gebhart/patrepeval huggingface dataset:
Toward hybrid force/position control for the Cerberus epicardial robot (2015)

Gene therapies have emerged as a promising treatment for congestive heart failure, yet they lack a method for minimally invasive, uniform delivery. To address this need we developed Cerberus, a minimally invasive parallel wire robot for cardiac interventions. Prior work on Cerberus was limited to controlling the device using only position feedback. In order to ensure safety for both the patient and the device, as well as to improve the performance of the device, this paper presents work on enhancing the existing system with force feedback capabilities. By modeling the statics of the system and developing a tension distribution optimization technique, existing position control schemes were modified to a hybrid force/position controller. Experimental results show that using a hybrid force-position control scheme as opposed to position decreases positioning error by 38%.
A versatile patterning process based on easily soluble sacrificial bilayers (2017)

Development of a microfabrication process is essential to embed fascinating physical properties of functional materials into mesoscopic devices. Different from well-investigated materials with established microfabrication process, newly-discovered materials often meet difficulty when scaling down into a mesoscopic size, because process damages cause serious deterioration of their functionalities. Here, we demonstrate a versatile lift-off method using a carefully designed sacrificial bilayer, composed of an easily soluble layer and a thermally stable rigid layer. In this method, the target films can be grown in optimum conditions, such as high temperature and high oxygen partial pressure, on the stable pre-patterned substrate with the inorganic sacrificial bilayer. After film deposition, measurable patterned devices can be obtained just by a short-time lift-off in a mild chemical solution. We carried out micron-scale patterning and electrical measurements by applying this technique to one of perovskite oxides, SrRuO3, and Fe-based chalcogenide superconductors, FeSe, both of which are incompatible with conventional photolithography and dry-etching processes. The demonstrated narrowest line width of 5 μm is successfully patterned with maintaining the almost identical properties of the pristine films, exemplifying that process damage is minimized. The demonstrated versatile patterning process expands the range of application of emerging functional materials in thin film devices.
Changes in dynamic medial tibiofemoral contact mechanics and kinematics after injury of the anterior cruciate ligament: A cadaveric model (2013)

The effects of tears of the anterior cruciate ligament on knee kinematics and contact mechanics during dynamic everyday activities, such as gait, remains unclear. The objective of this study was to characterize anterior cruciate ligament-deficient knee contact mechanics and kinematics during simulated gait. Nine human cadaveric knees were each augmented with a sensor capable of measuring dynamic normal contact stresses on the tibial plateau, mounted on a load-controlled simulator, and subjected to physiological, multidirectional, dynamic loads to mimic gait. Using a mixed model with random knee identifiers, confidence intervals were constructed for contact stress before and after anterior cruciate ligament transection at two points in the gait cycle at which axial force peaked (14% and 45% of the gait cycle). Kinematic and contact mechanics changes after anterior cruciate ligament transection were highly variable across knees. Nonetheless, a statistically significant increase in contact stress in the posterior-central aspect of the medial tibial plateau at 45% of the gait cycle was identified, the location of which corresponds to the location of degenerative changes that are frequently found in patients with chronic anterior cruciate ligament injury. The variability in the contact stress in other regions of the medial plateau at 45% of the gait cycle was partly explained by the variations in osseous geometry across the nine knees tested. At 14% of gait, there was no significant change in peak contact stress after anterior cruciate ligament transection in any of the four quadrants, and none of the possible explanatory variables showed statistical significance. Understanding the variable effect of anterior cruciate ligament injury on contact mechanics based on geometric differences in osseous anatomy is of paramount clinical importance and may be invaluable to select the best reconstruction techniques and counsel patients on their individual risk of subsequent chondral degeneration.
The response of selected human B cell lines to B cell growth and differentiation factors (1987)

