gebhart/patrepeval huggingface dataset:
Supplementary Table 1 from Ligand-Specific Antibodies to Insulin-Like Growth Factors Suppress Intestinal Polyp Formation in <i>Apc</i><sup>+/−</sup> Mice (2023)

Supplementary Table 1 from Ligand-Specific Antibodies to Insulin-Like Growth Factors Suppress Intestinal Polyp Formation in &lt;i&gt;Apc&lt;/i&gt;&lt;sup&gt;+/−&lt;/sup&gt; Mice
Effect of Separating Load Eccentricity on the Clamp Load Loss in a Bolted Joint Using a Strain Hardening Model (2011)

Abstract A nonlinear model is proposed for studying the effect of the eccentricity of applied tensile forces on the clamp load loss in bolted joints that were initially tightened beyond the bolt elastic limit while the joint remained in the elastic range. A closed form solution is obtained for the amount of clamp load loss due to a cyclic separating force. The proposed model takes into account two sources of nonlinearity, namely, the strain hardening behavior of the yielded bolt material as well as the nonlinear deformation behavior of the clamped plates under an external separating load. After the initial tightening of the fastener past its elastic limit, the subsequent application of a tensile separating force on the joint tends to increase the fastener tension in a nonlinear fashion, and, simultaneously, reduce the clamping force in the bolted joint from its initial value. Upon the removal of the cyclic tensile load, the bolted joint system reaches a new equilibrium point between the residual fastener tension and the joint clamping force. At the new equilibrium point, the fastener tension is reduced from its preload due to its plastic elongation; simultaneously, a partial yet permanent loss in the clamp load level takes place. Excessive clamp load loss may lead to joint leakage, fastener loosening, or fatigue failure. For a known amplitude of the external cyclic tensile load, the increase in bolt tension and corresponding reduction in the joint clamp load are highly sensitive to the eccentricity of the tensile load (from the bolt center). Variables studied include the eccentricity value of the separating load, rate of strain hardening of the bolt material, compressive and tensile stiffness of the clamped plates, bolt stiffness, bolt preload, and magnitude of the separating tensile load.
Effects of Estradiol Dose and Serum Estradiol Levels on Metabolic Measures in Early and Late Postmenopausal Women in the REPLENISH Trial (2020)

<b><i>Background:</i></b> To identify the association of estradiol (E2) dose and serum E2 levels with metabolic measures in early (<6 years) compared with late (≥10 years) postmenopausal women from the REPLENISH trial. <b><i>Material and Methods:</i></b> This is a <i>post hoc</i> analysis of a multicenter randomized clinical trial in the United States. Four doses of TX-001HR, an oral combination of E2 and progesterone (P4), and placebo were tested. This analysis included a total of 1,216 early and 297 late postmenopausal women. Linear mixed-effects models tested the association of E2 dose and serum E2 levels with changes in metabolic parameters; total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), triglyceride (TG), and glucose (GLUC) levels from six visits over 12 months, adjusted for the serum P4 level. <b><i>Results:</i></b> A higher E2 dose was significantly associated with lower TC (<i>p</i> = 0.02) and LDL-C (<i>p</i> = 0.002) and higher HDL-C (<i>p</i> = 0.04) levels in early, but not late, postmenopause. With longer time since menopause, the inverse association of E2 dose with TC and LDL-C and positive association with HDL-C were attenuated (interaction <i>p</i> < 0.05). Higher serum E2 levels were significantly associated with lower TC (<i>p</i> = 0.004), LDL-C (<i>p</i> = 0.0001), and fasting blood GLUC (<i>p</i> = 0.003) and higher TG (<i>p</i> = 0.002) levels in early postmenopause. <b><i>Conclusion:</i></b> E2 dose differentially affects metabolic measures among early compared with late postmenopausal women. No significant main effect of the serum P4 level was found. As the metabolic parameters studied are risk factors for cardiovascular events, these results support the timing hypothesis of E2 therapy and its cardiovascular benefits.
Stable MAGEC1/CT7 Inhibition by Short Hairpin RNA (shRNA) Does Not Affect Tumor Cell Proliferation and Invasive Potential in Sko-007 Multiple Myeloma Cell Line. (2009)

