gebhart/patrepeval huggingface dataset:
Assessment of Left Ventricular Ejection Fraction Calculation on Long-axis Views From Cardiac Magnetic Resonance Imaging in Patients With Acute Myocardial Infarction (2015)

To assess left ventricular ejection fraction (LVEF) accurately, cardiac magnetic resonance (CMR) can be indicated and lays on the evaluation of multiple slices of the left ventricle in short axis (CMRSAX). The objective of this study was to assess another method consisting of the evaluation of 2 long-axis slices (CMRLAX) for LVEF determination in acute myocardial infarction.One hundred patients underwent CMR 2 to 4 days after acute myocardial infarction. LVEF was computed by the area-length method on horizontal and vertical CMRLAX images. Those results were compared to reference values obtained on contiguous CMRSAX images in one hand, and to values obtained from transthoracic echocardiography (TTE) in the other hand. For CMRSAX and TTE, LVEF was computed with Simpson method. Reproducibility of LVEF measurements was additionally determined. The accuracy of volume measurements was assessed against reference aortic stroke volumes obtained by phase-contrast MR imaging.LVEF from CMRLAX had a mean value of 47 ± 8% and were on average 5% higher than reference LVEF from CMRSAX (42 ± 8%), closer to routine values from TTELAX (49 ± 8%), much better correlated with the reference LVEF from CMRSAX (R = 0.88) than that from TTE (R = 0.58), obtained with a higher reproducibility than with the 2 other techniques (% of interobserver variability: CMRLAX 5%, CMRSAX 11%, and TTE 13%), and obtained with 4-fold lower recording and calculation times than for CMRSAX. Apart from this, CMRLAX stroke volume was well correlated with phase-contrast values (R = 0.81).In patients with predominantly regional contractility abnormalities, the determination of LVEF by CMRLAX is twice more reproducible than the reference CMRSAX method, even though the LVEF is consistently overestimated compared with CMRSAX. However, the CMRLAX LVEF determination provides values closer to TTE measurements, the most available and commonly used method in clinical practice, clinical trials, and guidelines in ischemic cardiomyopathy. Moreover, LVEF determination by CMRLAX allows a 63% gain of acquisition/reading time compared with CMRSAX. Thus, despite the fact that LVEF obtained from CMRSAX remains the gold standard, CMRLAX should be considered to shorten the overall imaging acquisition and reading time as a putative replacement.
The Carboxyl Termini of KATP Channels Bind Nucleotides (2002)

ATP-sensitive potassium (K(ATP)) channels are expressed in many excitable, as well as epithelial, cells and couple metabolic changes to modulation of cell activity. ATP regulation of K(ATP) channel activity may involve direct binding of this nucleotide to the pore-forming inward rectifier (Kir) subunit despite the lack of known nucleotide-binding motifs. To examine this possibility, we assessed the binding of the fluorescent ATP analogue, 2',3'-O-(2,4,6-trinitrophenylcyclo-hexadienylidene)adenosine 5'-triphosphate (TNP-ATP) to maltose-binding fusion proteins of the NH(2)- and COOH-terminal cytosolic regions of the three known K(ATP) channels (Kir1.1, Kir6.1, and Kir6.2) as well as to the COOH-terminal region of an ATP-insensitive inward rectifier K(+) channel (Kir2.1). We show direct binding of TNP-ATP to the COOH termini of all three known K(ATP) channels but not to the COOH terminus of the ATP-insensitive channel, Kir2.1. TNP-ATP binding was specific for the COOH termini of K(ATP) channels because this nucleotide did not bind to the NH(2) termini of Kir1.1 or Kir6.1. The affinities for TNP-ATP binding to K(ATP) COOH termini of Kir1.1, Kir6.1, and Kir6.2 were similar. Binding was abolished by denaturing with 4 m urea or SDS and enhanced by reduction in pH. TNP-ATP to protein stoichiometries were similar for all K(ATP) COOH-terminal proteins with 1 mol of TNP-ATP binding/mole of protein. Competition of TNP-ATP binding to the Kir1.1 COOH terminus by MgATP was complex with both Mg(2+) and MgATP effects. Glutaraldehyde cross-linking demonstrated the multimerization potential of these COOH termini, suggesting that these cytosolic segments may directly interact in intact tetrameric channels. Thus, the COOH termini of K(ATP) tetrameric channels contain the nucleotide-binding pockets of these metabolically regulated channels with four potential nucleotide-binding sites/channel tetramer.
Accurate Approximate Methods for the Fully Developed Flow of Shear-Thinning Fluids in Ducts of Noncircular Cross Section (2019)

