gebhart/patrepeval huggingface dataset:
Safety Assessment of Advanced Imaging Sequences II: Simulations (2015)

An automatic approach for simulating the emitted pressure, intensity, and mechanical index (MI) of advanced ultrasound imaging sequences is presented. It is based on a linear simulation of pressure fields using Field II, and it is hypothesized that linear simulation can attain the needed accuracy for predicting MI and I(spta.3) as required by FDA. The method is performed on four different imaging schemes and compared to measurements conducted using the SARUS experimental scanner. The sequences include focused emissions with an F-number of 2 with 64 elements that generate highly nonlinear fields. The simulation time is between 0.67 and 2.8 ms per emission and imaging point, making it possible to simulate even complex emission sequences in less than 1 s for a single spatial position. The linear simulations yield a relative accuracy on MI between -12.1% and 52.3% and for I(spta.3) between -38.6% and 62.6%, when using the impulse response of the probe estimated from an independent measurement. The accuracy is increased to between -22% and 24.5% for MI and between -33.2% and 27.0% for I(spta.3), when using the pressure response measured at a single point to scale the simulation. The spatial distribution of MI and I(ta.3) closely matches that for the measurement, and simulations can, therefore, be used to select the region for measuring the intensities, resulting in a significant reduction in measurement time. It can validate emission sequences by showing symmetry of emitted pressure fields, focal position, and intensity distribution.
Nonvolatile Rewritable Frequency Tuning of a Nanoelectromechanical Resonator Using Photoinduced Doping (2020)

Arrays of nanoelectromechanical resonators (NEMS) have shown promise for a suite of applications, from nanomechanical information processing technologies to mass spectrometry. A fundamental challenge toward broader adoption of NEMS arrays is a lack of viable frequency tuning methods, which must simultaneously allow for persistent and reversible control of single resonators while also being scalable to large arrays of devices. In this work, we demonstrate an electro-optic tuning method for graphene-based NEMS where locally photoionized charge tensions a suspended membrane and tunes its resonance frequency. The tuned frequency state persists unchanged for several days in the absence of any external power, and the state can be repeatedly written and erased with a high degree of precision. We show the scalability of this technique by aligning the frequencies of several NEMS devices on the same chip, and we discuss implications of this tuning method for both single devices and programmable NEMS networks.
A Novel Bifunctional Phospholipase C That Is Regulated by Gα12 and Stimulates the Ras/Mitogen-activated Protein Kinase Pathway (2001)

Three families of phospholipase C (PI-PLCbeta, gamma, and delta) are known to catalyze the hydrolysis of polyphosphoinositides such as phosphatidylinositol 4,5-bisphosphate (PIP(2)) to generate the second messengers inositol 1,4,5 trisphosphate and diacylglycerol, leading to a cascade of intracellular responses that result in cell growth, cell differentiation, and gene expression. Here we describe the founding member of a novel, structurally distinct fourth family of PI-PLC. PLCepsilon not only contains conserved catalytic (X and Y) and regulatory domains (C2) common to other eukaryotic PLCs, but also contains two Ras-associating (RA) domains and a Ras guanine nucleotide exchange factor (RasGEF) motif. PLCepsilon hydrolyzes PIP(2), and this activity is stimulated selectively by a constitutively active form of the heterotrimeric G protein Galpha(12). PLCepsilon and a mutant (H1144L) incapable of hydrolyzing phosphoinositides promote formation of GTP-Ras. Thus PLCepsilon is a RasGEF. PLCepsilon, the mutant H1144L, and the isolated GEF domain activate the mitogen-activated protein kinase pathway in a manner dependent on Ras but independent of PIP(2) hydrolysis. Our findings demonstrate that PLCepsilon is a novel bifunctional enzyme that is regulated by the heterotrimeric G protein Galpha(12) and activates the small G protein Ras/mitogen-activated protein kinase signaling pathway.
Estrogen receptors in ductal carcinoma in situ of breast. (1990)