Abstract Abstract 4888 Introduction MAGEC1/CT7 gene encodes for a cancer testis (CT) antigen frequently expressed in multiple myeloma (MM) and may be a potential target for immunotherapy in this still incurable disease. This CT gene expression is restricted to malignant plasma cells and may be related with tumor progression, since it seems to play a role as a “gatekeeper” gene for other CT antigens and can be associated with a more aggressive phenotype. However, the exact function of this protein for tumor biology is not yet understood. Objective The aim of this study is to elucidate the role of MAGEC1/CT7 in the control of cellular proliferation, DNA synthesis and invasive potential of Sko-007 myeloma cell line. Material and Methods We used a short hairpin RNA (shRNA) specific for MAGEC1/CT7 gene that was previously inserted in the pRS (pRETROSUPER) retroviral vector. The pRS-shRNA-MAGEC1/CT7 construct was co-transfected with pCL-amphotropic packing vector in 293T cells to produce virus particles. Sko-007 myeloma cell line was transduced and selected for stable expression of shRNA-MAGEC1/CT7. Expression of MAGEC1/CT7 was analyzed by Western Blot and Real Time PCR (RQ-PCR). Functional studies included cell proliferation, 3H thymidine incorporation and invasion potential, using matrigel-coated transwell filters. Results Sko-007 was chosen to perform the initial functional studies since the basal MAGEC1/CT7 gene expression level was higher in this cell line when compared with the other myeloma cell lines (U266 and SK-MM-2). Sko-007wt (wild type) cell was divided into three derivatives, Sko-007ev (empty vector), Sko-007shMAGEC1/CT7Δ (antisense strand deleted – GC bases) and Sko-007shMAGEC1/CT7. MAGEC1/CT7 expression was approximately five times down regulated in Sko-007shMAGEC1/CT7 when compared with Sko-007wt, Sko-007ev, and Sko-007shMAGEC1/CT7Δ cells by RQ-PCR. Sko-007shMAGE1/CT7 had an 80% decrease in MAGEC1/CT7 protein expression when compared with Sko-007wt, Sko-007ev and Sko-007shMAGEC1/CT7Δ by Western Blot. Our preliminary functional assays did not show any change in cell proliferation and DNA synthesis when Sko-007shMAGEC1/CT7 was compared with Sko-007wt, Sko-007ev and Sko-007shMAGEC1/CT7Δ. Indeed, Sko-007 cell line has invasive potential, but no change was observed in Sko-007shMAGEC1/CT7 or other cells (Sko-007wt, Sko-007ev and Sko-007shMAGEC1/CT7Δ). Conclusions Expression of MAGEC1/CT7 mRNA could be inhibited by the shRNA strategy, but the concomitant reduction of its protein level did not seem to have impact in proliferation, DNA synthesis or in invasive potential of Sko-007 MM cell line (Supported CNPq and LICR São Paulo Branch). Disclosures No relevant conflicts of interest to declare.
High frequency attenuated total internal reflection light modulator (1992)

The modulation efficiency and bandwidth limitations of a new type of light modulator, the attenuated total internal reflection modulator (ATRM), are described. The ATRM is based on coupling a light beam to a surface plasmon wave, and its fabrication is compatible with GaAs integrated circuit technology. We demonstrate modulation to 22 GHz (the extrapolated 1.5 dB optical modulation bandwidth is 26 GHz) and show that devices with high modulation index can be built using existing materials.
Constrained Bayesian Active Learning of a Linear Classifier (2018)

In this paper, an on-line interactive method is proposed for learning a linear classifier. This problem is studied within the Active Learning (AL) framework where the learning algorithm sequentially chooses unlabelled training samples and requests their class labels from an oracle in order to learn the classifier with the least queries to the oracle possible. Additionally' a constraint is introduced into this interactive learning process which limits the percentage of the samples from one “unwanted” class under a certain threshold. An optimal AL solution is derived and implemented with a sophisticated, accurate and fast Bayesian Learning method, the Expectation Propagation (EP) and its performance is demonstrated through numerical simulations.
Patch-Seq Protocol to Analyze the Electrophysiology, Morphology and Transcriptome of Whole Single Neurons Derived From Human Pluripotent Stem Cells (2018)

