gebhart/patrepeval huggingface dataset:
Computational simulations of the total cavo-pulmonary connection: insights in optimizing numerical solutions (2004)

The Fontan procedure is a palliative surgical technique that is used to treat patients with congenital heart defects that include complex lesions such as those with a hypoplastic ventricle. In vitro, in vivo, and computational models of a set of modifications to the Fontan procedure, called the total cavopulmonary connection (TCPC), have been developed. Using these modeling methods, attempts have been made at finding the most energy efficient TCPC circuit. Computational modeling has distinct advantages to other modeling methods. However, discrepancies have been found in validation studies of TCPC computational models. There is little in the literature available to help explain and correct for such discrepancies. Differences in computational results can occur when choosing between steady flow versus transient flow numerical solvers. In this study transient flow solver results were shown to be more consistent with results from previous TCPC in vitro experiments. Using a transient flow solver we found complex fluctuating flow patterns can exist with steady inflow boundary conditions in computational models of the TCPC. To date such findings have not been reported in the literature. Furthermore, our computational modeling results suggest fluctuating flow patterns as well as the magnitudes of these secondary flow structures diminish if the TCPC offset between vena cavae is increased or if flanged connections are added. An association was found between these modifications and improvements in TCPC circuit flow efficiencies. In summary, development of accurate computational simulations in the validation process is critical to efforts in finding the most efficient TCPC circuits, efforts aimed at potentially improving the long term outcome for Fontan patients.
Temperature dependence of the Raman spectra of polycrystallineBa1−xSixTiO3 (2000)

We have studied the temperature dependence of the Raman spectra of ceramic bulk and thin-film samples of polycrystalline ${\mathrm{Ba}}_{1\ensuremath{-}x}{\mathrm{Sr}}_{x}{\mathrm{TiO}}_{3}$ $(x=0,$ 0.1, 0.2, and 0.3) in the range between room temperature and 350 \ifmmode^\circ\else\textdegree\fi{}C. The ferroelectric to paraelectric phase-transition temperatures ${(T}_{C})$ have been estimated from the loss of intensity for several phonon modes belonging to the tetragonal phase when the samples transform to the paraelectric cubic phase. Similar to single crystalline ${\mathrm{BaTiO}}_{3},$ broad first-order Raman features are found to persist well beyond ${T}_{C}$ in all the samples studied here. For bulk samples, the estimated values of ${T}_{C}$ from the Raman studies agree well with the ${T}_{C}$ values determined from the anomaly in the dielectric constant versus temperature measurements. For thin films, however, the temperature measurements of the dielectric constant do not show any anomaly and the Raman signature viz., the disappearance of several phonon modes at ${T}_{C},$ is used for determining ${T}_{C}.$ We find that the values of ${T}_{C}$ in thin films are higher than those of the bulk samples. This is attributed to the presence of intergrain stresses in the submicron size grains in the thin films which might prevent a complete phase transformation at the expected bulk ${T}_{C}.$ Furthermore, a new Raman mode has been seen at \ensuremath{\sim}620 ${\mathrm{cm}}^{\mathrm{\ensuremath{-}}1}$ in all the thin-film samples but not in bulk ceramics at all temperatures. This mode has also been observed in polycrystalline bulk ${\mathrm{BaTiO}}_{3}$ powder under high pressure and it most probably originates from the strain in the grain-boundary regions.
Inducible mismatch repair streamlines forward genetic approaches to target identification of cytotoxic small molecules (2023)

Orphan cytotoxins are small molecules for which the mechanism of action (MoA) is either unknown or ambiguous. Unveiling the mechanism of these compounds may lead to useful tools for biological investigation and in some cases, new therapeutic leads. In select cases, the DNA mismatch repair-deficient colorectal cancer cell line, HCT116, has been used as a tool in forward genetic screens to identify compound-resistant mutations, which have ultimately led to target identification. To expand the utility of this approach, we engineered cancer cell lines with inducible mismatch repair deficits, thus providing temporal control over mutagenesis. By screening for compound resistance phenotypes in cells with low or high rates of mutagenesis, we increased both the specificity and sensitivity of identifying resistance mutations. Using this inducible mutagenesis system, we implicate targets for multiple orphan cytotoxins, including a natural product and compounds emerging from a high-throughput screen, thus providing a robust tool for future MoA studies.
Remodeling the Endoplasmic Reticulum by Poliovirus Infection and by Individual Viral Proteins: an Autophagy-Like Origin for Virus-Induced Vesicles (2000)

