gebhart/patrepeval huggingface dataset:
Fluctuation Modes of a Twist-Bend Nematic Liquid Crystal (2016)

We report a dynamic light scattering study of the fluctuation modes in a thermotropic liquid crys- talline mixture of monomer and dimer compounds that exhibits the twist-bend nematic (NTB) phase. The results reveal a spectrum of overdamped fluctuations that includes two nonhydrodynamic and one hydrodynamic mode in the NTB phase, and a single nonhydrodynamic plus two hydrodynamic modes (the usual nematic optic axis or director fluctuations) in the higher temperature, uniaxial nematic phase. The properties of these fluctuations and the conditions for their observation are comprehensively explained by a Landau-deGennes expansion of the free energy density in terms of heliconical director and helical polarization fields that characterize the NTB structure, with the latter serving as the primary order parameter. A “coarse-graining” approximation simplifies the theoretical analysis, and enables us to demonstrate quantitative agreement between the calculated and experimentally determined temperature dependence of the mode relaxation rates.
Thesaurus-Based Hierarchical Semantic Grouping of Medical Terms in Information Extraction (2016)

In this paper we describe a semantic approach for grouping medical terms into a hierarchy of concepts based on the UMLS meta-thesaurus. The context of this work is Medical Recap, a Web system that automatically extracts risk information from PubMed abstracts, and then aggregates this knowledge into dependence graphs or Bayesian networks.
Fluorescence time-resolved imaging system embedded in an ultrasound prostate probe (2010)

Ultrasound imaging (US) of the prostate has a low specificity to distinguish tumors from the surrounding tissues. This limitation leads to systematic biopsies. Fluorescent diffuse optical imaging may represent an innovative approach to guide biopsies to tumors marked with high specificity contrast agents and therefore enable an early detection of prostate cancer. This article describes a time-resolved optical system embedded in a transrectal US probe, as well as the fluorescence reconstruction method and its performance. Optical measurements were performed using a pulsed laser, optical fibers and a time-resolved detection system. A novel fast reconstruction method was derived and used to locate a 45 µL ICG fluorescent inclusion at a concentration of 10 µM, in a liquid prostate phantom. Very high location accuracy (0.15 cm) was achieved after reconstruction, for different positions of the inclusion, in the three directions of space. The repeatability, tested with ten sequential measurements, was of the same order of magnitude. Influence of the input parameters (optical properties and lifetime) is presented. These results confirm the feasibility of using optical imaging for prostate guided biopsies.
Validity of thermal activation volume estimated by using Wohlfarth’s equation in perpendicular recording hard disk media (2008)

The physical volume of thermal switching unit, the activation volume for perpendicular recording media, has been investigated using the Wohlfarth equation based on micromagnetic simulation. It was found that the activation volume obtained from the Wohlfarth equation Vac-Wohlfarth exhibits significant field dependence, which is very different from direct observation of thermal switching process. This shows that Vac-Wohlfarth is invalid for perpendicular recording media. The reason for that was interpreted in terms of the narrow dispersion of the energy barrier for thermal switching, originating from the high degree of easy axes orientation along the direction perpendicular to the film plane.
Characterization and definition of a software stack for a reference experimental framework (2013)

In 2006, the US Army Research Laboratory (ARL) and the UK Ministry of Defence (MoD) established a collab­ orative research alliance with academia and industry, named the International Technology Alliance in Network and Information Science (ITA) 1 to address fundamental issues concerning Network and Information Sciences. Research performed under the ITA was extended through a collaboration between ARL and IBM UK to char­ acterize and define a software stack and tooling that will become the reference framework for network science experimentation. A key element to the success and validation of ITA theoretical research is experimentation in a controlled environment that can, as best as possible, emulate the real world conditions and context. Ex­ perimental validation in a network emulation environment contributes to the validation of theoretical concepts and algorithms, the investigation of more complex scenarios that span multiple research areas, exposing gaps in the theory that may need special attention, identifying additional areas where the research might focus and develop, and reproducible experimentation, which enables and facilitates the comparison of results from multiple executions of the same experiment. To accomplish these experimentation goals, the framework needs to foster the collaboration across multiple disciplines and facilitate the sharing of existing and new assets in a common emulation environment. The framework also needs to be extensible for the integration of new features, emula­ tion models, monitoring, and integration with real, external assets that can be linked to any given experiment. This paper discusses the work resulting from the ARL/ IBM UK collaboration to build a framework to support experimentations and foster collaboration within and across different research groups.
Development and evaluation of augmented reality audio systems (2009)

