gebhart/patrepeval huggingface dataset:
Bio-printing cell-laden Matrigel–agarose constructs (2016)

3D printing of biological architectures that mimic the structural and functional features of in vivo tissues is of great interest in tissue engineering and the development of transplantable organ constructs. Printable bio-inks that are compatible with cellular activities play critical roles in the process of 3D bio-printing. Although a variety of hydrogels have been used as bio-inks for 3D bio-printing, they inherit poor mechanical properties and/or the lack of essential protein components that compromise their performance. Here, a hybrid Matrigel-agarose hydrogel system has been demonstrated that possesses both desired rheological properties for bio-printing and biocompatibility for long-term (11 days) cell culture. The agarose component in the hybrid hydrogel system enables the maintenance of 3D-printed structures, whereas Matrigel provides essential microenvironments for cell growth. When human intestinal epithelial HCT116 cells are encapsulated in the printed Matrigel-agarose constructs, high cell viability and proper cell spreading morphology are observed. Given that Matrigel is used extensively for 3D cell culturing, the developed 3D-printable Matrigel-agarose system will open a new way to construct Matrigel-based 3D constructs for cell culture and tissue engineering.
ROTATIONAL ANALYSIS OF THE Nak $D^{1}\Pi \rightarrow X^{1}\Sigma^{+}$ FLUORESCENCE SERIES EXCITED BY AN ARGON ION LASER (1974)

Author Institution: Department of Chemistry, Columbia University; Quantum Electronics Division, National Bureau of Standards
Patient-oriented education and visual-aid intervention are inadequate to identify patients with potential capsule retention: a prospective randomized study (2019)

<b>Background/aims:</b> The key procedure-related risk with video capsule endoscopy (VCE) is capsule retention, which should be suspected in patients who have not reported capsule passage. The study aims were to determine the frequency of capsule passage visualization and the difference in self-reporting of capsule passage between patients who receive patient-oriented education (POE) and patients who receive POE and a visual aid intervention in the form of a wrist band (WB). <b>Methods:</b> This was a prospective randomized study that enrolled patients undergoing VCE. Patients were randomly assigned to a POE group versus a POE and WB group. POE consisted of verbal education and an information booklet. Both groups received instructions to notify the study team regarding capsule passage. <b>Results:</b> Sixty patients (mean age 57 ± 18 years; 61% female) were included. A total of 57 patients were included in the analysis (3 lost to follow-up; 28 in POE group; 29 in WB group). Capsule passage status was reported by 68% without significant difference between POE and WB groups (72% vs. 64%; <i>p</i> = .51). Capsule passage status was obtained from all 57 patients with the addition of a proactive follow-up. Only 56% (<i>n</i> = 32) reported visualizing capsule passage. Of the remaining patients who did not visualize capsule passage, 60% (<i>n</i> = 15) reported on this without significant difference between the POE and WB groups (<i>p</i> = .23). <b>Conclusions:</b> Lack of visualization of capsule passage is a poor indicator of retention. Self-reporting of VCE passage status is suboptimal and the addition of a visual aid did not improve this parameter.
Leakage current reduction in sequential circuits by modifying the scan chains (2004)

Input vector control is an effective technique for reducing the leakage current of combinational VLSI circuits when these circuits are in the sleep mode. In this paper a design technique for applying the minimum leakage input to a sequential circuit is proposed. Our method uses the built-in scan-chain in a VLSI circuit to drive it with the minimum leakage vector when it enters the sleep mode. Using these scan registers eliminates the area and delay overhead of the additional circuitry that would otherwise be needed to apply the minimum leakage vector to the circuit. We show how the proposed technique can be used for several different scan-chain architectures and present the experimental results on the MCNC91 benchmark circuits.
Search for Dark Matter and Supersymmetry with a Compressed Mass Spectrum in the Vector Boson Fusion Topology in Proton-Proton Collisions at s=8  TeV (2017)