A number of investigators have suggested treatment of precursor lesions for invasive breast cancer such as ductal carcinoma in situ with antiestrogen. However, very little information is available on the incidence of estrogen receptor in such lesions and the probability of treatment success. Fourteen formalin-fixed tissue specimens of intraductal carcinoma in situ from 14 female patients aged 40 to 66 years were evaluated for the presence of estrogen receptor by immunoperoxidase technique using estrogen receptor antibody. Eight of the 14 lesions (57%) were positive for estrogen receptor. The incidence of estrogen receptor in intraductal carcinoma in situ is very similar to that of invasive carcinoma of breast, leading to the speculation that ER-positive invasive carcinoma originates from ER-positive precursor lesions. Since only 70 per cent of positive receptor lesions are expected to respond to antiestrogens, it appears that only 40 per cent of patients with ductal carcinoma in situ of breast will benefit from endocrine therapy.
A global perspective on multivariate calibration methods (1993)

Abstract This paper consists of two distinct but related parts. In the first part a geometric theory of generalized inverses is presented and a methodology based on this theory is developed and applied to solve the K‐matrix and P‐matrix forms of Beer's law. It is shown that most currently accepted and practiced methods for solving these forms of Beer's law are just special cases of this geometric theory of generalized inverses. In addition, this geometric theory is used to explain why the current methods work and why they fail. In the second part a general methodology that includes as special cases least squares, principal component regression, partial least squares 1 and 2, continuum regression plus a variety of other described and undescribed methodologies is presented and then applied to solve the P‐matrix formulation of Beer's law. This general methodology, like the first, is also geometric in nature and relies on an understanding of projections. The main emphasis of this paper is one of perspective, which, if understood, provides the proper foundation for answering the general but extremely hard and possibly unanswerable question “what is the best method?”.
A Systematic Literature Review (2009)

The Bernese periacetabular osteotomy is com- monly used to treat symptomatic acetabular dysplasia. Although periacetabular osteotomy is becoming a more common surgical intervention to relieve pain and improve function, the strength of clinical evidence to support this procedure for these goals is not well defined in the litera- ture. We therefore performed a systematic review of the literature to define the level of evidence for periacetabular osteotomy, to determine deformity correction, clinical results, and to determine complications associated with the procedure. Thirteen studies met our inclusion criteria. Eleven studies were Level IV, one was Level III, and one was Level II. Radiographic deformity correction was consistent and improvement in hip function was noted in all studies. Most studies did not correlate radiographic and clinic outcomes. Clinical failures were commonly associ- ated with moderate to severe preoperative osteoarthritis and conversion to THA was reported in 0% to 17% of cases. Major complications were noted in 6% to 37% of the procedures. These data indicate periacetabular osteotomy provides pain relief and improved hip function in most patients over short- to midterm followup. The current evidence is primarily Level IV. Level of Evidence: Level IV, therapeutic study. See Guidelines for Authors for a complete description of levels of evidence.
Beyond Generative Models: Superfast Traversal, Optimization, Novelty, Exploration and Discovery (STONED) Algorithm for Molecules using SELFIES (2021)

Inverse design allows the design of molecules with desirable properties using property optimization. Deep generative models have recently been applied to tackle inverse design, as they possess the ability to optimize molecular properties directly through structure modification using gradients. While the ability to carry out direct property optimizations is promising, the use of generative deep learning models to solve practical problems requires large amounts of data and is very time-consuming. In this work, we propose STONED – a simple and efficient algorithm to perform interpolation and exploration in the chemical space, comparable to deep generative models. STONED bypasses the need for large amounts of data and training times by using string modifications in the SELFIES molecular representation. We achieve comparable performance on typical benchmarks without any training. We demonstrate applications in high-throughput virtual screening for the design of drugs, photovoltaics, and the construction of chemical paths, allowing for both property and structure-based interpolation in the chemical space. We anticipate our results to be a stepping stone for developing more sophisticated inverse design models and benchmarking tools, ultimately helping generative models achieve wide adoption.
Fosfomycin: Mechanism and Resistance (2017)