Teknillinen korkeakoulu Elektroniikan, tietoliikenteen ja automaation tiedekunta Signaalinkäsittelyn ja akustiikan laitos
Molecular Basis for Kv1.5 Channel Block (2003)

Kv1.5 channels conduct the ultrarapid delayed rectifier current (IKur) that contributes to action potential repolarization of human atrial myocytes. Block of these channels has been proposed as a treatment for atrial arrhythmias. Here we report a novel and potent inhibitor of Kv1.5 potassium channels, N-benzyl-N-pyridin-3-yl-methyl-2-(toluene-4-sulfonylamino)-benzamide hydrochloride (S0100176), which exhibits features consistent with preferential block of the open state. The IC50 of S0100176 for Kv1.5 expressed in Xenopus oocytes was 0.7 microm. Ala-scanning mutagenesis within the pore helix and the S6 segment, regions that form the walls of the central cavity, was combined with voltage clamp analysis to identify point mutations that altered drug affinity. This approach identified Thr-479, Thr-480, Val-505, Ile-508, and Val-512 as the most important residues for block by S0100176. Mutations of these key residues to Ala or other amino acids caused marked changes in the IC50 of S0100176 (p<0.01). For example, the IC50 of S0100176 increased 362-fold for T480A, 26-fold for V505A, 150-fold for I508A, and 99-fold for V512A. We used modeling to dock S0100176 into the inner cavity of a Kv1.5 pore homology model that was generated based on the crystal structure of KcsA. The docking predicted that the five residues identified by the Ala scan were positioned less than 4.5 A from the compound. Based on the homology models, the positions of the five amino acids identified to interact with S0100176 face toward the central cavity and overlap with putative binding sites for other blockers and voltage-gated potassium channels.
Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer in water (1988)

An efficient procedure is noted for computing absolute free energies of binding for complexes in solution. Two series of computer simulations are required in which the substrate is annihilated in the solvent by itself and in the solvated complex. For illustration, the free energy of binding for two methane-like particles at their contact separation of 4 Å has been computed in TIP4P water. Though several alternatives are possible, in this case, Monte Carlo simulations were employed with statistical perturbation theory in the NPT ensemble at 25 °C and 1 atm. The results for the free energy of binding as well as for the potential of mean force are consistent with prior findings from the integral equation theory of Pratt and Chandler.
Supplementary Table 2 from Transcriptional Profiling Identifies Cyclin D1 as a Critical Downstream Effector of Mutant Epidermal Growth Factor Receptor Signaling (2023)

Supplementary Table 2 from Transcriptional Profiling Identifies Cyclin D1 as a Critical Downstream Effector of Mutant Epidermal Growth Factor Receptor Signaling
Dysphagia Without Endoscopically Evident Disease: To Dilate Or Not? (2001)