All positive-strand RNA viruses of eukaryotes studied assemble RNA replication complexes on the surfaces of cytoplasmic membranes. Infection of mammalian cells with poliovirus and other picornaviruses results in the accumulation of dramatically rearranged and vesiculated membranes. Poliovirus-induced membranes did not cofractionate with endoplasmic reticulum (ER), lysosomes, mitochondria, or the majority of Golgi-derived or endosomal membranes in buoyant density gradients, although changes in ionic strength affected ER and virus-induced vesicles, but not other cellular organelles, similarly. When expressed in isolation, two viral proteins of the poliovirus RNA replication complex, 3A and 2C, cofractionated with ER membranes. However, in cells that expressed 2BC, a proteolytic precursor of the 2B and 2C proteins, membranes identical in buoyant density to those observed during poliovirus infection were formed. When coexpressed with 2BC, viral protein 3A was quantitatively incorporated into these fractions, and the membranes formed were ultrastructurally similar to those in poliovirus-infected cells. These data argue that poliovirus-induced vesicles derive from the ER by the action of viral proteins 2BC and 3A by a mechanism that excludes resident host proteins. The double-membraned morphology, cytosolic content, and apparent ER origin of poliovirus-induced membranes are all consistent with an autophagic origin for these membranes.
Supplementary Figures from Targeting the SUMO Pathway Primes All-<i>trans</i> Retinoic Acid–Induced Differentiation of Nonpromyelocytic Acute Myeloid Leukemias (2023)

&lt;p&gt;Supplementary Figure 1: Inhibition of SUMOylation increases morphological changes associated with ATRA-induced differentiation. Supplementary Figure 2: Effect of SENP overexpression on total and chromatin bound proteins. Supplementary Figure 3: Inhibition of the SUMO pathway increases the differentiation of primary AML cells. Supplementary Figure 4: Inhibition of the SUMO pathway induces the differentiation of primary non-APL AML cells.Supplementary Figure 5: Inhibition of the SUMO pathway increases the death of primary AML cells.&lt;/p&gt;
Threshold reduction and CW operation of LPE grown GaInAsP/AlGaAs red-light injection lasers with the 670nm wavelength (1990)

The objective of this paper is to report a remarkable threshold current density reduction (~ 1KA/cm2) of 670nm wavelength GaInAsP/AlGaAs lasers[l], and the room temperature CW operation of the GaInAsP/AlGaAs VSIS laser
ToxTree: descriptor-based machine learning models for both hERG and Nav1.5 cardiotoxicity liability predictions (2021)

Drug-mediated blockade of the voltage-gated potassium channel(hERG) and the voltage-gated sodium channel (Nav1.5) can lead to severe cardiovascular complications. This rising concern has been reflected in the drug development arena, as the frequent emergence of cardiotoxicity from many approved drugs led to either discontinuing their use or, in some cases, their withdrawal from the market. Predicting potential hERG and Nav1.5 blockers at the outset of the drug discovery process can resolve this problem and can, therefore, decrease the time and expensive cost of developing safe drugs. One fast and cost-effective approach is to use in silico predictive methods to weed out potential hERG and Nav1.5 blockers at the early stages of drug development. Here, we introduce two robust 2D descriptor-based QSAR predictive models for both hERG and Nav1.5 liability predictions. The machine learning models were trained for both regression, predicting the potency value of a drug, and multiclass classification at three different potency cut-offs (i.e. 1$μ$M, 10$μ$M, and 30$μ$M), where ToxTree-hERG Classifier, a pipeline of Random Forest models, was trained on a large curated dataset of 8380 unique molecular compounds. Whereas ToxTree-Nav1.5 Classifier, a pipeline of kernelized SVM models, was trained on a large manually curated set of 1550 unique compounds retrieved from both ChEMBL and PubChem publicly available bioactivity databases. The proposed hERG inducer outperformed most metrics of the state-of-the-art published model and other existing tools. Additionally, we are introducing the first Nav1.5 liability predictive model achieving a Q4 = 74.9% and a binary classification of Q2 = 86.7% with MCC = 71.2% evaluated on an external test set of 173 unique compounds. The curated datasets used in this project are made publicly available to the research community.
Optical approach for determining strain anisotropy in quantum wells (2003)

