocenes: An Experimental and Theoretical Study (2017)

A series of allyl ansa-lanthanidocenes, [{Me2C(C5H4)(Flu)}Nd(1,3-C3H3(SiMe3)2)2]K (Flu = 9-fluorenyl; 1-Nd-K(allyl)) and {R2C(C5H4)(R′R′Flu)}Ln(1,3-C3H3(SiMe3)2)(THF)x (R = Me, R′ = 2,7-tBu2, Ln = Y (2-Y), Sc (2-Sc), x = 0; Ln = La (2-La), Pr (2-Pr), Nd (2-Nd), Sm (2-Sm), x = 1; R = Me, R′ = oct = octamethyloctahydrodibenzo, Ln = Nd, x = 1 (3-Nd); R = Ph, R′ = H, Ln = Nd, x = 1 (4-Nd); R = Me, R′ = 3,6-tBu2, Ln = Nd, x = 1 (5-Nd)), were prepared in good yields and characterized by NMR spectroscopy (for diamagnetic complexes 2-Sc, 2-Y, and 2-La) and by single-crystal X-ray diffraction (1-Nd-K(allyl), 2-La, 2-Pr, 2-Nd, 2-Sm, and 4-Nd). Those complexes, especially 1-Nd-K(allyl), 2-Nd, 4-Nd, 2-La, and 2-Sm, act as single-component catalyst precursors for polymerization of styrene (in bulk or in aliphatic hydrocarbon solutions, (nBu)2Mg as scavenger, Tpolym = 60–140 °C), affording highly syndiotactic polystyrene (sPS) ([r]5 = 63–88%; Tm up to 260 °C). High productivities (up to 4560 kg(sPS) mol(Ln)−1 h–1) were achieved at 120–140 °C, at low catalyst loadings ([St]/[Nd] = 20 000–76 000 equiv), with 2-Nd and 2-Pr. On the other hand, precursors having bulky substituents on the fluorenyl moieties in 3,6-positions (3-Nd, 5-Nd) or based on small ionic radius metals (2-Y, 2-Sc) were poorly or not active under standard polymerization conditions. These results have been rationalized by DFT computations, which included the solvent, carried out on the putative 1-Nd, and the isolated 2-Nd and 5-Nd complexes. Three consecutive styrene insertions were studied, and it was revealed that (i) the formation of sPS is thermodynamically controlled by two effects—minimization of repulsions between fluorenyl/styrene phenyl ring and (in the initiation phase) fluorenyl/SiMe3 substituents of the allyl ligand—and (ii) the presence of bulky substituents on the fluorenyl moiety does not influence the activation barrier of monomer insertion, but it may destabilize thermodynamically the insertion product.
Field of view extension and truncation correction for MR‐based human attenuation correction in simultaneous MR/PET imaging (2014)

The proposed technique successfully extends the MR FoV in MR-based attenuation correction and shows an improvement of PET quantification in whole-body MR/PET hybrid imaging. In comparison to the PET-based completion of the truncated body contour, the proposed method is also applicable to specialized PET tracers with little uptake in the arms and might reduce the computation time by obviating the need for iterative calculations of the PET emission data beyond those required for reconstructing images.
Site-Resolved Contributions to the Magnetic-Anisotropy Energy and Complex Spin Structure of Fe/MgO Sandwiches (2018)

The magnetic properties of ultrathin Fe layers are important in spintronics, but their complex electronic and temperature-dependent properties lead to intricate surface effects that are difficult to predict. The authors use a combination of first-principles and spin-dynamics calculations to study magnetism in MgO/Fe/MgO sandwiches. Surprisingly, they find a noncollinear surface spin structure, due to competition between surface antiferromagnetic coupling and Dzyaloshinskii-Moriya interactions. These results reveal the true complexity of MgO/Fe/MgO ultrathin films, with implications for skyrmionic devices.
Robust prognostic prediction model developed with integrated biological markers for acute myocardial infarction (2022)