The human brain is composed of a complex assembly of about 171 billion heterogeneous cellular units (86 billion neurons and 85 billion non-neuronal glia cells). A comprehensive description of brain cells is necessary to understand the nervous system in health and disease. Recently, advances in genomics have permitted the accurate analysis of the full transcriptome of single cells (scRNA-seq). We have built upon such technical progress to combine scRNA-seq with patch-clamping electrophysiological recording and morphological analysis of single human neurons <i>in vitro</i>. This new powerful method, referred to as Patch-seq, enables a thorough, multimodal profiling of neurons and permits us to expose the links between functional properties, morphology, and gene expression. Here, we present a detailed Patch-seq protocol for isolating single neurons from <i>in vitro</i> neuronal cultures. We have validated the Patch-seq whole-transcriptome profiling method with human neurons generated from embryonic and induced pluripotent stem cells (ESCs/iPSCs) derived from healthy subjects, but the procedure may be applied to any kind of cell type <i>in vitro</i>. Patch-seq may be used on neurons <i>in vitro</i> to profile cell types and states in depth to unravel the human molecular basis of neuronal diversity and investigate the cellular mechanisms underlying brain disorders.
Long term disease-free survival and T cell and antibody responses in women with high-risk Her2+ breast cancer following vaccination against Her2 (2007)

ClinicalTrials.gov NCT00005956.
Comparison of capacitive and frequential readout when scaling accelerometers down from Micro- to Nano- Electro Mechanical Systems (2012)

This paper shows the effect of scaling silicon accelerometers down from MEMS to NEMS. It models both electronics and Brownian noise sources for both capacitive and resonant devices, and computes the minimum detectable signal attainable. Computed results are remarkably close to published experimental results. It shows the relatively low influence of the quality factor and of the beam width in the resonant case. Different scaling rules are investigated, and it appears that resonant sensing may satisfy some new application requirements, in particular for critical dimensions below a few hundreds of nm, when it is better resolved than capacitive sensing.
The cost of overweight and obesity in Australia (2010)

The total annual direct cost of overweight and obesity in Australia in 2005 was $21 billion, substantially higher than previous estimates. There is financial incentive at both individual and societal levels for overweight and obese people to lose weight and/or reduce WC.
Help, hope, and hype: Ethical dimensions ofneuroprosthetics (2017)

Accountability, responsibility, privacy, and security are key
Lignin Impact on Fiber Degradation:  Increased Enzymatic Digestibility of Genetically Engineered Tobacco (Nicotiana tabacum) Stems Reduced in Lignin Content (1997)

Cell wall digestibility, lignin content, and lignin composition were analyzed in transgenic tobacco altered in the expression of the phenylpropanoid biosynthetic enzymes caffeic acid 3-O-methyltransferase (COMT) and l-phenylalanine ammonia-lyase (PAL). Reduction of COMT activity by antisense technology resulted in reduced lignin content accompanied by an increased syringyl (S)/guaiacyl (G) monomer ratio, as determined by pyrolysis/GC/MS and measurement of lignin methoxyl content by wet chemistry. These results resemble those obtained by reduction of flux of lignin precursors into the phenylpropanoid pathway by PAL suppression, which results in drastically reduced lignin with sharply increased methoxyl content. Enzymatic digestibility of cell walls from stem internodes was improved in the transgenic lines and was highly negatively correlated with lignin concentration (r = −0.97). Although lignin composition was also affected, lignin concentration was the overriding factor influencing cell wall digestibility. The results provide a basis for new strategies for lignin modification to improve digestibility of forages. Keywords: Lignin; genetic engineering; digestibility; tobacco
Acoustic time-reversal experiments in the nonlinear regime (1999)