Fosfomycin, a natural product antibiotic, has been in use for >20 years in Spain, Germany, France, Japan, Brazil, and South Africa for urinary tract infections (UTIs) and other indications and was registered in the United States for the oral treatment of uncomplicated UTIs because of Enterococcus faecalis and Escherichia coli in 1996. It has a broad spectrum, is bactericidal, has very low toxicity, and acts as a time-dependent inhibitor of the MurA enzyme, which catalyzes the first committed step of peptidoglycan synthesis. Whereas resistance to fosfomycin arises rapidly in vitro through loss of active transport mechanisms, resistance is rarely seen during therapy of UTIs, seemingly because of the low fitness of the resistant organisms. Recently, interest has grown in the use of fosfomycin against multidrug-resistant (MDR) pathogens in other indications, prompting the advent of development in the United States of a parenteral formulation for use, initially, in complicated UTIs. Whereas resistance has not been problematic in the uncomplicated UTI setting, it remains to be seen whether resistance remains at bay with expansion to other indications.
Synergistic Catalysis by “Polymeric Microzymes and Inorganic Nanozymes”: The 1+1&gt;2 Effect for Intramolecular Cyclization of Peptides (2017)

In this work, we developed an efficient "molecularly imprinted polymer microzymes and inorganic magnetic nanozymes" synergistic catalysis strategy for the formation of disulfide bonds in peptides. The polymeric microzymes showed excellent selectivity toward the template peptide as well as the main reactant (linear peptide), and the Fe<sub>3</sub>O<sub>4</sub> magnetic nanoparticle (MNP) nanozymes inhibited the intermolecular reaction during the formation of disulfide bonds in peptides. As a result, the integration of the two different artificial enzymes in one process facilitates the intramolecular cyclization in high product yields (59.3%) with excellent selectivity. Mechanism study indicates the synergistic effect was occurred by using a "reversed solid phase synthesis" strategy with an enhanced shift of reaction balance to product generation. We believe the synergistic catalysis by "polymeric microzymes and inorganic nanozymes" presented in the present work may open new opportunities in creation of multifunctional enzyme mimics for sensing, imaging, and drug delivery.
The plant activator BTH promotes Ornithogalum dubium and O. thyrsoides differentiation and regeneration in vitro (2012)

Benzothiadiazole (BTH) is a structural analogue of salicylic acid (SA) which is widely recognized for its role in elicitation of systemic acquired resistance in a broad range of plant species. Here, BTH was applied to cell cultures of the bulbous ornamental plants Ornithogalum dubium and O. thyrsoides, showing a strong effect on rates of differentiation and morphogenesis. Morphogenic cell clusters in liquid Murashige and Skoog (MS) medium containing 1-naphthaleneacetic acid (NAA) and 6-benzylaminopurine (BAP) were used for all treatments. The calluses were washed thoroughly and activated with increasing concentrations of BTH. Following the induction, calli were grown on a solid MS medium without growth regulators (MS) or on a comparable media with NAA and BAP (M-206). The calli treated with BTH displayed a dose dependent increase in formation of meristematic centres followed by enhanced shoot formation compared to controls. Microscopic analyses revealed increased differentiation to cell organelles and a strengthening of the cell wall. A stronger response to BTH was observed in MS than in M-206 medium. A similar effect on calli differentiation was obtained by three weeks darkness followed by light exposure. The dark/light positive effect on differentiation was further augmented by BTH in a synergistic fashion. It is suggested that BTH enhances the rates of morphogenesis in Ornithogalum cultures by triggering a plant regulator-like activity.
Optimization of CD34+ Cell Selection Using Immunomagnetic Beads: Implications for Use in Cryopreserved Peripheral Blood Stem Cell Collections (1997)

Isolation of CD34+ cells from bone marrow, umbilical cord blood, and mobilized peripheral blood stem cell (PBSC) collections has many potential clinical benefits. The aim of this study was to evaluate the use of the ISOLEX 300 system to select hematopoietic precursors and determine the effectiveness at depleting contaminating tumor cells from cryopreserved/thawed PBSC. Median recovery of CD34+ cells and CFU-GM colonies was 71% and 51.5%, respectively, using a protocol optimized for our laboratory. A mean 2.9 log10 decrease in contaminating breast carcinoma cells was seen after the selection process. Selected CD34+ cells underwent a second round of cryopreservation/thawing while retaining 85.6% viability and 72.3% recovery of CFU-GM colonies.
Challenges of Investigating Fluid-Elastic Lock-In of a Shallow Cavity and a Cantilevered Beam at Low Mach Numbers (2005)