Commonly used prediction methods for acute myocardial infarction (AMI) were created before contemporary percutaneous coronary intervention was recognized as the primary therapy. Although several studies have used machine learning techniques for prognostic prediction of patients with AMI, its clinical application has not been achieved. Here, we developed an online application tool using a machine learning model to predict in-hospital mortality in patients with AMI. A total of 2,553 cases of ST-elevation AMI were assigned to 80% training subset for cross validation and 20% test subset for model performance evaluation. We implemented random forest classifier for the binary classification of in-hospital mortality. The selected best feature set consisted of ten clinical and biological markers including max creatine phosphokinase, hemoglobin, heart rate, creatinine, systolic blood pressure, blood sugar, age, Killip class, white blood cells, and c-reactive protein. Our model achieved high performance: the area under the curve of the receiver operating characteristic curve for the test subset, 0.95: sensitivity, 0.89: specificity, 0.91: precision, 0.43: accuracy, 0.91 respectively, which outperformed common scoring methods. The freely available application tool for prognostic prediction can contribute to risk triage and decision-making in patient-centered modern clinical practice for AMI.
Sustainable Polysulfides for Oil Spill Remediation: Repurposing Industrial Waste for Environmental Benefit (2018)

Abstract Crude oil and hydrocarbon fuel spills are a perennial threat to aquatic environments. Inexpensive and sustainable sorbents are needed to mitigate the ecological harm of this pollution. To address this need, this study features a low‐density polysulfide polymer that is prepared by the direct reaction of sulfur and used cooking oils. Because both sulfur and cooking oils are hydrophobic, the polymer has an affinity for hydrocarbons such as crude oil and diesel fuel and can rapidly remove them from seawater. Through simple mechanical compression, the oil can be recovered and the polymer can be reused in oil spill remediation. The polysulfide is unique because it is prepared entirely from repurposed waste: sulfur is a by‐product of the petroleum industry and used cooking oil can be used as a comonomer. In this way, sulfur waste from the oil industry is used to make an effective sorbent for combatting pollution from that same sector.
Rough Electrode Creates Excess Capacitance in Thin-Film Capacitors (2017)

The parallel-plate capacitor equation is widely used in contemporary material research for nanoscale applications and nanoelectronics. To apply this equation, flat and smooth electrodes are assumed for a capacitor. This essential assumption is often violated for thin-film capacitors because the formation of nanoscale roughness at the electrode interface is very probable for thin films grown via common deposition methods. In this work, we experimentally and theoretically show that the electrical capacitance of thin-film capacitors with realistic interface roughness is significantly larger than the value predicted by the parallel-plate capacitor equation. The degree of the deviation depends on the strength of the roughness, which is described by three roughness parameters for a self-affine fractal surface. By applying an extended parallel-plate capacitor equation that includes the roughness parameters of the electrode, we are able to calculate the excess capacitance of the electrode with weak roughness. Moreover, we introduce the roughness parameter limits for which the simple parallel-plate capacitor equation is sufficiently accurate for capacitors with one rough electrode. Our results imply that the interface roughness beyond the proposed limits cannot be dismissed unless the independence of the capacitance from the interface roughness is experimentally demonstrated. The practical protocols suggested in our work for the reliable use of the parallel-plate capacitor equation can be applied as general guidelines in various fields of interest.
Two-Layer Coding in Distributed Storage Systems With Partial Node Failure/Repair (2016)

We a distributed storage system where parts of the stored packets in storage nodes are subject to being lost. In a process, termed as the partial repair, the lost packets in a faulty node are recovered by the transmitted packets from other storage nodes and the available packets in the faulty node. To improve reliability of the stored data, and reduce the transmission costs, we propose a scheme that implements two-layer coding for storing files in the system. We study the minimum possible partial-repair bandwidth, and the codes that achieve the optimal bound.
Adaptive Piecewise Linear Predistorters for Nonlinear Power Amplifiers With Memory (2012)