It is not known whether patients with symptoms of dysphagia but normal upper endoscopy benefit from empiric esophageal dilation. The aim of this prospective study was to determine whether patients with solid food dysphagia and normal upper endoscopy have symptomatic benefit from empiric dilation using a through-the-scope balloon.Patients who were seen for complaints of solid food dysphagia and who had normal endoscopic examinations at our institution from 1998 through 1999 were identified. Those patients who had agreed before sedation to participate in the study, if eligible, were randomized to either sham or balloon dilation using an 18-mm through-the-scope balloon at the time of esophagogastroduodenoscopy. All potentially eligible patients who had given provisional consent completed a dysphagia questionnaire and a 10-cm visual analog dysphagia scale before endoscopy. Follow-up questionnaires were completed on day 1 and at 3 months and 6 months after the procedure. The primary endpoint of the study was the patient's self-assessment of difficulty swallowing, based on the questionnaires.A total of 83 patients met the study criteria and were randomized to balloon dilation (n = 43) or sham (n = 40). The two groups were comparable in age, sex, severity of baseline dysphagia. and use of antireflux medication. Improvement in dysphagia comparing sham to balloon on day 1 was 66% versus 67% (p = 0.99); at 3 months it was 82% versus 76% (p = 0.56); and at 6 months it was 84% versus 73% (p = 0.38). There were no reported complications in either group.The data from this prospective randomized, controlled study do not support the practice of empiric dilation in patients with symptoms of dysphagia without an endoscopically evident cause of dysphagia.
Effect of operational parameters and their interplay in differential cross-phase-modulation wavelength converters (2006)

DXPM wavelength-converters are analyzed via simulations to quantify sensitivity to device parameters. 0.2 rad phase-drift causes 3-dB power-penalty. Optimal operating conditions are shown to depend on input signal parameters pointing to the requirement of adaptive optimization.
Cardiac contractility modulation for the treatment of moderate to severe HF (2020)

<b>Introduction</b>: Heart failure (HF) affects over 6 million Americans and approximately 650,000 new cases are diagnosed annually, with patients evenly split between HFrEF and HFpEF. Recent advances in therapy for these patients have been limited to pharmaceutical agents, with CRT remaining the most reliable device therapy option since its advent almost twenty years ago. In 2019, after almost two decades without the introduction of a new device therapy for the treatment of moderate HF, the FDA approved CCM® therapy, delivered by the Optimizer Smart device, for patients with NYHA Class III HF who are on guideline-directed medical therapy (GDMT), in normal sinus rhythm (NSR), and with EF ranging from 25% to 45%, and who are ineligible for CRT.<b>Areas covered</b>: Multiple clinical trials support the use of CCM to improve quality of life, functional class, and 6-min hall walk distance. This article will discuss the science behind CCM therapy, the presumed mechanisms of action, the pre-clinical studies that shaped subsequent endeavors, and the clinical trials that support its use.<b>Expert opinion</b>: The introduction of CCM therapy bridges a therapeutic gap for patients with few or no other therapeutic options for NYHA III heart failure.
The α‐kinases TRPM6 and TRPM7, but not eEF‐2 kinase, phosphorylate the assembly domain of myosin IIA, IIB and IIC (2008)

TRPM6 and TRPM7 encode channel-kinases. While these channels share electrophysiological properties and cellular functions, TRPM6 and TRPM7 are non-redundant genes raising the possibility that the kinases have distinct substrates. Here, we demonstrate that TRPM6 and TRPM7 phosphorylate the assembly domain of myosin IIA, IIB and IIC on identical residues. Whereas phosphorylation of myosin IIA is restricted to the coiled-coil domain, TRPM6 and TRPM7 also phosphorylate the non-helical tails of myosin IIB and IIC. TRPM7 does not phosphorylate eukaryotic elongation factor-2 (eEF-2) and myosin II is a poor substrate for eEF-2 kinase. In conclusion, TRPM6 and TRPM7 share exogenous substrates among themselves but not with functionally distant alpha-kinases.
Parathyroid hormone receptors in GtoPdb v.2021.3 (2021)

The parathyroid hormone receptors (nomenclature as agreed by the NC-IUPHAR Subcommittee on Parathyroid Hormone Receptors [49]) are class B G protein-coupled receptors. The parathyroid hormone (PTH)/parathyroid hormone-related peptide (PTHrP) receptor (PTH1 receptor) is activated by precursor-derived peptides: PTH (84 amino acids), and PTHrP (141 amino-acids) and related peptides (PTH-(1-34), PTHrP-(1-36)). The parathyroid hormone 2 receptor (PTH2 receptor) is activated by the precursor-derived peptide TIP39 (39 amino acids). [125I]PTH may be used to label both PTH1 and PTH2 receptors. The structure of a long-active PTH analogue (LA-PTH, an hybrid of PTH-(1-13) and PTHrP-(14-36)) bound to the PTH1 receptor-Gs complex has been resolved by cryo-electron microscopy [147]. Another structure of a PTH-(1-34) analog bound to a thermostabilized inactive PTH1 receptor has been obtained with X-ray crytallography [34].
Induced expression of syndecan in healing wounds. (1991)