At low flow Mach numbers, fluid-elastic lock-in may occur when a shear layer instability interacts with an adjoining or nearby structure and the resulting vibration of the structure reinforces the shear layer instability. Despite the significant amount of study of lock-in with acoustic resonators, fluid-elastic lock-in of a shear layer fluctuation over a cavity and a structural resonator is not well understood and has not been thoroughly studied. Design of an experimental system is described and preliminary diagnostics are addressed as a basis for a platform for developing a fundamental understanding of the feedback mechanism, analytical models for predicting and describing fluid-elastic lock-in conditions, and the roles of the fluid and structural dynamics in the process. Features of the system investigated here include design for characterization of modal excitation of a beam-like structure from the shear layer fluctuation, isolation of the predominant instability source to the shear layer fluctuation over the cavity, variation of the cavity size to identify critical parameters that govern fluid-elastic lock-in, and alteration of the inflow boundary layer momentum thickness. So far, lock-in between the cavity and the distributed elastic resonator has not been achieved. Further investigations to determine the role of the source and resonator attributes are underway.
Formation of Cell Junctions Between Grafted and Host Cardiomyocytes at the Border Zone of Rat Myocardial Infarction (1999)

These findings indicate that grafted cardiomyocytes foster electrical pathways with host counterparts through the gap junction and suggest that the environment in infarcted hearts could influence the localization of gap junctions, desmosomes, and adherens junctions.
50–200 GHz Silicon–Germanium Heterojunction Bipolar Transistor BICMOS Technology and a Computer-Aided Design Environment for 2–50+ GHz Very Large-Scale Integration Mixed-Signal ICs (2002)

Silicon–germanium (SiGe) heterojunction bipolar transistor (HBT) BICMOS technology is a stable, ultra-high performance, semiconductor technology capable of supporting mixed-signal, very large-scale integration (VLSI) circuit designs for a variety of emerging communication applications. This technology is supported by a computer-aided design (CAD) system that supports a variety of high-performance circuit designs, mixed-signal circuit block reuse, and the ability to accurately predict circuit performance at the highest frequencies. This paper summarizes the progress this technology has made in recent years in moving from the research laboratory to a production environment. We also specifically address performance, operating voltage, reliability and integration considerations for using 100–200 GHz SiGe HBTs in high-speed (10–40 Gb/s) network ICs, an application space previously only addressed by InP technology. All indications are that SiGe will be very successful at addressing this new application space, and all facets of the networking IC market.
Competence for collagenase gene expression by tissue fibroblasts requires activation of an interleukin 1 alpha autocrine loop. (1995)

The enzyme collagenase (EC 3.4.24.7), a key mediator in biological remodeling, can be induced in early-passage fibroblasts by a wide variety of agents and conditions. In contrast, at least some primary tissue fibroblasts are incompetent to synthesize collagenase in response to many of these stimulators. In this study, we investigate mechanisms controlling response to two of the conditions in question: (i) trypsin or cytochalasin B, which disrupt actin stress fibers, or (ii) phorbol 12-myristate 13-acetate (PMA), which activates growth factor signaling pathways. We demonstrate that collagenase expression stimulated by trypsin or cytochalasin B is regulated entirely through an autocrine cytokine, interleukin 1 alpha (IL-1 alpha). The IL-1 alpha intermediate also constitutes the major mechanism by which PMA stimulates collagenase expression, although a second signaling pathway(s) contributes to a minor extent. Elevation of the IL-1 alpha level in response to stimulators is found to be sustained by means of an autocrine feedback loop in early-passage fibroblast cultures. In contrast, fibroblasts freshly isolated from the tissue are incompetent to activate and sustain the IL-1 alpha feedback loop, even though they synthesize collagenase in response to exogenous IL-1. We conclude that this is the reason why tissue fibroblasts are limited, in comparison with subcultured fibroblasts, in their capacity to synthesize collagenase. Activation of the IL-1 alpha feedback loop, therefore, seems likely to be an important mechanism by which resident tissue cells adopt the remodeling phenotype.
National Institute of Biomedical Imaging and Bioengineering Point-of-Care Technology Research Network: Advancing Precision Medicine (2016)

To advance the development of point-of-care technology (POCT), the National Institute of Biomedical Imaging and Bioengineering established the POCT Research Network (POCTRN), comprised of Centers that emphasize multidisciplinary partnerships and close facilitation to move technologies from an early stage of development into clinical testing and patient use. This paper describes the POCTRN and the three currently funded Centers as examples of academic-based organizations that support collaborations across disciplines, institutions, and geographic regions to successfully drive innovative solutions from concept to patient care.
Holographic imaging with a nanometer resolution using compact table-top EUV laser (2009)