A first search for pair production of dark matter candidates through vector boson fusion in proton-proton collisions at sqrt[s]=8 TeV is performed with the CMS detector. The vector boson fusion topology enhances missing transverse momentum, providing a way to probe supersymmetry, even in the case of a compressed mass spectrum. The data sample corresponds to an integrated luminosity of 18.5 fb^{-1}, recorded by the CMS experiment. The observed dijet mass spectrum is consistent with the standard model expectation. In an effective field theory, dark matter masses are explored as a function of contact interaction strength. The most stringent limit on bottom squark production with mass below 315 GeV is also reported, assuming a 5 GeV mass difference with respect to the lightest neutralino.
Neurologic Deficit Following Percutaneous Vertebral Stabilization (2007)

Percutaneous vertebroplasty and kyphoplasty have been reported to be safe options for the treatment of painful osteoporotic vertebral fractures. Although complications are infrequent, there remains the potential for catastrophic neurologic injury. Physicians performing these procedures need to be aware of these potential complications and be prepared to respond in an emergent manner (surgically) if a need arises.
Light assisted poling and the photorefractive effect in lithium niobate (2009)

Light assisted poling (LAP) in LiNbO&lt;sub&gt;3&lt;/sub&gt; is examined under the "light" of the photorefractive effect for both congruently melting and MgO doped crystals. Experimental results suggest that a photo-induced space charge is responsible for the effect.
Microfluidic flow switching via localized acoustic streaming controlled by surface acoustic waves (2018)

We propose an acoustic flow switching device that utilizes high-frequency surface acoustic waves (SAWs) produced by a slanted-finger interdigitated transducer. As the acoustic field induced by the SAWs was attenuated in the fluid, it produced an acoustic streaming flow in the form of a pair of symmetrical microvortices, which induced flow switching between two fluid streams in a controlled manner. The microfluidic device was composed of a piezoelectric substrate attached to a polydimethylsiloxane (PDMS) microchannel having an H-shaped junction that connected two fluid streams in the middle. The two immiscible fluids, separated by the PDMS wall, flowed in parallel, briefly came in contact at the junction, and separated again into the downstream microchannels. The acoustic streaming flow induced by the SAWs rotated the fluid streams within the microchannel cross-section, thereby altering the respective positions of the two fluids and directing them into the opposite flow paths. The characteristics of the flow switching mechanism were investigated by tuning the input voltage and the flowrates. On-demand acoustic flow switching was successfully achieved without additional moving parts inside the microchannel. This technique may be useful for fundamental studies that integrate complex experimental platforms into a single chip.
Artificial Intelligence Methods for Rapid Vascular Access Aneurysm Classification in Remote or In-Person Settings (2021)

This is the first quality improvement project to show that an AI instrument can reliably grade vascular access aneurysms in a noninvasive way, allowing rapid assessments to be made on patients who would otherwise be at risk for highly morbid events. Moreover, these AI-assisted assessments can be made without having to schedule separate appointments and potentially even via telehealth.
Mucosal morphology in Barrett’s esophagus: interobserver agreement and role of narrow band imaging (2008)

Interobserver agreement for the classification of mucosal morphology was moderate. Although NBI was rated more highly than HR-WLE for imaging quality, this did not result in improved interobserver agreement or increased yield for identifying early neoplasia in Barrett's esophagus. This applied to non-expert as well as expert endoscopists.
Metabolic Phenotype Modulation by Caloric Restriction in a Lifelong Dog Study (2013)