The fully developed laminar flow of Non-Newtonian fluids in ducts has broad application in engineering. The power-law viscosity model is utilized most often in the engineering literature, but it is deficient for many fluids as it does not admit limiting Newtonian viscosities at low and high shear rates. The goal of this work is to demonstrate two approximate but accurate and efficient methods for computing the pressure gradient in ducts of noncircular cross section for shear-thinning fluids following a general viscosity curve. Both methods predict the pressure gradient to better than 1% as established by full numerical solutions for ten cross-sectional shapes, a result representing an order-of-magnitude improvement over previous approximate methods. In the first method, an approach recently proposed and demonstrated to be accurate for a circular duct is shown to be equally applicable to noncircular ducts. In the second method, a widely used approach for noncircular ducts based on a generalization of the Rabinowitsch–Mooney equation is improved through an alternate evaluation of its parameters. Both methods require one-time numerical solutions of the power-law viscosity model for a duct shape of interest, and the necessary results are tabulated for the ten cross-sectional shapes analyzed. It is additionally demonstrated that the pressure-gradient error of the second method is approximately halved by simply replacing the hydraulic diameter with a viscous diameter obtained from the Hagen–Poiseuille equation.
H3PO2-Catalyzed Intramolecular Stereospecific Substitution of the Hydroxyl Group in Enantioenriched Secondary Alcohols by N-, O-, and S-Centered Nucleophiles to Generate Heterocycles (2019)

The direct intramolecular stereospecific substitution of the hydroxyl group in enantiomerically enriched secondary benzylic, allylic, propargylic, and alkyl alcohols was successfully accomplished by phosphinic acid catalysis. The hydroxyl group was displaced by O-, S-, and N-centered nucleophiles to provide enantioenriched five-membered tetrahydrofuran, pyrrolidine, and tetrahydrothiophene as well as six-membered tetrahydroquinolines and chromanes in up to a 99% yield and 100% enantiospecificity with water as the only byproduct. Mechanistic studies using both experiments and calculations have been performed for substrates generating 5-membered heterocycles. Rate studies show dependences in a catalyst, an internal nucleophile, and an electrophile, however, independence in an external nucleophile, an electrophile, or water. Kinetic isotope effect studies show an inverse KIE of kH/kD = 0.79. Furthermore, phosphinic acid does not promote SN1 reactivity. Computational studies support a bifunctional role of the phosphinic acid in which activation of both nucleofuge and nucleophile occurs in a bridging SN2-type transition state. In this transition state, the acidic hydrogen of phosphinic acid protonates the leaving hydroxyl group simultaneously as the oxo group partially deprotonates the nucleophile. Thereby, phosphinic acid promotes the substitution of the nonderivatized hydroxyl group in enantioenriched secondary alcohols by uncharged nucleophiles with conservation of the chirality from the alcohol to the heterocycle.
Pseudoprolines (Pro) in Drug Design: Direct Insertion of Pro Systems into Cyclosporin C (2000)

