gebhart/patrepeval huggingface dataset:
Estimating heritability using family and unrelated individuals data (2011)

For the family data from Genetic Analysis Workshop 17, we obtained heritability estimates of quantitative traits Q1 and Q4 using the ASSOC program in the S.A.G.E. software package. ASSOC is a family-based method that estimates heritability through the estimation of variance components. The covariate-adjusted mean heritability was 0.650 for Q1 and 0.745 for Q4. For the unrelated individuals data, we estimated the heritability of Q1 as the proportion of total variance that can be accounted for by all single-nucleotide polymorphisms under an additive model. We examined a novel ordinary least-squares method, a naïve restricted maximum-likelihood method, and a calibrated restricted maximum-likelihood method. We applied the different methods to all 200 replicates for Q1. We observed that the ordinary least-squares method yielded many estimates outside the interval [0, 1]. The restricted maximum-likelihood estimates were more stable than the ordinary least-squares estimates. The naïve restricted maximum-likelihood method yielded an average estimate of 0.462 ± 0.1, and the calibrated restricted maximum-likelihood method yielded an average of 0.535 ± 0.121. Our results demonstrate discrepancies in heritability estimates using the family data and the unrelated individuals data.
Sparse placement of electronic switching nodes for low blocking in translucent optical networks (2002)

Abstract- We evaluate the performance of optical network designs using relatively few switch nodes at which wavelength conversion and electronic regeneration is possible. A simple heuristic for placing the fewest such nodes to reach a given blocking probability is based on the ranked frequency of shortest-path routes transiting each node. This strategy is found to be efficient in designing a “translucent ” optical network with sparse electronic switch placement that performs very close in blocking to that of an “opaque ” optical network. In addition, we apply a new 2-D Dijkstra’s algorithm for routing and wavelength assignment in the resultant translucent optical network. Simulation results indicate that a translucent optical network with sparse electronic switch placement based on the heuristic has much lower blocking than a fully transparent optical network when the constraint of the maximum transparent distance before regeneration is also considered. Moreover by placing the switches according to the heuristic, lightpath blocking can approach that of a fully opaque network with significantly fewer electronic switches in total. In our results, lightpath blocking as low as the fully opaque network case was obtained with electronic switches selectively placed at approximately 1 node in 3 on average. The heuristic also performs well against random searching for an effective subset of electronic switch nodes and performs better than a prior optimal
Abstract A143: Vaccination of a concatenated L2 fusion protein with L1 VLP or capsomeres for broad protection against HPV infection (2010)

Abstract Background: Immunization with L1 major capsid protein in the form of the pentavalent capsomeres or 360mer virus-like particles (VLPs) generates high and long-lived titers of neutralizing antibodies and protection primarily against the human papillomavirus (HPV) type from which the vaccine was derived. Consequently, multivalent L1 VLP vaccines have been developed to expand the breadth of coverage, e.g. Cervarix which contains L1 VLPs that are derived from HPV16 and HPV18 and formulated in alum and monophosphoryl lipid A (MPL) adjuvant. Vaccination with L2 minor capsid protein induces lower titer, but more broadly neutralizing and protective antibody responses in animals. To enhance cross-protection we generated multi-type L2 proteins by fusing cross-neutralizing epitopes of divergent HPV types, e.g. 11-88×5 that is a concatamer of L2 residues 11–88 of HPV1, HPV5, HPV6, HPV16 and HPV18. Objectives: A low cost HPV vaccine that yields cross-protective antibodies and broad protection against more than a dozen oncogenic HPV types is urgently needed. We sought to combine the advantages of each protective antigen by immunization with titrated doses of multi-type L2 11-88×5 in alum+MPL, or with either HPV16 L1 capsomeres or Cervarix and to assess the importance of adjuvant for L2 dose sparing. Methods: Mice were vaccinated three times every alternate week and bled two weeks later. Serum antibody titers were determined by ELISA using HPV16 L1 VLP or L2 11-88×5antigen, as well as in vitro HPV pseudovirion neutralization assays. Results: The absolute titers and dose response to 11-88×5 were similar in mice vaccinated with 11-88×5 alone or in combination with either L1 capsomeres or VLPs. HPV16 L1 VLP generated significantly higher HPV16 neutralization titers than L1 capsomeres, and the capsomeres induce higher titers than 11-88×5. Importantly, the serum IgG titers specific to HPV16 L1 VLP were not influenced by vaccination with L1 capsomeres or VLP in the presence of L2 11-88×5. The in vitro neutralization titers elicited by vaccination with 11-88×5 in the combinations tested were not significantly different at two weeks after immunization but there was a trend at four months for reduced cross-neutralization when 11-88×5 was combined with L1 VLP but not capsomeres. Conclusions: There is no evidence of interference between the L1 and L2 serum antibody response to co-administration of L1 capsomeres, but not VLP, with multi-type L2 vaccines based on neutralization titers. Citation Information: Cancer Prev Res 2010;3(1 Suppl):A143.
Oil viscosity measurement by ultrasonic reflectance (2001)