Anisotropic in-plane strain arises in quantum-well systems by design or unintentionally. We propose two methods of measuring the in-plane strain anisotropy based on the optical polarization anisotropy that arises with anisotropic in-plane strain. One method uses purely optical means to determine the strain anisotropy in quantum wells under a compressive strain that is spatially varying. A second approach, applicable to quantum wells under tensile strain or with strain that does not vary with position, requires the application of a uniaxial in-plane stress. Although the second method is experimentally more difficult, it allows analysis of systems that would otherwise be inaccessible.
Human Herpesvirus-6 (HHV-6) Infection in Allogeneic Bone Marrow Transplant Recipients: Evidence of a Marrow-Suppressive Role for HHV-6 In Vivo (1993)

Sixteen adults were studied for the first 100 days after allogeneic bone marrow transplant to assess the pathogenic role of human herpesvirus-6 (HHV-6) infection in patients with unexplained febrile illnesses. HHV-6 was directly isolated from the blood of 6 patients. Analysis of the clinical courses of these 16 patients revealed otherwise unexplained posttransplant marrow suppression in 5 patients. Idiopathic marrow suppression occurred more frequently in patients with concurrent HHV-6 viremia (4/6) than in those from whom HHV-6 was not isolated from peripheral blood (1/10, P < .05). An etiologic role for the virus was also supported by isolation of HHV-6 from the bone marrow of all 4 patients at the time of marrow suppression and by in vitro colony-forming unit (cfu) assays that demonstrated that HHV-6 could inhibit cfu-granulocyte-macrophage and burst-forming unit-erythroid growth from human bone marrow. By restriction enzyme mapping, all clinical isolates were type B, suggesting that bone marrow transplant recipients may be preferentially infected with and reactivate this HHV-6 subtype. This study implicates HHV-6 as a novel cause of bone marrow suppression in marrow transplant recipients.
Wave propagation and vibration in intelligent nanoplates: A mechanical modeling approach (2021)

In this article, wave propagation responses of a double-layer magneto-electro-viscoelastic (DLMEVE) nanoplate as an intelligent material is studied via modified couple stress and nonlocal strain gradient hypotheses to investigate magnitude of surface layers changes. Both, real and imaginary parts of wave propagation responses are considered and investigated based on the Kelvin–Voigt model of viscoelastic nanoplate model. A refined plate model is applied to extent the governing equations through the modified couple stress and Kelvin–Voigt models. Hamilton’s principle will be employed to determine equilibrium equations to be solved analytically. The motivation of the present research is investigating small-scale coefficients, visco-Pasternak foundation, orthotropic angle effects, and also other effective parameters on the increasing and diminishing of surface layers of the DLMEVE nanoplate in a wave propagation analysis for both real and imaginary responses.
Bit Wear Control and Optimization in Autonomous Rotary Steerable Drilling (2017)

Abstract Directional Steering System (DSS) has been established for well drilling in the oilfield in order to accomplish high reservoir productivity and to improve accessibility of oil reservoirs in complex locations. Rotary Steerable System (RSS) is the current state of the art in directional drilling. In this work, we address the problem of real time control of RSS with unknown formation friction and rock strength. The work presents an online control scheme for real time optimization of drilling parameters to (1) maximize rate of penetration, (2) minimize the deviation from the planned well bore trajectory, and (3) assess the degree of bit wear. Nonlinear model for the drilling operation was developed using energy balance equation, where rock specific energy is used to calculate the minimum power required for a given rate of penetration. The bit wear is mathematically represented using Bourgoyne model. Detailed mathematical formulation and computer simulation were used for evaluation of the performance of the proposed technique, based on real well data. The obtained results showed excellent ability to accommodate the changes in the formation properties. In addition, the rate of bit wear has been optimized.
Event-Related Potential (ERP) Measures in Auditory Development Research (2007)