We have studied the expression of an integral cell surface proteoglycan, syndecan, during the healing of cutaneous wounds, using immunohistochemical and in situ hybridization methods. In normal mouse skin, both syndecan antigen and mRNA were found to be expressed exclusively by epidermal and hair follicle cells. After incision and subsequent suturing, remarkably increased amounts of syndecan on the cell surfaces of migrating and proliferating epidermal cells and on hair follicle cells adjacent to wound margins were noted. This increased syndecan expression was shown to be a consequence of greater amounts of syndecan mRNA. Induction was observed already 1 d after wounding, was most significant at the time of intense cell proliferation, and was still observable 14 d after incision. The migrating cells of the leading edge of the epithelium also showed enhanced syndecan expression, although clearly less than that seen in the proliferating epithelium. The merging epithelial cells at the site of incision showed little or no syndecan expression; increased syndecan expression, however, was detected during later epithelial stratification. When wounds were left unsutured, in situ hybridization experiments also revealed scattered syndecan-positive signals in the granulation tissue near the migrating epidermal sheet. By immunohistochemical analysis, positive staining in granulation tissue was observed around vascular endothelial cells in a subpopulation of growing capillaries. Induction of syndecan in granulation tissue both at the protein and mRNA levels was temporally and spatially highly restricted. Granulation tissue, which formed in viscose cellulose sponge cylinders placed under the skin of rats, was also found to produce 3.4 and 2.6 kb mRNA species of syndecan similar to that observed in the normal murine mammary epithelial cell line, NMuMG. These results suggest that syndecan may have a unique and important role as a cell adhesion and a growth factor-binding molecule not only during embryogenesis but also during tissue regeneration in mature tissues.
ChemInform Abstract: Synthesis of Function‐Oriented 2‐Phenyl‐2H‐chromene Derivatives Using L‐Pipecolinic Acid and Substituted Guanidine Organocatalysts. (2010)

Abstract An organocatalytic oxa‐Mannich/aldol reaction is developed to give chromenes in high yields without the need of a co‐catalyst.
Stability of symplectic finite-difference time-domain methods (2002)

Problems with slowly varying electromagnetic fields may be difficult to treat using finite-difference time-domain (FDTD) method. FDTD method was extended to symplectic FDTD methods to resolve the problems. Stability of schemes is a key to the efficient calculation of these problems. The stability of newly developed symplectic FDTD methods is examined. The developed symplectic FDTD methods show better stability than the conventional FDTD method.
Three-Step, “One-Pot” Radiosynthesis of 6-Fluoro-3,4-Dihydroxy-l-Phenylalanine by Isotopic Exchange (2009)

The pathway to 6-(18)F-fluoro-L-DOPA by isotopic exchange not only is more efficient but also is suited to automation as a "one-pot" procedure.
Chronic Kidney Disease and Postoperative Morbidity After Elective Orthopedic Surgery (2010)

A substantial minority of patients with CKD undergoing elective orthopedic procedures are at increased risk of prolonged morbidity and hospital stay. Preoperative eGFR may enhance perioperative risk stratification beyond traditional risk factors.
Diversity-Based Media Search (2022)

In this paper, we outline a method for searching a set of information based on both the individual diversity of the constituent elements of the set as well as its overall ensemble diversity. Using the example of searching user accounts on Instagram, we are able to perform searches based on the representative diversity (across race, age, gender, body type, skin tone, and disability) of the posts as well as the overall diversity of the search results.
Facile Purification of Honokiol (I) and Its Antiviral and Cytotoxic Properties. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Impact of β2 integrin deficiency on mouse natural killer cell development and function (2011)