Modeling aging and age-related pathologies presents a substantial analytical challenge given the complexity of gene-environment influences and interactions operating on an individual. A top-down systems approach is used to model the effects of lifelong caloric restriction, which is known to extend life span in several animal models. The metabolic phenotypes of caloric-restricted (CR; n = 24) and pair-housed control-fed (CF; n = 24) Labrador Retriever dogs were investigated by use of orthogonal projection to latent structures discriminant analysis (OPLS-DA) to model both generic and age-specific responses to caloric restriction from the ¹H NMR blood serum profiles of young and older dogs. Three aging metabolic phenotypes were resolved: (i) an aging metabolic phenotype independent of diet, characterized by high levels of glutamine, creatinine, methylamine, dimethylamine, trimethylamine N-oxide, and glycerophosphocholine and decreasing levels of glycine, aspartate, creatine and citrate indicative of metabolic changes associated largely with muscle mass; (ii) an aging metabolic phenotype specific to CR dogs that consisted of relatively lower levels of glucose, acetate, choline, and tyrosine and relatively higher serum levels of phosphocholine with increased age in the CR population; (iii) an aging metabolic phenotype specific to CF dogs including lower levels of liproprotein fatty acyl groups and allantoin and relatively higher levels of formate with increased age in the CF population. There was no diet metabotype that consistently differentiated the CF and CR dogs irrespective of age. Glucose consistently discriminated between feeding regimes in dogs (≥312 weeks), being relatively lower in the CR group. However, it was observed that creatine and amino acids (valine, leucine, isoleucine, lysine, and phenylalanine) were lower in the CR dogs (<312 weeks), suggestive of differences in energy source utilization. ¹H NMR spectroscopic analysis of longitudinal serum profiles enabled an unbiased evaluation of the metabolic markers modulated by a lifetime of caloric restriction and showed differences in the metabolic phenotype of aging due to caloric restriction, which contributes to longevity studies in caloric-restricted animals. Furthermore, OPLS-DA provided a framework such that significant metabolites relating to life extension could be differentiated and integrated with aging processes.
Ethanol Production by Saccharomyces cerevisiae Immobilized in Hollow-Fiber Membrane Bioreactors (1983)

Saccharomyces cerevisiae ATCC 4126 was grown within the macroporous matrix of asymmetric-walled polysulfone hollow-fiber membranes and on the exterior surfaces of isotropic-walled polypropylene hollow-fiber membranes. Nutrients were supplied and products were removed by single-pass perfusion of the fiber lumens. Growth of yeast cells within the macrovoids of the asymmetric-walled membranes attained densities of greater than 10 cells per ml and in some regions accounted for nearly 100% of the available macrovoid volume, forming a tissue-like mass. A radial distribution of cell packing existed across the fiber wall, indicating an inadequate glucose supply to cells located beyond 100 mum from the lumen surface. By comparison, yeast cell growth on the exterior surfaces of the isotropic-walled membranes resulted in an average density of 3.5 x 10 viable cells per ml. Ethanol production by reactors containing isotropic polypropylene fibers reached a maximum value of 26 g/liter-h based on the total reactor volume. Reactor performance depended on the fiber packing density and on the glucose medium flow rate and was limited by low nutrient and product transport rates. The inhibition of ethanol production and the reduction in fermentation efficiency arose primarily from the accumulation of CO(2) gas within the sealed reactor shell space.
Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa (2008)

Natural antisense transcripts (NATs) have been shown to play important roles in post-transcriptional regulation through the RNA interference pathway. We have combined pyrophosphate-based high-throughput sequencing and computational analysis to identify and analyze, in genome scale, cis-NAT and trans-NAT small RNAs that are derived under normal conditions and in response to drought and salt stresses in the staple plant Oryza sativa. Computationally, we identified 344 cis-NATs and 7,142 trans-NATs that are formed by protein-coding genes. From the deep sequencing data, we found 108 cis-NATs and 7,141 trans-NATs that gave rise to small RNAs from their overlapping regions. Consistent with early findings, the majority of these 108 cis-NATs seem to be associated with specific conditions or developmental stages. Our analyses also revealed several interesting results. The overlapping regions of the cis-NATs and trans-NATs appear to be more enriched with small RNA loci than non-overlapping regions. The small RNAs generated from cis-NATs and trans-NATs have a length bias of 21 nt, even though their lengths spread over a large range. Furthermore, >40% of the small RNAs from cis-NATs and trans-NATs carry an A as their 5'-terminal nucleotides. A substantial portion of the transcripts are involved in both cis-NATs and trans-NATs, and many trans-NATs can form many-to-many relationships, indicating that NATs may form complex regulatory networks in O. sativa. This study is the first genome-wide investigation of NAT-derived small RNAs in O. sativa. It reveals the importance of NATs in biogenesis of small RNAs and broadens our understanding of the roles of NAT-derived small RNAs in gene regulation, particularly in response to environmental stimuli.
Progressive Compression of Triangle Meshes (2023)