Between birth and 2 years of age, the human cortex undergoes tremendous development, with region-specific and layer-specific patterns of synaptic maturation, overgrowth, and pruning that are undoubtedly influenced by environmental input and complex patterns of neurotransmitter expression (e.g., Huttenlocher & Dabholkar, 1997; Moore & Guan, 2001). During this period, the newborn, who is totally dependent on caregivers for survival, turns into a walking, talking, thinking, self-aware being. These anatomical and functional changes across development should be reflected in vivo in the electrical brain activity that can be measured at the scalp.
Cytoplasmic Mg2+ concentration in platelets: implications for determination of Ca2+ with aequorin (1988)

The concentration of cytoplasmic ionized Mg2+ ([Mg2+]i) varies considerably among different cell types. It has not been measured in platelets. Incorrect estimates of this value could markedly affect many intracellular investigations, including calibration of measurements of platelet cytoplasmic ionized Ca2+ concentration ([Ca2+]i) with the photoprotein aequorin and other Ca2+-sensitive probes. [Mg2+]i was measured in washed, gel-filtered human platelets suspended in modified Tyrode buffer by two methods: 31P-nuclear magnetic resonance (NMR) spectroscopy of intact platelets and null-point titration in platelets selectively permeabilized with digitonin. The 31P-NMR spectra demonstrated that the [Mg2+]i, as calculated from the chemical shift values of ATP resonances, was 0.23 +/- 0.02 (SD) mM in unstimulated platelets. The mean [Mg2+]i as determined by null-point titration was 0.3 +/- 0.1 mM (range: 0.1-0.6 mM). When this [Mg2+]i value was used to construct a Ca2+-calibration curve for aequorin, the indicated [Ca2+]i values in resting and stimulated platelets were lower than those obtained from curves based on previously assumed values for [Mg2+]i (1.0-1.25 mM). This finding largely resolves the discrepancy between resting [Ca2+]i as determined by aequorin or by quin2, fura-2, and indo-1.
Mechanical properties of glass continuous poly(cyclohexylethylene) block copolymers (2012)

Abstract The bulk mechanical properties of linear triblock and pentablock copolymers that self‐assemble into hexagonally packed cylinders with glassy, unentangled matrices of poly(cyclohexylethylene) (PCHE for a homopolymer, C for a block copolymer) with rubbery poly(ethylene‐ alt ‐propylene) (P) and semicrystalline polyethylene (E) minority components are examined. The tensile properties of high C content CEC triblock copolymer could not be quantified; however, CPC can plastically deform under uniaxial strain, unlike brittle PCHE. Both CECEC and CPCPC pentablock copolymers exhibited ductile tensile behavior, but the tensile properties of blends of these two pentablock copolymers show that the addition of crystallinity in the minority phase prevents strain softening after yielding and necking, which indicates that these samples deform only via crazing. On the other hand, the white gage region of CPCPC and the ability of CPCPC to neck indicate that high C content materials deform via shear yielding and crazing when the minority component is a rubbery material. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2012
Polarization Effects and UV Emission in Highly Excited Quaternary AlInGaN Quantum Wells (2001)

We report on UV photoluminescence (PL) dynamics in highly excited quaternary AlxInyGa1—x—yN epilayers and multiple quantum wells (MQWs). At low temperature, in MQWs we have observed new PL band which appeared at low excitation on the long-wave side of the spectrum and we show it to arise from localized carriers (excitons). The strong blue-shift of PL maximum with excitation intensity in MQWs is caused by localized state filling and screening of piezoelectric and spontaneous polarization electric field.
Loss of PDZK1 Causes Coronary Artery Occlusion and Myocardial Infarction in Paigen Diet-Fed Apolipoprotein E Deficient Mice (2009)

These results show that Paigen-diet fed PDZK1/apoE dKO mice represent a new animal model useful for studying coronary heart disease and suggest that PDZK1 may represent a valuable target for therapeutic intervention.
Utility of Multiparametric Magnetic Resonance Imaging Suspicion Levels for Detecting Prostate Cancer (2013)