Until now, time-reversal mirrors (TRM) were only used in a low power regime for which nonlinearities can be neglected. Here, their behavior is investigated in a higher power regime compelling nonlinearities to be taken into account. If one considers the acoustic wave equation in a weakly nonlinear medium, the time-reversal invariance holds. Thus, Burger’s equation is invariant when time and direction of propagation are simultaneously reversed. In a nonlinear medium, the shape of a sinusoid changes continuously during propagation as energy is transferred to harmonics. The inverse process would take place after reflection on a TRM. This property holds as long as the shock distance is not reached, otherwise the shock discontinuity implies an irreversible change of the entropy and the time-reversal invariance is broken. These results are confirmed by a finite differences simulation of Burger’s equation. However, experiments are very difficult to carry out because of the limited bandwidth of transducers. Nevertheless, for 1-D problems and an antisymmetric wave packet, a time reversal is equivalent to a reflection on a pressure release interface. This trick has been used to conduct an experiment giving qualitative good agreements with the simulation. a)Also at Lab. de Modélisation en Mécanique, Univ. Paris VI, CNRS UMR 7607, 4 place jussieu, F75252 Paris Cedex 05, France.
A Compact Disc-Recordable Compatible Digital Versatile Disc Pickup with a Lens for 780 nm and 650 nm Wavelengths (1998)

Two types of compact disc-recordable(CD-R) compatible digital versatile disc (DVD) pickups have been developed. One has separate conjugate points for DVD and compact disc(CD) readouts. The other has a common conjugate point for DVD and CD readouts. Optical and signal properties are considered for both types. Both types have been shown to exhibit good qualities for practical use.
Commentary on: Human Adipose Tissue-Derived Stromal/Stem Cells Promote Migration and Early Metastasis of Head and Neck Cancer Xenografts (2015)

Autologous fat grafting for soft tissue reconstruction was first reported by Neuber in 1893 for the correction of facial defects.1 While this technique was largely ignored until the late 1970s, the procedure has now grown exponentially due to its vast degree of applications in soft tissue reconstruction and aesthetic augmentation. Despite its surging popularity, fat graft survival remains highly variable, ranging from 40 to 50 percent graft volume retention.2 While a relatively high degree of graft resorption may be undesirable, the procedure is extremely safe, with few minor complications such as calcification or cyst formation. Much research has been performed to evaluate the variables most highly associated with graft viability, including graft volume, suction pressure, shear stress, and centrifugation. Another major area of investigation to improve graft retention is the application of adipose-derived stromal/stem cells (ASC).

ASCs are cells present within the stromal vascular fraction of adipose tissue and serve as progenitor or stem cells with the potential to self-renew or differentiate into multiple cell lineages including adipocytes, osteocytes, chondrocytes, and even cardiomyocytes.3 These cells are believed to strongly influence their local environment through paracrine effects via the expression of growth factors and cytokines, leading to cell growth, differentiation, and angiogenesis. Supplementation of …
Thermal microactuators for surface-micromachining processes (1995)

Microelectromechanical systems must include large-deflection actuators to create devices which can interact mechanically with their surroundings. Electrostatic actuators with large nonresonant motion require high voltages and large surface areas to produce useful forces. Large-deflection thermal actuators have been fabricated in electroplated metal processes, but the choice of materials is limited, and the high conductivity of metal means these devices need a high current to generate the required heat. Thus, there is a need for a low voltage actuator with a large nonresonant deflection which can be fabricated in integrated circuit compatible surface-micromachining processes. The device described in this paper has a simple, flexible, and reliable design which overcomes the limitations of other actuators. It is a low voltage, medium current thermal actuator which can be designed to move laterally in a controllable, nonresonant motion. Typical actuators are 200 micrometers long, 18 micrometers wide, and deflect 10 micrometers at the tip with a drive current of 5 mA at 5 volts. A wide range of layout geometries allows this type of actuator to be fabricated in any surface-micromachining process that includes a releasable, current-carrying layer. An empirical model is presented to describe the devices fabricate in a commercially available surface-micromachining process. Arrays of actuators were fabricated to test the effect of different device dimensions on maximum achievable deflection as a funciton of applied current. Actuators can be combined to produce more force and have been integrated with other micromechanical structures. Applications of these actuators include linear and rotating motors, compliant micromechanisms, latches, micro-relays, variable capacitators and tweezers.
New Monotone Span Programs from Old. (2004)