Fifteen human B cell lines were tested for their ability to respond to B cell growth and differentiation factors present in phytohemagglutinin-conditioned medium. Five lines responded significantly: CESS showed an increase in IgG production only, HFB1 and BALM1 showed an increase in proliferation only and L4 and BALM4 showed an increase in both IgG production and proliferation. When four of the responding lines (CESS, HFB1, L4 and BALM4) were cultured with human recombinant-derived interleukin 1, interleukin 2, interleukin 4 or interferon-gamma no significant response was seen. CESS, L4 and BALM4 all increased IgG production in response to partially purified B cell growth factor (Cellular Products, Inc., Sera-Lab., Crawley Down, GB) and B cell differentiation factor-containing supernatant from the T24 bladder carcinoma cell line. HFB1, L4 and BALM4 all showed increased tritiated thymidine incorporation in response to purified B cell growth factor but not in response to B cell differentiation factor-containing supernatant. These lines may prove useful in the study of B cell growth and differentiation factors and their receptors.
Modulation of cell migration by integrin-mediated cytoskeletal linkages and ligand-binding affinity. (1996)

Integrin cell surface adhesion receptors play a central role in mediating cell migration. We have developed a model system consisting of CHO cells ectopically expressing the alpha IIb beta 3 integrin to study integrin affinity and cytoskeletal interactions during cell migration. The alpha IIb beta 3 integrins are suited for study of integrin receptors during cell migration because they are well characterized with respect to ligand binding, cytoskeletal interactions, and signal transduction, and mutants with altered receptor function are available. The alpha IIb beta 3 receptor specifically mediates migration of alpha IIb beta 3-transfected CHO cells. The migration of transfected CHO cells was studied on a fibrinogen substrate both by time lapse videomicroscopy and by random and haptotactic transwell assays. Haptotactic and random transwell assays measured distinct aspects of migration, with the random transwell assay correlating most closely with time lapse videomicroscopy. Mutations in the cytoplasmic domains that increase ligand affinity or activation of the alpha IIb beta 3 receptor into a high affinity state by the LIBS6 antibody decreased the migration rate. Likewise, mutations that increase cytoskeletal organization without affecting affinity also decreased the migration rate. In contrast, truncation of the beta chain, which alters cytoskeletal associations as assayed by absence of focal adhesions, decreased haptotactic migration while increasing random migration. These effects on the migration rate were partially compensated for by altering substrate concentration, demonstrating optimum substrate concentrations that supported maximal migration. For example, cells expressing integrins locked in the high affinity state showed maximal migration at lower substrate concentrations than cells expressing low affinity receptor. Together, these results implicate the strength of adhesion between cell and substrate, as modulated by receptor affinity, organization of adhesive complexes, and substrate concentration, as important regulators of cell migration rate. Further, we demonstrate a dominant effect of high affinity integrin in inhibiting migration regardless of the organization of adhesive complexes. These observations have potential implications for tumor metastasis and its therapy.
Bionanofabrication: engineering biomaterials for in situ remodeling and drug delivery (2016)

Presentation given at the Materials Science Research Seminar Series on Friday, February 26, 2016, 1 – 2 PM.
Observation of wavelength bistability in 850nm Vertical- Cavity Semiconductor Optical Amplifiers (VCSOAs) (2006)

The experimental observation of wavelength bistability in an 850nm VCSOA is reported. Clockwise hystereses are obtained with input wavelength sweeping when the input power is kept constant. Results are in good agreement with theoretical predictions.
Measurement of shear waves in tissue (2002)

The wavelength of a propagating pulse of shear wave within tissue is related to the local shear modulus and density through the speed of propagation. If the pulse does not produce standing waves, then the wavelength is a function of the tissue properties and not boundary conditions. Methods for imaging such waves using ultrasound and magnetic resonance imaging have recently been developed. The MRI method, termed Magnetic Resonance Elastography, can measure displacements in all three dimensions and is sensitive to motion of the order of 100 nanometers. The ultrasound method can measure in one plane very quickly and is sensitive to displacements of fractions of micrometers. Local wavelength of the propagating shear waves can be measured using specially modified filters. Shear modulus can then be estimated if density is known or assumed. Applications of this method reminiscent of palpation but in three dimensions and at any depth in the tissue are possibilities.
Agonists of the A2A adenosine receptor reduce inflammation and hypoxia‐induced pulmonary damage in transgenic sickle cell mice (2006)