Multiparametric magnetic resonance imaging is a clinically useful modality to detect and characterize prostate cancer, particularly in men with higher grade disease.
Impact of Self‐Absorption and Cavity Effects on the Electroluminescence Spectra of Thin‐Film Solar Cells (2022)

Thin‐film organic and perovskite solar cells have seen tremendous advances in recent years. A common technique to characterize the low‐energy states in these solar cells is electroluminescence spectroscopy. Stemming from their thin film nature, however, the outcoupled electroluminescence spectra of these devices are affected by cavity effects and self‐absorption. Herein, a modeling approach is developed taking into account self‐absorption, cavity effects, and a nonhomogeneous emission profile, to correct the outcoupled spectrum, thereby yielding the intrinsically emitted spectrum. The modeling approach is then employed to structurally investigate the impact of these effects for a variety of active layer thicknesses, complex refractive indices, device structures, and emission profiles. The data presented uncover trends and provide guidelines that enable gauging the impact of self‐absorption and cavity effects on the electroluminescence spectra of a large set of thin‐film devices.
Texture refinement framework for improved video coding (2009)

H.264/AVC standard offers an efficient way of reducing the noticeable artefacts of former video coding schemes, but it can be perfectible for the coding of detailed texture areas. This paper presents a conceptual coding framework, utilizing visual perception redundancy, which aims at improving both bit-rate and quality on textured areas. The approach is generic and can be integrated into usual coding scheme. The proposed scheme is divided into three steps: a first algorithm analyses texture regions, with an eye to build a dictionary of the most representative texture sub-regions (RTS). The encoder preserves then them at a higher quality than the rest of the picture, in order to enable a refinement algorithm to finally spread the preserved information over textured areas. In this paper, we present a first solution to validate the framework, detailing then the encoder side in order to define a simple method for dictionary building. The proposed H.264/AVC compliant scheme creates a dictionary of macroblocks
Free-space optical communications using encoding of data on different orbital-angular-momentum modes (2016)

Free-space optical communications can play a significant role in line-of-sight links. In general, data can be encoded on the amplitude, phase, or temporal position of the optical wave. Importantly, there are environments for which ever-more information is desired for a given amount of optical energy. This can be accomplished if there are more degrees-of-freedom that the wave can occupy to provide higher energy efficiency for a given capacity (i.e., bits/photon). Traditionally, free-space optical links have used only a single beam, such that there was little opportunity for a wave to occupy more than one spatial location, thereby not allowing the spatial domain to be used for data encoding. Recently, space- and mode-multiplexing has been demonstrated to simultaneously transmit multiple data-carrying free-space beams. Each spatially overlapping mode was orthogonal to other modes and carried a unique amount of orbital-angular-momentum (OAM). In this paper, we consider that OAM modes could be a data-encoding domain, such that a beam could uniquely occupy one of many modes, i.e., 4 modes would provide 4 possible states and double the bits of information for the same amount of energy. In the past, such OAM-based encoding was shown at kHz data rates. We will present the architecture and experimental results for OAM-based data encoding for a free-space 1.55-&mu;m data link under different system parameters. Key features of the results include: (a) encoding on several modes is accomplished using a fast switch, and (b) low bit-error-rates are achieved at &gt;Gbit/s, which is orders-of-magnitude faster than previous results.
Multitarget Stool DNA Test Performance in an Average-Risk Colorectal Cancer Screening Population (2019)

In an average-risk screening population, the MT-sDNA test has an increased sensitivity for detecting advanced precancerous lesions compared with FIT alone. AAs with a high risk of progression were not detected with significantly higher sensitivity by MT-sDNA or FIT.
The Dilemma of Narcissistic Leadership: Overcoming Resistance to Consultations (2016)

In response to growing corporate interest in assessments of toxic leaders, this paper presents a description of a consultation within an organization suffering through significant dysfunction and deficit leadership. Identified are obstacles faced by consultants when assessing and attempting to act upon destructive leader behavior. The central role of the consultant is described in innovating and enacting interventions intended to empower and transform a struggling organization from deficit to abundance leadership.