This paper details the first publicly available implementation of the progressive mesh compression algorithm described in the paper entitled "Compressed Progressive Meshes" [R. Pajarola and J. Rossignac, IEEE Transactions on Visualization and Computer Graphics, 6 (2000), pp. 79-93]. Our implementation is generic, modular, and includes several improvements in the stopping criteria and final encoding. Given an input 2-manifold triangle mesh, an iterative simplification is performed, involving batches of edge collapse operations guided by an error metric. During this compression step, all the information necessary for the reconstruction (at the decompression step) is recorded and compressed using several key features: geometric quantization, prediction, and spanning tree encoding. Our implementation allowed us to carry out an experimental comparison of several settings for the key parameters of the algorithm: the local error metric, the position type of the resulting vertex (after collapse), and the geometric predictor.
The effect of inertia on the intrinsic viscosity of polymers (1974)

Abstract For the model of an elastic dumbbell, i.e., two beads connected by a Hookean spring, the Langevin equations for the beads are formulated. It is taken into account that the friction force contains terms resulting from the inertia of the liquid. The contribution of the dumbbell to the viscosity is calculated from the rate of energy dissipation. When the inertia of the liquid is neglected, the viscosity contribution reduces to Kramers' result and is independent of the mass of the beads. When the inertia terms are added, the result is nearly independent of this mass, but shows a dependence on the density of the liquid. In liquids of low viscosity, the extra term resulting from the inertia may be as large as 25% of the total viscosity contribution.
Fetal brain during a binge drinking episode: a dynamic susceptibility contrast MRI fetal brain perfusion study (2010)

We assessed the effects of a single episode of maternal alcohol intoxication on fetal brain blood perfusion in three pregnant dams (baboons) at the 24th week of pregnancy using dynamic susceptibility contrast magnetic resonance imaging. After the oral administration of alcohol, there was a four-fold increase in the peak contrast concentrations in the fetal brain. In addition, we observed a two- to three-fold increase in the contrast uptake and washout rates in the fetal brain. The underlying mechanisms of these changes are unknown, but we hypothesized that these could include the alcohol-mediated changes in placental permeability and fetal cerebral blood flow. Our findings indicate that alcohol intoxication produces profound changes, which may detrimentally influence neurodevelopmental processes in the brain.
Light-Emitting Silicon Nanocrystals and Photonic Structures in Silicon Nitride (2006)

In this paper, we review our main results on the optical and electrical properties of light-emitting silicon nanocrystals (Si-ncs) obtained from the thermally induced nucleation in amorphous silicon-rich nitride (SRN) films deposited either by plasma-enhanced chemical vapor deposition (PE-CVD) or magnetron sputtering. In particular, we discuss the Si-ncs microscopic light emission mechanism combining the optical data with the first-principle calculations of the absorption/emission Stokes shifts and recombination lifetimes. In addition, we report on the electrical injection characteristics of simple p-i-n device structures showing efficient bipolar transport and room temperature electroluminescence, and demonstrate efficient energy sensitization of erbium (Er) ions from the Si-ncs embedded in the SRN matrices. We further show that the light-emitting nanocrystals in SRN can be embedded in aperiodic photonic environments, where the localized optical modes can be used to significantly enhance the Si-ncs emission intensity at different emission wavelengths. These results suggest that the Si-ncs embedded in the SRN matrices have a large potential for the fabrication of optically active photonic devices based on the Si technology
A MACHINE-LEARNING APPROACH FOR MEASURING ARTICULAR CARTILAGE DAMAGE IN THE KNEE (2021)

Objectives Articular cartilage damage is a primary outcome of pre-clinical and clinical studies evaluating meniscal and cartilage repair or replacement techniques. Recent studies have quantitativel...
Atomic-scale diffractive imaging of sub-cycle electron dynamics in condensed matter (2015)

Abstract For interaction of light with condensed-matter systems, we show with simulations that ultrafast electron and X-ray diffraction can provide a time-dependent record of charge-density maps with sub-cycle and atomic-scale resolutions. Using graphene as an example material, we predict that diffraction can reveal localised atomic-scale origins of optical and electronic phenomena. In particular, we point out nontrivial relations between microscopic electric current and density in undoped graphene.
Exciton-Dominated Core-Level Absorption Spectra of Hybrid Organic–Inorganic Lead Halide Perovskites (2018)