Abstract Pulses of shear‐mode ultrasound (center frequency 10 MHz) are reflected from the surface of a series of vegetable and synthetic high‐viscosity calibration oils at a range of temperatures (5–50°C). For all samples and temperatures there is a single negative correlation between the magnitude of the echo from the interface between the delay‐line and the sample and the viscosity of the sample. Similar experiments with longitudinal ultrasonic waves show the amount of sound reflected decreased with increasing viscosity, but there is no single correlation for all samples.
Prehabilitation and rehabilitation using data-driven, parcel-guided transcranial magnetic stimulation treatment for brain tumor surgery (2022)

Improved knowledge of the neuroplastic potential of the brain connectome has facilitated the advancement of neuromodulatory treatments for brain tumor patients especially in the perioperative period. More recently, the idea of inducing neuroplastic changes before surgery as “prehabilitation” has been suggested in low-grade gliomas with favorable data. However, it is uncertain the degree to which this treatment with transcranial magnetic stimulation (TMS) would benefit patients with high-grade gliomas, especially with additional rehabilitation after surgery and targets defined by personalized connectomic data. The current report details a case of a patient with recurrent glioblastoma in the right motor area 2 years after previous total resection. Given the desire for a more aggressive recurrent surgery in a highly functional area, the authors decided to proceed with “prehabilitation” by stimulating the surrounding motor cortices around the lesion to turn down the motor cortex connectivity before the recurrent surgery and then completing “rehabilitation” after the surgery. Structural-functional connectomic analyses were completed using Infinitome software based on an individualized patient brain atlas using machine-learning based parcellations. Repetitive TMS was employed, specifically using continuous and intermittent theta burst stimulation protocols. Prehabilitation consisted of using continuous theta burst stimulation at the estimated surgical entry point parcel and intermittent theta burst stimulation at adjacent parcellations for a total of 10 days with 5 sessions per day per target leading up until the surgery. A gross-total resection was obtained, but the patient woke up with left-sided hemiparesis. Resting-state functional magnetic resonance imaging derived connectivity demonstrated a case of a primarily pure cingulate-motor resection causing hemiplegia with an intact corticospinal tract and supplementary motor area. Functional connectivity outliers in cingulate-motor parcels were identified and compared with connectivity matrices from a healthy control atlas. Anomalies, parcels defined as functioning significantly outside a normal range, were chosen as rehabilitation TMS targets to be similarly treated for a total of 10 days with 5 sessions per day per target approximately two weeks after surgery. By using continuous theta burst stimulation on hyperconnected parcels and intermittent theta burst stimulation on hypoconnected parcels, the patient demonstrated significant motor improvement with only 4+/5 strength in the left arm 1 month after surgery. This report demonstrates for the first time the feasibility of using TMS treatment for glioblastoma surgery near “eloquent” cortices as a means of prehabilitation before surgery and rehabilitation after surgery. This parcel-guided approach for TMS treatment based on the cortical site of entry and individualized connectivity analyses allowed for maximal tumor resection and minimal long-term neurologic deficits.
Comparing ExoVis, Orientation Icon, and In-Place 3D Visualization Techniques (2003)