The insertion of acetals that exhibit variable structural features into complex peptides such as cyclosporin C (CsC) results in oxazolidine derivatives (pseudoprolines, psiPro) of tailored physico-chemical and biological properties. N,O-Acetalation of the 2-threonine hydroxyl group and the preceding amide nitrogen of CsC is achieved by treating the molecule with a number of both arylated and non-arylated dimethyl acetals. The psiPro-containing CsC derivatives exhibit enhanced conformational backbone rigidity, as suggested by analytical HPLC, NMR spectroscopy and by kinetic measurements on binding with their receptor protein cyclophilin A (CypA) that were not time-dependent. IC50 values for calf-thymus CypA were obtained by kinetic evaluation of its cis-->trans isomerase activity. The choice of the para-substituted aryl dimethyl acetals allows the inhibitory properties of the corresponding derivatives to be modulated to either prodrugs or moderately strongly binding cyclosporin C derivatives.
Data from Intraductal Transplantation Models of Human Pancreatic Ductal Adenocarcinoma Reveal Progressive Transition of Molecular Subtypes (2023)

&lt;div&gt;Abstract&lt;p&gt;Pancreatic ductal adenocarcinoma (PDAC) is the most lethal common malignancy, with little improvement in patient outcomes over the past decades. Recently, subtypes of pancreatic cancer with different prognoses have been elaborated; however, the inability to model these subtypes has precluded mechanistic investigation of their origins. Here, we present a xenotransplantation model of PDAC in which neoplasms originate from patient-derived organoids injected directly into murine pancreatic ducts. Our model enables distinction of the two main PDAC subtypes: intraepithelial neoplasms from this model progress in an indolent or invasive manner representing the classical or basal-like subtypes of PDAC, respectively. Parameters that influence PDAC subtype specification in this intraductal model include cell plasticity and hyperactivation of the RAS pathway. Finally, through intratumoral dissection and the direct manipulation of &lt;i&gt;RAS&lt;/i&gt; gene dosage, we identify a suite of &lt;i&gt;RAS&lt;/i&gt;-regulated secreted and membrane-bound proteins that may represent potential candidates for therapeutic intervention in patients with PDAC.&lt;/p&gt;Significance:&lt;p&gt;Accurate modeling of the molecular subtypes of pancreatic cancer is crucial to facilitate the generation of effective therapies. We report the development of an intraductal organoid transplantation model of pancreatic cancer that models the progressive switching of subtypes, and identify stochastic and RAS-driven mechanisms that determine subtype specification.&lt;/p&gt;&lt;p&gt;&lt;i&gt;See related commentary by Pickering and Morton, p. 1448&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;&lt;i&gt;This article is highlighted in the In This Issue feature, p. 1426&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Analytical reaction-diffusion model and the modeling of nitrogen-enhanced negative bias temperature instability (2006)

An analytical reaction-diffusion (RD) model within the framework of the standard RD model is proposed to describe the negative bias temperature instability (NBTI) process in a wide time scale covering the three regimes of reaction, transition, and diffusion. The experimental NBTI results for the nitrided gate oxides at various nitrogen concentrations are well described by this analytical model. The modeling of nitrogen-enhanced NBTI degradation based on this model has provided us some very useful information. It has shown that with increasing nitrogen concentration, the initial neutral defect density and/or forward reaction rate increase̸s, leading to the enhancement of interface trap generation in all the three regimes. At the same time, the diffusion of H species in nitrided oxides also increases, causing a further enhancement of interface trap generation in the diffusion regime.
Oxide Nanoelectronics on Demand (2009)

Electronic confinement at nanoscale dimensions remains a central means of science and technology. We demonstrate nanoscale lateral confinement of a quasi-two-dimensional electron gas at a lanthanum aluminate-strontium titanate interface. Control of this confinement using an atomic force microscope lithography technique enabled us to create tunnel junctions and field-effect transistors with characteristic dimensions as small as 2 nanometers. These electronic devices can be modified or erased without the need for complex lithographic procedures. Our on-demand nanoelectronics fabrication platform has the potential for widespread technological application.
Clinical Scenarios in Acute Kidney Injury: Pre-Renal Acute Kidney Injury (2016)