Abstract. In this paper we provide several known and one new constructions of new linear secret sharing schemes (LSSS) from existing ones. This constructions are well-suited for didactic purposes, which is a main goal of this paper. It is well known that LSSS are in one-to-one correspondence with monotone span programs (MSPs). MSPs introduced by Karchmer and Wigderson, can be viewed as a linear algebra model for computing a monotone function (access structure). Thus the focus is in obtaining a MSP computing the new access structure starting from the MSPs that compute the existing ones, in the way that the size of the MSP after the transformation is well defined. Next we define certain new operations on access structures and prove certain related properties. 1
Enzyme‐linked immunosorbent assay is a viable method for determining release kinetics of cardiac myosin binding protein‐C following isoproterenol‐induced cardiac injury (1073.8) (2014)

Cardiac myosin binding protein‐C (cMyBP‐C) is shown to be released into the bloodstream following myocardial infarction (MI), suggesting its potential as a biomarker post‐MI. To explore this further, dose‐ and time‐dependent effects on cMyBP‐C release into circulation can be determined following isoproterenol (ISO) administration, an established model of drug‐induced cardiac injury in mice. The objective is to establish a quantitative enzyme‐linked immunosorbent assay (ELISA) that is specific and sensitive in measuring concentrations of cMyBP‐C in serum samples. To determine cMyBP‐C in serum samples following ISO‐induced injury, sandwich ELISA was developed using monoclonal and polyclonal antibodies against cMyBP‐C. To generate a standard graph, cMyBP‐C N’ recombinant peptide (40 kDa) was used to determine inter‐ and intra‐plate coefficient of variability (CV,%), as well as the respective recovery (%) values. The sandwich ELISA assay for quantifying serum concentrations of cMyBP‐C was established with an average lower limit of detection of 0.36 ng/ml and upper limit of detection up to 2000 ng/ml, indicating the assay can detect cMyBP‐C within the working range of our experiment. Furthermore, an inter‐ and intra‐plate variability of 4.7% and 4.2%, respectively, suggests a reproducible assay. The average inter‐ and intra‐plate recoveries were, 101% and 103%, illustrating the accuracy of the assay in measuring cMyBP‐C concentration. Using this assay, future experiments will be conducted to measure the exact amount of cMyBP‐C in the mice serum post‐cardiac injury. Grant Funding Source : American Physiological Society ‐ Undergraduate Summer Research Fellowship
Photoembossing of Periodic Relief Structures Using Polymerization‐ Induced Diffusion: A Combinatorial Study (2005)

Photoembossing is a solvent-free photolithographic technique for the production of polymeric relief microstructures (see Figure). A combinatorial methodology to explore the influence of different parameters (e.g., processing temperature, binder content, photoinitiator content) on the resultant relief structure is presented using an acrylate-based model system. Results are discussed in the framework of a diffusion-polymerization model.
Innate imprinting of resident alveolar macrophages by a preceding allergic bronchial inflammation increases the inflammatory reactivity through autocrine IFN-β. (141.18) (2010)

Abstract Macrophages play an important and dynamic role in the initiation, propagation and resolution of inflammation. We investigated the dynamics of resident alveolar macrophages (rAM) and its pathophysiological consequences in experimental asthma. Using CD45 chimeric mice and intratracheal instilled fluorescent microparticles to distinguish resident from elicited AM, we observed a near complete disappearance of rAM during consecutive allergen challenges. As a consequence, after clearance of inflammation, inflammation-experienced rAM replaced the initial population of rAM. Strikingly, these secondary rAM showed a markedly altered responsiveness to LPS stimulation. Especially genes induced by IFN-β showed strongly increased expression in secondary rAM as opposed to their near absent induction in primary rAM. This switch from an IFN-β deficient to an IFN-β adequate phenotype increased the inflammatory sensitivity of secondary rAM as observed with rAM from IFN-β -/- mice. Also the basal differentiation status of secondary rAM was modified, dependent on the nature of the preceding allergic inflammation. M2-biased differentiation was seen following eosinophilic asthma while M1-biased differentiation was present following neutrophilic hypersensitivity pneumonitis. Taken together, these observations indicate innate imprinting of rAM by preceding allergic inflammation in the lungs.