We present a novel algorithm for simultaneous visual hull reconstruction and rendering by exploiting off-the-shelf graphics hardware. The reconstruction is accomplished by projective texture mapping in conjunction with the alpha test. Parallel to the reconstruction, rendering is also carried out in the graphics pipeline. We texture the visual hull view-dependently with the aid of fragment shaders, such as nVIDIA's register combiners. Both reconstruction and rendering are done in a single rendering pass. We achieve frame rates of more than 80 fps on a standard PC equipped with a commodity graphics card. The performance is significantly faster than that of previously reported similar systems.
Lithium, an anti-psychotic drug, greatly enhances the generation of induced pluripotent stem cells (2011)

Somatic cells can be reprogrammed into induced pluripotent stem cells (iPSCs) by defined factors. The low efficiency of reprogramming and genomic integration of oncogenes and viral vectors limited the potential application of iPSCs. Here we report that Lithium (Li), a drug used to treat mood disorders, greatly enhances iPSC generation from both mouse embryonic fibroblast and human umbilical vein endothelial cells. Li facilitates iPSC generation with one (Oct4) or two factors (OS or OK). The effect of Li on promoting reprogramming only partially depends on its major target GSK3β. Unlike other GSK3β inhibitors, Li not only increases the expression of Nanog, but also enhances the transcriptional activity of Nanog. We also found that Li exerts its effect by promoting epigenetic modifications via downregulation of LSD1, a H3K4-specific histone demethylase. Knocking down LSD1 partially mimics Li's effect in enhancing reprogramming. Our results not only provide a straightforward method to improve the iPSC generation efficiency, but also identified a histone demethylase as a critical modulator for somatic cell reprogramming.
An Efficient Algorithm for a Weighted Cooperative Spectrum Sensing in Cognitive Networks (2017)

In this paper, a novel approach is proposed for a weighted cooperative spectrum sensing (WCSS) in cognitive radio networks (CRNs) aiming to maximize the probability of detection under a given probability of false alarm. In CRNs, Cooperative Spectrum Sensing (CSS) scheme is used to get over the problem of hidden terminal, fading and shadowing. The proposed algorithm can be applied for single and double thresholds energy detector. Our goal is to have an efficient WCSS with less complexity and high performance. The existing works showed that finding the optimal weights for probability of detection maximization is a difficult problem. Therefore, we propose a closed form suboptimal solution using the generalized eigenvalue that outperform some of the existing works in terms of performance and complexity. The proposed approach is compared to particle swarm optimization (PSO), equal gain combining (EGC), modified deflection coefficient (MDC) in terms of complexity and performance. Our results show that the proposed approach outperforms all these methods especially when the users receive different signal to noise ratio (SNR).
Exploring the space between smoothed and non-smooth total variation for 3D iterative CT reconstruction (2019)

Because total variation (TV) is non-differentiable, iterative reconstruction using a TV penalty comes with technical difficulties. To avoid these, it is popular to use a smooth approximation of TV instead, which is defined using a single parameter, herein called &delta;, with the convention that the approximation is better when &delta; is smaller. To our knowledge, it is not known how well image reconstruction with this approximation can approach a converged non-smooth TV-regularized result. In this work, we study this particular question in the context of X-ray computed tomography (CT). Experimental results are reported with real CT data of a head phantom and supplemented with a theoretical analysis. To address our question, we make proficient use of a generalized iterative soft-thresholding algorithm that allows us to handle TV and its smooth approximation in the same framework. Our results support the following conclusions. First, images reconstructed using the smooth approximation of TV appears to smoothly converge towards the TV result as &delta; tends to zero. Second, the value of δ does not need to be overly small to obtain a result that is essentially equivalent to TV, implying that numerical instabilities can be avoided. Last, though it is smooth, the convergence with &delta; is not particularly fast, as the mean absolute pixel difference decreases only as &radic;&delta; in our experiments. Altogether, we conclude that the approximation is a theoretically valid way to approximate the non-smooth TV penalty for CT, opening the door to safe utilization of a wide variety of optimization algorithms.
Constitutive Behavior and Temperature Effects in NR and SBR Under Variable Amplitude and Multiaxial Loading Conditions (2007)