Polymerization of deoxygenated HbS is the primary event in the molecular pathogenesis of sickle cell disease (SCD). Recently it has been proposed that chronic inflammation plays an important role in the etiology of vaso‐occlusive crisis (VOC) and long‐term pathologic manifestations of SCD. SCD patients and transgenic mice (NY‐S) expressing human betaS globin exhibit increased plasma levels of pro‐inflammatory cytokines, increased numbers of circulating endothelial cells, leukocytosis, and elevated expression of cell‐surface activation markers on leukocytes and endothelial cells. Adenosine acts through the A2A adenosine receptor (A2AAR) found on bone marrow‐derived cells to inhibit inflammation. We used hypoxia/reoxygenation to trigger VOC in NY‐S mice and assessed plasma cytokine levels, hypoxia‐induced lung inflammation and pulmonary function following the subcutaneous administration of the highly selective adenosine A2A receptor agonist, ATL146e (10 ng/kg/min). Compared to vehicle treated NY‐S mice, ATL146e‐treated mice displayed: 1) decreased plasma IL‐6 levels; 2) reduced severity of hypoxia‐induced vascular congestion as evidenced by pulmonary histology; 3) decreased pulmonary hypoxia based on 2‐nitroimidazole hypoxia staining in lung tissue sections and in vivo pulmonary accumulation of BRU59‐21, a 99mTc‐labeled 2‐nitroimidazole; and 4) improved pulmonary function (decreased breathing frequency and minute volume, increased expiratory time) as measured using whole‐body plethysmography. These data suggest that A2A adenosine agonists may be clinically useful for the treatment of sickle cell crisis. NIH grant #PO1 HL073361.
Measurement of the muon reconstruction performance of the ATLAS detector using 2011 and 2012 LHC proton–proton collision data (2014)

This paper presents the performance of the ATLAS muon reconstruction during the LHC run with $$pp$$ collisions at $$\sqrt{s}=7$$ –8 TeV in 2011–2012, focusing mainly on data collected in 2012. Measurements of the reconstruction efficiency and of the momentum scale and resolution, based on large reference samples of $${J/\psi \rightarrow \mu \mu }$$ , $$Z \rightarrow \mu \mu $$ and $${\Upsilon \rightarrow \mu \mu }$$ decays, are presented and compared to Monte Carlo simulations. Corrections to the simulation, to be used in physics analysis, are provided. Over most of the covered phase space (muon $$|\eta |<2.7$$ and $$5 \lesssim p_{\mathrm{T}}\lesssim 100$$ GeV) the efficiency is above $$99\,\%$$ and is measured with per-mille precision. The momentum resolution ranges from $$1.7\,\%$$ at central rapidity and for transverse momentum $$p_{\mathrm{T}}\simeq 10$$ GeV, to $$4\,\%$$ at large rapidity and $$p_{\mathrm{T}}\simeq 100$$ GeV. The momentum scale is known with an uncertainty of $$0.05\,\%$$ to $$0.2\,\%$$ depending on rapidity. A method for the recovery of final state radiation from the muons is also presented.
Recent advances in relativistic A6 magnetron research - mode control (2012)

Summary form only given. In a companion abstract we presented recent improvements in the start-up and efficiency of the A6 magnetron with radial extraction and axial extraction (MDO) [1]. Here we describe recent advances in mode switching and mode control.
Radiofrequency energy deposition and radiofrequency power requirements in parallel transmission with increasing distance from the coil to the sample (2015)

For parallel transmission, the distance between coils and object can be optimized to reduce SAR and minimize RF power requirements associated with homogeneous excitation.
Phase retrieval of widefield microscopy point spread functions (2001)

The three-dimensional imaging properties of a light microscope are traditionally described through an intensity point spread function (PSF) or its Fourier transform, the optical transfer function (OTF). However, the imaging properties can be more compactly described by a generalized two-dimensional pupil function. Use of the pupil function allows easy modification of an observed PSF to introduce known aberrations, a much more difficult task when using a PSF or OTF. Unfortunately, it is not straightforward to determine the complex-valued pupil function from the measured intensity PSF, because of the lack of phase information. This is the problem of phase retrieval. Several phase retrieval algorithms have been developed for two-dimensional imaging in astronomy. We have modified one such algorithm to be appropriate for the high-aperture, non-paraxial case of high resolution light microscopy. PSFs reconstructed from phase-retrieved pupil functions, modified by calculated aberrations closely reproduce the features of measured, aberrated PSFs.
LUNGx Challenge for computerized lung nodule classification (2016)