In a combined theoretical and experimental work, we investigate X-ray absorption near-edge structure spectroscopy of the I L<sub>3</sub> and the Pb M<sub>5</sub> edges of the methylammonium lead iodide (MAPbI<sub>3</sub>) hybrid inorganic-organic perovskite and its binary phase PbI<sub>2</sub>. The absorption onsets are dominated by bound excitons with sizable binding energies of a few hundred millielectronvolts and pronounced anisotropy. The spectra of both materials exhibit remarkable similarities, suggesting that the fingerprints of core excitations in MAPbI<sub>3</sub> are essentially given by its inorganic component, with negligible influence from the organic groups. The theoretical analysis complementing experimental observations provides the conceptual insights required for a full characterization of this complex material.
The C K L L first-derivative x-ray photoelectron spectroscopy spectra as a fingerprint of the carbon state and the characterization of diamondlike carbon films (1987)

The C KLL spectra from natural diamond, graphite, and single-crystal β-SiC have been investigated using x-ray photoelectron spectroscopy and first-derivative x-ray excited Auger electron spectroscopy (XAES). It is shown that the XAES spectra is essentially the same as that obtained with conventional AES with the added benefits of no electron beam (e-beam) damage, enhanced fine structure, and the simultaneous acquisition of the C 1s and valence-band spectra. The C KLL XAES fine structure provides a fingerprint of the carbon bonding state and the C 1s and valence-band spectra provide insight into the origin of this fine structure. Diamondlike carbon films fabricated by hydrogen gas reactive sputtering of graphite on Si were also investigated. The XAES C KLL spectra in conjunction with the valence-band spectra verifies the tetrahedral C–C bonding in these films even though the AES spectra shows a graphitelike structure; indicative of e-beam damage.
Scaffolds: 3D Structural Patterns in Scalable, Elastomeric Scaffolds Guide Engineered Tissue Architecture (Adv. Mater. 32/2013) (2013)

Microfabricated biodegradable scaffolds with 3D structural patterns are created by semi-automated layer-by-layer assembly of elastomeric polymer sheets with through-pores, as described by Lisa E. Freed and co-workers on page 4459. The 3D pore network architecture defined by the relative alignment of layers directed cell and muscle-like fiber orientation in skeletal and cardiac muscle. In this picture, heart cell bundles weave through a pore network created in a multi-layer poly(glycerol sebacate) (PGS) scaffold.
Correction: Benefits of Aldosterone Receptor Antagonism in Chronic Kidney Disease (BARACK D) trial–a multi-centre, prospective, randomised, open, blinded end-point, 36-month study of 2,616 patients within primary care with stage 3b chronic kidney disease to compare the efficacy of spironolactone 25 mg once daily in addition to routine care on mortality and cardiovascular outcomes versus routine care alone: study protocol for a randomized controlled trial (2022)

Correction: Benefits of Aldosterone Receptor Antagonism in Chronic Kidney Disease (BARACK D) trial-a multi-centre, prospective, randomised, open, blinded end-point, 36-month study of 2,616 patients within primary care with stage 3b chronic kidney disease to compare the efficacy of spironolactone 25 mg once daily in addition to routine care on mortality and cardiovascular outcomes versus routine care alone: study protocol for a randomized controlled trial
Nonlinear GaInAs/AlInAs/InP quantum cascade laser sources for wavelength generation in the 2.7-70 μm wavelength range (2011)

In this paper we describe the design and performance of nonlinear quantum cascade laser sources for near-infrared and terahertz applications. Our devices are based on monolithically integrated mid-infrared quantum cascade lasers and passive nonlinear structures which provide a giant nonlinear response for the pumping frequency. Such design concept can be applied for both short-wavelength and long-wavelength generation. In our work, short-wavelength devices were based on the concept of second-harmonic generation whereas long-wavelength devices utilized difference-frequency generation. With this approach we demonstrate room-temperature operation down to 2.7 &mu;m for near-infrared devices and up to 70 &mu;m at 210 K for terahertz devices. The performance of our nonlinear devices is very sensitive to the resonance condition for the pump and nonlinearity. We demonstrate that, once resonant, nonlinear powers in the mW range are available.