Abstract Holographic 2D/3D imaging with nanometer resolution using short wavelength extreme ultraviolet (EUV) light is presented in this paper. Gabor’s holograms were recorded with a highly coherent table top EUV laser with different numerical apertures demonstrating ultimately a spatial resolution of 46+/−2 nm, comparable with the illumination wavelength, in 2D holographic imaging. Three dimensional images were obtained from a single high numerical aperture hologram recorded in a high resolution photoresist and numerically reconstructed at different image planes, allowing numerical optical sectioning with a lateral resolution ∼170 nm and depth resolution of 2.4 µm. The holograms were recorded in a high resolution photoresist and digitized with an atomic force microscope. To assess the spatial resolution of the numerical reconstructions of the holograms a correlation method was used. The algorithm allows for simultaneous estimation of the resolution and the feature size of the image under analysis.
Concept Space Synset Manager Tool (2014)

The IndoWordNet 1 Consortium consists of member institutions developing WordNet using the expansion approach.The WordNets developed using expansion approach are very much influenced by the source language and may not reflect the richness of the target language (Walawalikar et al., 2010).And therefore the IndoWordNet Community decided to develop concepts which were specific to their respective language viz.language-specific concepts which will help in increasing the WordNet coverage.Besides the above requirement it was also felt that it should be possible to maintain additional information about the concepts i.e. an image, document describing the concept, links to websites and other resources, etc.In this paper, we discuss a Concept Space Synset Management Tool (CSS) 2 which was developed to assist creation of language specific concepts/synsets and manage their linkages to other Indian language WordNets.
Cholecystokinin-A receptor ligands based on the .kappa.-opioid agonist tifluadom (1990)

Tifluadom, a kappa-opioid agonist and cholecystokinin-A (CCK-A) receptor antagonist, was utilized as a model to prepare a series of 2-(aminomethyl)- and 3-(aminomethyl)-1,4-benzodiazepines. These compounds were tested in vitro as inhibitors of the binding of [125I]CCK to rat pancreas and guinea pig brain receptors. All compounds with IC50's less than 100 microM proved to have greater affinity for the CCK-A receptor, with the most potent analogue, 6e, having an IC50 of 0.16 microM. The benzodiazepines described in this study are simultaneously CCK-A and opioid receptor ligands. The ramification of this dichotomy on current concepts of peptide hormone action are discussed. These results further demonstrate the versatility of the benzodiazepine core structure for designing nonpeptide ligands for peptide receptors and the ability to fine-tune the receptor interactions of these benzodiazepines by appropriate structure modifications.
Stereoselective Synthesis of the LM Ring Moiety of Ciguatoxin: Reagent Control of Asymmetric Dihydroxylation (1997)

Abstract Stereoselective synthesis of the LM ring moiety of ciguatoxin was achieved from (R)-(E)-1-benzyloxy-2-hydroxy-3-pentene via Ireland-Claisen rearrangement, iodolactonization, and reagent-controlled asymmetric dihydroxylation.
Formation and Ring Expansion of Germaplatinacycles via Dehydrogenative Ge−Ge and Ge−Pt Bond-Forming Reactions (2009)

The bis(germyl)platinum complex [Pt(GeHPh2)2(dmpe)] (1) (dmpe = 1,2-bis(dimethylphosphino)ethane) reacts with a small excess of H2GePh2 at 90 °C to produce four-membered germaplatinacycle [Pt(GePh2GePh2GePh2)(dmpe)] (2). Further reaction of 2 with excess H2GePh2 at 90 °C forms tetragermaplatinacyclopentane [Pt(GePh2GePh2GePh2GePh2)(dmpe)] (3), while 3 is obtained also by the direct reaction of excess H2GePh2 with 1 for a prolonged period. Complexes 1−3 were characterized by X-ray crystallography and NMR spectroscopy. Germaplatinacycles 2 and 3 react with H3GePh to cause cleavage of the Pt−Ge bonds and formation of the oligogermanes H(GePh2)3H and H(GePh2)4H, respectively.