Knowledge of the stress response of a material to the applied deformations is necessary for many engineering analysis and applications. This paper addresses the observed effects of load sequencing, Mullins effect, and multiaxial loading on the constitutive behavior of rubber under variable amplitude conditions for a series of experiments using multiaxial ring test specimens. Two filled rubber materials were used and compared in this study; natural rubber, which strain crystallizes, and styrene butadiene rubber (SBR), which does not. A pseudoelastic approach is used to model the cyclic stress-strain response for both materials. The implications of inelasticity when using hyperelastic material models are also discussed. Based on temperature results for the multiaxial ring specimen obtained via a thermal imaging system for SBR, a model capable of accurately predicting surface temperature for the multiaxial ring specimen as a function of hysteresis area and test frequency has been developed.
Fluorescence-based Sensing of 2,4,6-Trinitrotoluene (TNT) Using a Multi-channeled Poly(methyl methacrylate) (PMMA) Microimmunosensor (2010)

Fluorescence immunoassays employing monoclonal antibodies directed against the explosive 2,4,6-trinitrotoluene (TNT) were conducted in a multi-channel microimmunosensor. The multi-channel microimmunosensor was prepared in poly (methyl methacrylate) (PMMA) via hot embossing from a brass molding tool. The multi-channeled microfluidic device was sol-gel coated to generate a siloxane surface that provided a scaffold for antibody immobilization. AlexaFluor-cadaverine-trinitrobenzene (AlexaFluor-Cad-TNB) was used as the reporter molecule in a displacement immunoassay. The limit of detection was 1-10 ng/mL (ppb) with a linear dynamic range that covered three orders of magnitude. In addition, antibody crossreactivity was investigated using hexahydro-1,3,5-triazine (RDX), HMX, 2,4-dinitrotoluene (DNT), 4-nitrotoluene (4-NT) and 2-amino-4,6-DNT.
Can a Shaft Brush be Safely Applied on a Motor in a Class I Hazardous Location? (2015)

Some inverter-fed motors, particularly at higher power ratings, are supplied with a shaft brush in order to help mitigate bearing currents. As more inverters are applied to motors in Class I Division 1/Zone 1 and Class I Division 2/Zone 2 locations, there is a need to understand whether a shaft brush can be safely applied in such an environment. This paper addresses the physics of why this is a concern and a methodology to evaluate the relative safety of two example cases. These issues are considered from the perspective of users, manufacturers of inverters and motors, and certifying bodies. The question posed in the title of this paper is answered by considering whether the addition of a shaft brush to an inverter-fed motor in a Class I hazardous location makes the system more safe or less safe.
Closed-Loop Insulin Therapy Improves Glycemic Control in Children Aged &lt;7 Years (2012)

Closed-loop insulin delivery decreases the severity of overnight hyperglycemia without increasing the incidence of hypoglycemia. The therapy is better able to reestablish target glucose levels in advance of a subsequent meal. Younger children with type 1 diabetes may reap significant benefits from closed-loop therapy.
Gaussian-2 theory using reduced Mo/ller–Plesset orders (1993)

Two variations of Gaussian-2 (G2) theory are presented. In the first, referred to as G2 (MP2) theory, the basis-set-extension energy corrections are obtained at the 2nd order Mo/ller–Plesset (MP2) level and in the second, referred to as G2(MP3) theory, they are obtained at the MP3 level. The methods are tested out on the set of 125 systems used for validation of G2 theory [J. Chem Phys. 94, 7221 (1991)]. The average absolute deviation of the G2(MP2) and G2(MP3) theories from experiment are 1.58 and 1.52 kcal/mol, respectively, compared to 1.21 kcal/mol for G2 theory. The new methods provide significant savings in computational time and disk storage.
A role for intracellular calcium downstream of G-protein signaling in undifferentiated human embryonic stem cell culture (2012)