Natural killer (NK) cells are innate immune cells that express members of the leukocyte β2 integrin family in humans and mice. These CD11/CD18 heterodimers play critical roles in leukocyte trafficking, immune synapse formation, and costimulation. The cell-surface expression of one of these integrins, CD11b/CD18, is also recognized as a major marker of mouse NK-cell maturation, but its function on NK cells has been largely ignored. Using N-ethyl-N-nitrosourea (ENU) mutagenesis, we generated a mouse carrying an A → T transverse mutation in the Itgb2 gene, resulting in a mutation that prevented the cell-surface expression of CD18 and its associated CD11a, CD11b, and CD11c proteins. We show that β2 integrin-deficient NK cells have a hyporesponsive phenotype in vitro, and present an alteration of their in vivo developmental program characterized by a selective accumulation of c-kit(+) cells. NK-cell missing-self recognition was partially altered in vivo, whereas the early immune response to mouse cytomegalovirus (MCMV) infection occurred normally in CD18-deficient mice. Therefore, β2 integrins are required for optimal NK-cell maturation, but this deficiency is partial and can be bypassed during MCMV infection, highlighting the robustness of antiviral protective responses.
Supplementary Tables 1 and 2 from Immunologic Recognition of a Shared p53 Mutated Neoantigen in a Patient with Metastatic Colorectal Cancer (2023)

&lt;p&gt;Supplementary Tables 1 and 2&lt;/p&gt;
Parallel Connection of Two Three-Phase Three-Switch Buck-Type Unity-Power-Factor Rectifier Systems With DC-Link Current Balancing (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Connecting three-phase rectifier systems in parallel shows many advantages as compared to a single rectifier system with higher output power, such as higher reliability, smaller current and voltage ripple components, lower filtering effort, or higher system bandwidth. However, current unbalance or circulating currents can occur for modular design. In this paper, the parallel connection of two three-phase three-switch buck-type unity-power-factor pulsewidth-modulation rectifier systems is experimentally investigated for a 10-kW digital-signal-processor-controlled prototype. A space vector modulation scheme is employed showing all the advantages of an interleaved operation. Three control schemes for active dc-link current balancing are described employing an additional free-wheeling state that allows to influence the rate of change of the dc-link currents and can therefore be used for dc-link current balancing. The control schemes differ concerning control action and additional switching losses. Simulation and experimental results confirm the theoretical considerations: The dc-link current-balancing capability of the different control methods is compared, and the influence of the additional free-wheeling state on switching losses and operation behavior is investigated. The most advantageous control method, which employs a hysteresis controller and shows limited switching losses, is selected. The analysis of the mains behavior shows an improvement as compared to a single rectifier operation. </para>
Negative Feedback Regulation and Desensitization of Insulin- and Epidermal Growth Factor-stimulated p21ras Activation (1995)

Insulin and epidermal growth factor receptors transmit signals for cell proliferation and gene regulation through formation of active GTP-bound p21ras mediated by the guanine nucleotide exchange factor Sos. Sos is constitutively bound to the adaptor protein Grb2 and growth factor stimulation induces association of the Grb2/Sos complex with Shc and movement of Sos to the plasma membrane location of p21ras. Insulin or epidermal growth factor stimulation induces a rapid increase in p21ras levels, but after several minutes levels decline toward basal despite ongoing hormone stimulation. Here we show that deactivation of p21ras correlates closely with phosphorylation of Sos and dissociation of Sos from Grb2, and that inhibition of mitogen-activated protein (MAP) kinase kinase (also known as extracellular signal-related kinase (ERK) kinase, or MEK) blocks both events, resulting in prolonged p21ras activation. These data suggest that a negative feedback loop exists whereby activation of the Raf/MEK/MAP kinase cascade by p21ras causes Sos phosphorylation and, therefore, Sos/Grb2 dissociation, limiting the duration of p21ras activation by growth factors. A serine/threonine kinase downstream of MEK (probably MAP kinase) mediates this desensitization feedback pathway.