Approximately 70% of community-acquired cases of acute kidney injury are attributed to pre-renal causes. In most of these cases, the underlying kidney function may be normal, but decreased renal perfusion associated with low intravascular volume or decreased arterial pressure can determine a reduced glomerular filtration rate (GFR). Autoregulatory mechanisms can partially compensate renal perfusion reduction in order to maintain GFR. In patients with pre-existing chronic kidney disease, however, these mechanisms are impaired, and the susceptibility to develop acute-on-chronic renal failure is higher.
Optimizing Timeout-Based Sleep Algorithms (2005)

For wireless sensor networks that are expected to have a long lifetime while operating on limited energy resources, energy efficiency is a major concern (1). In particular, it is well known that idle listening of the radio causes significant waste of energy; a power management technique (2) to deal with this problem is to switch to the lower energy consumption SLEEP mode during idle times. The effectiveness of this technique depends on (i) the duration of idle times (ii) the power consumption and performance characteristics of the sensor node and (iii) the sleep schedule/algorithm. A significant body of work focuses today on developing sleep schedules to meet energy and performance requirements. A class of simple, thus easy to implement, algorithms can be based on timeouts: nodes switch from ON to SLEEP, when the radio has been idle for longer than a Timeout period; clearly, the choice of Timeout becomes a critical parameter. In this extended abstract, we propose and analyze fixed timeout algo- rithms for a single sensor node, to minimize energy consumption. First, we consider the case that nothing is known about the duration of idle times; we choose a fixed timeout based on the power consumption characteristics of the node, and we prove that the energy consumed by this fixed timeout algorithm is at most twice the energy consumed by an offline algorithm. Second, we consider that the distribution of idle times is known and we show how to choose a fixed timeout value so as to minimize the average energy consumption; as a concrete example, we analyze the interesting case of Poisson packet arrivals. We are currently working on several extensions of this WIP, including (i) adaptive timeouts (ii) network-wide algorithms and (iii) performance metrics such as delay and connectivity.
Apodization scheme for hardware-efficient beamformer (2016)

3D ultrasound is an emerging diagnostic technique that extends standard ultrasound imaging by capturing volumes, instead of planes. This brings completely new diagnostic opportunities, among which the possibility of disjoining image acquisition and analysis, thus enabling remote diagnosis, which would bring obvious medical and economic benefits. Unfortunately, 3D ultrasound is several orders of magnitude more computationally complex than 2D imaging. Therefore, algorithmic improvements to simplify the processing are mandatory in order to conceive cheap, portable, low-power imagers. The kernel of the 3D imaging process, called beamforming, consists essentially of computing delay and apodization profiles. We have previously devised an approximation of the delay calculation stage, which dramatically reduces hardware complexity. Unfortunately, this approximation introduces an intrinsic degree of inaccuracy that can be characterized as added image noise. In this paper, we identify an efficient approximated approach to the calculation of apodization profiles, that additionally minimizes (-76%) the error introduced during delay calculation. Together, these two techniques enable an efficient computation of 3D ultrasound images.
Steady‐state first‐pass perfusion (SSFPP): A new approach to 3D first‐pass myocardial perfusion imaging (2013)

A new approach to first-pass myocardial perfusion is presented that obviates the need for magnetization preparation and provides high signal-to-noise ratio.
Aerosol: A Novel Vehicle for Pharmacotherapy in Neonates (2018)

The present review iteratively describes the difficulties in achieving optimized aerosol drug delivery in neonates. We suggest possible technical solutions aimed at improving delivery and developing a platform for increased reliability and reproducibility of dosing such that new and existing medications may exploit the potential advantages of aerosol therapy in the neonate population.
Distinct positions of genetic and oral histories: Perspectives from India (2022)