Multiple signalling pathways maintain human embryonic stem cells (hESC) in an undifferentiated state. Here we sought to define the significance of G protein signal transduction in the preservation of this state distinct from other cellular processes. Continuous treatment with drugs targeting G(αs)-, G(α-i/o)- and G(α-q/11)-subunit signalling mediators were assessed in independent hESC lines after 7days to discern effects on normalised alkaline phosphatase positive colony frequency vs total cell content. This identified PLCβ, intracellular free calcium and CAMKII kinase activity downstream of G(α-q/11) as of particular importance to the former. To confirm the significance of this finding we generated an agonist-responsive hESC line transgenic for a G(α-q/11) subunit-coupled receptor and demonstrated that an undifferentiated state could be promoted in the presence of an agonist without exogenously supplied bFGF and that this correlated with elevated intracellular calcium. Similarly, treatment of unmodified hESCs with a range of intracellular free calcium-modulating drugs in biologically defined mTESR culture system lacking exogenous bFGF promoted an hESC phenotype after 1week of continuous culture as defined by co-expression of OCT4 and NANOG. At least one of these drugs, lysophosphatidic acid significantly elevates phosphorylation of calmodulin and STAT3 in this culture system (p<0.05). These findings substantiate a role for G-protein and calcium signalling in undifferentiated hESC culture.
Antibody barriers to going viral (2019)

Antibody neutralization of a virus in vitro is often associated with protection against viral exposure in vivo, but the mechanisms operational in vivo are often unclear. By investigating a large number of antibodies, Earnest et al. (https://doi.org/10.1084/jem.20190736) show the importance of antibody effector function in neutralizing antibody protection against an emerging alphavirus in a mouse model.
First serological investigation of Peste des Petits Ruminants and Rift Valley Fever in Tunisia. (2009)

National audience
Neural Precursors Derived from Embryonic Stem Cells, but Not Those from Fetal Ventral Mesencephalon, Maintain the Potential to Differentiate into Dopaminergic Neurons After Expansion In Vitro (2006)

Neural precursors (NPs) derived from ventral mesencephalon (VM) normally generate dopaminergic (DA) neurons in vivo but lose their potential to differentiate into DA neurons during mitogenic expansion in vitro, hampering their efficient use as a transplantable and experimental cell source. Because embryonic stem (ES) cell-derived NPs (ES NP) do not go through the same maturation process during in vitro expansion, we hypothesized that expanded ES NPs may maintain their potential to differentiate into DA neurons. To address this, we expanded NPs derived from mouse embryonic day-12.5 (E12.5) VM or ES cells and compared their developmental properties. Interestingly, expanded ES NPs fully sustain their ability to differentiate to the neuronal as well as to the DA fate. In sharp contrast, VM NPs almost completely lost their ability to become neurons and tyrosine hydroxylase-positive (TH(+)) neurons after expansion. Expanded ES NP-derived TH(+) neurons coexpressed additional DA markers such as dopa decarboxylase and DAT (dopamine transporter). Furthermore, they also expressed other midbrain DA markers, including Nurr1 and Pitx3, and released significant amounts of DA. We also found that these ES NPs can be cryopreserved without losing their proliferative and developmental potential. Finally, we tested the in vivo characteristics of the expanded NPs derived from J1 ES cells with low passage number. When transplanted into the mouse striatum, the expanded NPs as well as control NPs efficiently generated DA neurons expressing mature DA markers, with approximately 10% tumor formation in both cases. We conclude that ES NPs maintain their developmental potential during in vitro expansion, whereas mouse E12.5 VM NPs do not.
A Mathematical Model Comparing Solute Kinetics in Low- and High-BMI Hemodialysis Patients (2007)

These results suggest that higher mortality for smaller dialysis patients may be mediated by higher time average toxin concentration, especially for solutes with a low mass-transfer coefficient value.
Preparation of Pb(ZrxTi1 - x)O3 Films on Trench Structure for High-Density Ferroelectric Random Access Memory (2004)

The growth characteristics of Pb(ZrxTi1 - x)O3 thin films on three-dimensional (3D) electrodes were investigated for the application to high-density ferroelectric random access memory (FeRAM) devices. PZT films have been grown on Ir coated trench structures having aspect ratio of 1.2 by liquid delivery-metal organic chemical vapor deposition (LD-MOCVD). Atomic layer deposited (ALD) Ir electrode showed good step coverage and electrical properties. MOCVD PZT films showed step coverage of 90% at the deposition temperature of 500°C, while it is decreased to 63% at 550°C. Compositional non-uniformity of PZT along the sidewall was greatly affected by the types of the metal organic sources.