We propose novel direct and indirect learning predistorters (PDs) that employ a new baseband simplicial canonical piecewise linear (SCPWL) function. The performance of the proposed PDs is easily controlled by varying the number of segments of the SCPWL function. When comparing to polynomial-based PDs, our SCPWL-based PDs are more robust for modeling strong nonlinearities and are less sensitive to input noise. In particular, we show that noise appearing in the feedback path of an indirect learning SCPWL-PD has negligible effect on the performance while the polynomial counterpart suffers from a noise-induced coefficient bias. We consider adaptive implementations of both Hammerstein-based and memory-based SCPWL PDs; the former featuring less parameters to be identified while the latter renders more straightforward parameter identification. When deriving the PD algorithms, we avoid a separate PA identification step which allows for a true real-time, or sample-by-sample, implementation without an alternating PA and PD identification procedure. However, to arrive at efficient sample-by-sample algorithms for Hammerstein PDs we need to bypass the problem of the associated nonconvex cost function. This is done by employing a modified, linear-in-the-parameter, Wiener model whose parameters can be explicitly or implicitly used for both indirect and direct learning. Extensive simulations confirm that the proposed SCPWL PDs outperform their polynomial counterparts, especially when noise is present in the feedback path of the indirect learning structure. The same is also verified by circuit level simulations on the Freescale MRF6S23100H class-AB PA in an 802.16d WiMAX system.
Photonic crystal laser lift-off GaN light-emitting diodes (2006)

We report on the fabrication and study of laser lift-off GaN-based light-emitting diodes, thinned down to the microcavity regime, incorporating two-dimensional photonic crystal diffraction gratings. Angle-resolved measurements reveal the photonic behavior of the devices, which strongly depends on the GaN thickness. Data point out the detrimental role of metal absorption. We explore theoretically the possibility to limit this loss channel.
Prostaglandin E2 Stimulates Granulocyte Colony-Stimulating Factor Production via the Prostanoid EP2 Receptor in Mouse Peritoneal Neutrophils (2005)

G-CSF is a hemopoietic growth factor involved in granulocytic differentiation of progenitor cells. In this study, we investigated the effects of PGE2 on G-CSF production in murine peritoneal neutrophils in vitro and in vivo. PGE2 augmented LPS-primed G-CSF release from peritoneal neutrophils. This augmentation was mimicked by a type E prostanoid receptor (EP)2-selective agonist but not by other EP-specific agonists. Indeed, the effect of PGE2 on G-CSF release was abolished in neutrophils isolated from EP2-deficient mice. PGE2 and an EP2 agonist have the ability to stimulate G-CSF gene expression even in the absence of LPS. In the casein-induced peritonitis model, the appearance of G-CSF in the casein-injected peritoneal cavity associated well with the timing of neutrophil infiltration as well as PGE2 levels in exudates, with a peak value at 6 h postinjection. Inhibition of endogenous PG synthesis by indomethacin resulted in a marked decrease in G-CSF content and neutrophil number in the peritoneal cavity. Moreover, EP2-deficient mice exhibited a strikingly reduced G-CSF content in peritoneal exudates with comparable responses in neutrophil migration and local PGE2 production at 6 h postinjection. These results suggest that the PGE2-EP2 system contributes to the local production of G-CSF during acute inflammation.
On the impact of 2G and 3G network usage for mobile phones' battery life (2009)

Over the last years mobile phones had a remarkable evolution. From a simple device for voice communication, it became a full blown multimedia device with multiple features and appealing services. In parallel with the introduction of novel services, mobile devices became more and more energy-hungry reducing the operational time for the user. To extend the battery life of mobile phones is one of the top priorities for mobile phones' manufacturers. This paper presents results of power and energy consumption measurements conducted on mobile phones for 2G and 3G networks. The services under investigation were text messaging, voice and data. The paper reports larger energy consumption in 3G networks for text messaging and voice services than energy consumption in 2G networks. On the other side the 3G networks become more energy friendly when large volumes of data have to be downloaded. The results imply that mobile phones should switch the network in dependency of the service used to save the maximum amount of energy. As this handover consumes energy, we include its analysis in our measurements.
Malignant hypertension in childhood (1941)

Essential hypertension remains one of the most important problems in clinical medicine. Until the cause is discovered both nomenclature and classification must of necessity be provisional and incomplete. Nevertheless in recent years, increasing attention has been given to this subject and certain definite advances made. This applies particularly to the so-called malignant type of primary or essential hypertension. Malignant hypertension may be defined as a progressive, generalized, vascular disorder associated with gross- hypertension, in which renal dysfunction is a secondary and late manifestation. The condition is predominantly one of middle life and in consequence its occurrence in childhood has received little notice. For this reason the following on July 28,