Abstract Over the past decade, genomic data has contributed to several insights on global human population histories. These studies have been met both with interest and critically, particularly by populations with oral histories that are records of their past and often reference their origins. While several studies have reported concordance between oral and genetic histories, there is potential for tension that may stem from genetic histories being prioritized or used to confirm community-based knowledge and ethnography, especially if they differ. To investigate the interplay between oral and genetic histories, we focused on the southwestern region of India and analyzed whole-genome sequence data from 158 individuals identifying as Bunt, Kodava, Nair, and Kapla. We supplemented limited anthropological records on these populations with oral history accounts from community members and historical literature, focusing on references to non-local origins such as the ancient Scythians in the case of Bunt, Kodava, and Nair, members of Alexander the Great’s army for the Kodava, and an African-related source for Kapla. We found these populations to be genetically most similar to other Indian populations, with the Kapla more similar to South Indian tribal populations that maximize a genetic ancestry related to Andaman Islanders. We did not find evidence of additional genetic sources in the study populations than those known to have contributed to many other present-day South Asian populations. Our results demonstrate that oral and genetic histories may not always provide consistent accounts of population origins and motivate further community-engaged, multi-disciplinary investigations of non-local origin stories in these communities.
Structure‐Based Inhibitor Design of Human Hematopoietic Prostaglandin D Synthase (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Anionic fluorophore-assisted fabrication of gold microstructures inside a hydrogel by multi-photon photoreduction (2020)

The fabrication of accentuated gold microstructures is demonstrated by multi-photon photoreduction inside an anionic fluorophore-containing hydrogel. We attempted to facilitate gold-ion photoreduction near the focal point of laser pulses, expecting the donation of electrons by the oxidation of fluorophores in the vicinity of gold ions. The presence of anionic FITC-dextran also inhibited the spontaneous reduction in untargeted zones, which is attributed to the coordination of gold ions and the anionic FITC-dextran. Simultaneous facilitation and inhibition are promising for the fabrication of dense metal microstructures in the targeted zone while maintaining the hydrogel’s light permeability.
A novel optical access network: Software-defined FlexPON (2014)

We propose a novel software defined FlexPON. Experimentally demonstrated adaptive bit loading flexible link supports different capacity (9.6Gb/s- 200Mb/s) at different OPB and up to 44dB OPB is verified at 10/20/30km fiber.
In situ cell-type-specific cell-surface proteomic profiling in mice (2022)

Cell-surface proteins (CSPs) mediate intercellular communication throughout the lives of multicellular organisms. However, there are no generalizable methods for quantitative CSP profiling in specific cell types in vertebrate tissues. Here, we present in situ cell-surface proteome extraction by extracellular labeling (iPEEL), a proximity labeling method in mice that enables spatiotemporally precise labeling of cell-surface proteomes in a cell-type-specific environment in native tissues for discovery proteomics. Applying iPEEL to developing and mature cerebellar Purkinje cells revealed differential enrichment in CSPs with post-translational protein processing and synaptic functions in the developing and mature cell-surface proteomes, respectively. A proteome-instructed in vivo loss-of-function screen identified a critical, multifaceted role for Armh4 in Purkinje cell dendrite morphogenesis. Armh4 overexpression also disrupts dendrite morphogenesis; this effect requires its conserved cytoplasmic domain and is augmented by disrupting its endocytosis. Our results highlight the utility of CSP profiling in native mammalian tissues for identifying regulators of cell-surface signaling.
Vidgets (2019)

We present Vidgets , a family of mechanical widgets, specifically push buttons and rotary knobs that augment mobile devices with tangible user interfaces. When these widgets are attached to a mobile device and a user interacts with them, the widgets' nonlinear mechanical response shifts the device slightly and quickly, and this subtle motion can be detected by the accelerometer commonly equipped on mobile devices. We propose a physics-based model to understand the nonlinear mechanical response of widgets. This understanding enables us to design tactile force profiles of these widgets so that the resulting accelerometer signals become easy to recognize. We then develop a lightweight signal processing algorithm that analyzes the accelerometer signals and recognizes how the user interacts with the widgets in real time. Vidgets widgets are low-cost, compact, reconfigurable, and power efficient. They can form a diverse set of physical interfaces that enrich users' interactions with mobile devices in various practical scenarios. We demonstrate their use in three applications: photo capture with single-handed zoom, control of mobile games, and making a playable mobile music instrument.