The purpose of this work is to describe the LUNGx Challenge for the computerized classification of lung nodules on diagnostic computed tomography (CT) scans as benign or malignant and report the performance of participants' computerized methods along with that of six radiologists who participated in an observer study performing the same Challenge task on the same dataset. The Challenge provided sets of calibration and testing scans, established a performance assessment process, and created an infrastructure for case dissemination and result submission. Ten groups applied their own methods to 73 lung nodules (37 benign and 36 malignant) that were selected to achieve approximate size matching between the two cohorts. Area under the receiver operating characteristic curve (AUC) values for these methods ranged from 0.50 to 0.68; only three methods performed statistically better than random guessing. The radiologists' AUC values ranged from 0.70 to 0.85; three radiologists performed statistically better than the best-performing computer method. The LUNGx Challenge compared the performance of computerized methods in the task of differentiating benign from malignant lung nodules on CT scans, placed in the context of the performance of radiologists on the same task. The continued public availability of the Challenge cases will provide a valuable resource for the medical imaging research community.
3rd World Congress on Oxidation Catalysis : proceedings of the 3rd World Congress on Oxidation Catalysis, San Diego, CA, U.S.A., 21-26 September 1997 (1997)

Featured lectures plenary lectures. Part A: structure selectivity/activity correlation lower alkane oxidation fine chemicals and pharmaceuticals engineering and environmental applications. Part B: methane activation combustion catalyst preparation alternate oxidants oxidation of olefins and aromatics oxidation in confined structures theoretical, computational and modelling studies. Part C: additional oxidation studies.
HYPOXIA AND REPRODUCTIVE HEALTH: Hypoxic regulation of preimplantation embryos: lessons from human embryonic stem cells (2020)

Development of the preimplantation embryo is reliant on nutrients present in the milieu of the reproductive tract. While carbohydrates, amino acids, lipids, and micronutrients are often considered when discussing preimplantation embryo nutrition, environmental oxygen is frequently overlooked. Although oxygen is not classically considered a nutrient, it is an important component of the in vitro culture environment and a critical regulator of cellular physiology. Oxygen is required to sustain an oxidative metabolism but when oxygen becomes limited, cells mount a physiological response driven by a family of transcription factors termed 'hypoxia inducible factors' which promote expression of a multitude of oxygen sensitive genes. It is this hypoxic response that is responsible not only for the switch to a glycolytic metabolism but also for a plethora of other cellular responses. There has been much debate in recent years over which environmental oxygen tension is preferential for the culture of preimplantation embryos. The review will evaluate this question and highlights how research using human embryonic stem cells can inform our understanding of why culturing under physiological oxygen tensions may be beneficial for the development of embryos generated through clinical in vitro fertilisation.
Author Correction: Non-Abelian generalizations of the Hofstadter model: spin–orbit-coupled butterfly pairs (2021)

A Correction to this paper has been published: https://doi.org/10.1038/s41377-021-00519-4
Peptides and proteins in a confined environment: NMR spectra at natural isotopic abundance (2007)

Confinement of proteins and peptides in a small inert space mimics the natural environment of the cell, allowing structural studies in conditions that stabilize folded conformations. We have previously shown that confinement in polyacrylamide gels (PAGs) is sufficient to induce a change in the viscosity of the aqueous solution without changing the composition and temperature of the solvent. The main limitation of a PAG to run NMR experiments in a confined environment is the need for labelling the peptides. Here we report the use of the agarose gel to run the NMR spectra of proteins and peptides. We show that agarose gels are completely transparent in NMR experiments, relieving the need for labelling. Although it is necessary to expose biomolecules to fairly high temperatures during sample preparation, we believe that this is not generally an obstacle to the study of peptides, and found that the method is also compatible with temperature-resistant proteins. The mesh of agarose gels is too wide for direct effects of confinement on the stability of proteins but confinement can be easily exploited to interact the proteins with other reagents, including crowding macromolecules that can eventually lead to fold stabilization. The use of these gels is ideally suited for low-temperature studies; we show that a very flexible peptide at subzero temperatures is stabilized into a well-folded conformation.
High‐Performance Solution‐Deposited n‐Channel Organic Transistors and their Complementary Circuits (2007)

High-performance, n-channel organic transistors are prepared from an air-stable, n-type organic semiconductor, and their complementary organic circuits, in which both p- and n-channel materials are solution deposited, are presented. Ring oscillators and D flip-flops fabricated from the transistors operate in air without passivation or packaging.
Bacterial Second Messenger Cyclic di-AMP Modulates the Competence State in Streptococcus pneumoniae (2019)

<i>Streptococcus pneumoniae</i> (the pneumococcus) is a naturally competent organism that causes diseases such as pneumonia, otitis media, and bacteremia. The essential bacterial second messenger cyclic di-AMP (c-di-AMP) is an emerging player in the stress responses of many pathogens. In <i>S. pneumoniae</i>, c-di-AMP is produced by a diadenylate cyclase, CdaA, and cleaved by phosphodiesterases Pde1 and Pde2. c-di-AMP binds a transporter of K<sup>+</sup> (Trk) family protein, CabP, which subsequently halts K<sup>+</sup> uptake via the transporter TrkH. Recently, it was reported that Pde1 and Pde2 are essential for pneumococcal virulence in mouse models of disease. To elucidate c-di-AMP-mediated transcription that may lead to changes in pathogenesis, we compared the transcriptomes of wild-type (WT) and Δ<i>pde1</i> Δ<i>pde2</i> strains by transcriptome sequencing (RNA-Seq) analysis. Notably, we found that many competence-associated genes are significantly upregulated in the Δ<i>pde1</i> Δ<i>pde2</i> strain compared to the WT. These genes play a role in DNA uptake, recombination, and autolysis. Competence is induced by a quorum-sensing mechanism initiated by the secreted factor competence-stimulating peptide (CSP). Surprisingly, the Δ<i>pde1</i> Δ<i>pde2</i> strain exhibited reduced transformation efficiency compared to WT bacteria, which was c-di-AMP dependent. Transformation efficiency was also directly related to the [K<sup>+</sup>] in the medium, suggesting a link between c-di-AMP function and the pneumococcal competence state. We found that a strain that possesses a V76G variation in CdaA produced less c-di-AMP and was highly susceptible to CSP. Deletion of <i>cabP</i> and <i>trkH</i> restored the growth of these bacteria in medium with CSP. Overall, our study demonstrates a novel role for c-di-AMP in the competence program of <i>S. pneumoniae</i><b>IMPORTANCE</b> Genetic competence in bacteria leads to horizontal gene transfer, which can ultimately affect antibiotic resistance, adaptation to stress conditions, and virulence. While the mechanisms of pneumococcal competence signaling cascades have been well characterized, the molecular mechanism behind competence regulation is not fully understood. The bacterial second messenger c-di-AMP has previously been shown to play a role in bacterial physiology and pathogenesis. In this study, we provide compelling evidence for the interplay between c-di-AMP and the pneumococcal competence state. These findings not only attribute a new biological function to this dinucleotide as a regulator of competence, transformation, and survival under stress conditions in pneumococci but also provide new insights into how pneumococcal competence is modulated.
Education for All : The Cost of Accessibility (2005)

The goal of Education for All (EFA) is&#13;\n to provide universal access to primary education throughout&#13;\n the world. To accomplish this goal, as many as 10 million&#13;\n classrooms will be built in developing countries by 2015. A&#13;\n key objective of the program is to ensure that no child is&#13;\n denied access to education because of disability. Access to&#13;\n all schools is necessary to ensure that children with&#13;\n disabilities can participate independently in a mainstreamed&#13;\n environment since most villages will have only one school&#13;\n building. The related construction costs, if any, are not a&#13;\n barrier to providing access and are insignificant when&#13;\n compared to the benefits. Children who are educated with&#13;\n their peers have greater opportunities to become productive&#13;\n members of their societies and be more integrated socially&#13;\n in their communities.