gebhart/patrepeval huggingface dataset:
Exploiting induced pluripotent stem cell-derived macrophages to unravel host factors influencing Chlamydia trachomatis pathogenesis (2017)

Chlamydia trachomatis remains a leading cause of bacterial sexually transmitted infections and preventable blindness worldwide. There are, however, limited in vitro models to study the role of host genetics in the response of macrophages to this obligate human pathogen. Here, we describe an approach using macrophages derived from human induced pluripotent stem cells (iPSdMs) to study macrophage-Chlamydia interactions in vitro. We show that iPSdMs support the full infectious life cycle of C. trachomatis in a manner that mimics the infection of human blood-derived macrophages. Transcriptomic and proteomic profiling of the macrophage response to chlamydial infection highlighted the role of the type I interferon and interleukin 10-mediated responses. Using CRISPR/Cas9 technology, we generated biallelic knockout mutations in host genes encoding IRF5 and IL-10RA in iPSCs, and confirmed their roles in limiting chlamydial infection in macrophages. This model can potentially be extended to other pathogens and tissue systems to advance our understanding of host-pathogen interactions and the role of human genetics in influencing the outcome of infections.
Linear machining technique using nanosecond pulsed laser for forming single-point cutting tool made of nano-polycrystalline diamond (2017)

A linear machining technique using a nanosecond pulsed laser, adaptable for forming a single-point cutting tool made of nano-polycrystalline diamond, was developed. A basic study to find the principal rules of linear machining was conducted by forming an inclined face against the beam axis that is coincided with the Z axis. The face was formed by conducting repeatedly a set of machining processes, comprising linear machining to remove chips and zero-cut machining to remove the residual stock. It was verified through a machining test that the removal depth in the Z direction was independent of the inclined angle of the face. In addition, the stock removal in the Z direction coincided with the sum of the applied depths of cut in the Z direction when the residual stock removal in each machining step was eliminated by the zero-cut machining. These basic rules made it possible to accurately fabricate a convex dimple with a diameter of 0.2 mm, during which the inclined angle of the machined face against the beam axis varied at every position, by repeatedly conducting the set of machining processes. Also, it was verified through the forming test of a single-point cutting tool with a nose radius of 0.4 mm that the linear machining technique enabled the fabrication of the tool with a shape accuracy better than 1 μm and a cutting edge radius of less than 250 nm.
Ablation Versus Amiodarone for Treatment of Persistent Atrial Fibrillation in Patients With Congestive Heart Failure and an Implanted Device (2016)

URL: http://www.clinicaltrials.gov. Unique identifier: NCT00729911.
Fast planar object detection and tracking via edgel templates (2012)

We describe an efficient method to detect and track planar objects using a template of edge segments. Such segments are selected at multiple scales based on gradient magnitude; their positions and orientations are used to determine a canonical reference frame where the descriptor is computed based on quantized orientation. The resulting descriptors are efficiently matched using logical operations, and tracked between frames. The method yields pose estimates that are robust to scale changes, foreshortening, partial occlusions, and is suitable for use in augmented reality and human-computer interaction.
Minimum time trajectory planning for dual robot systems (2003)

The problem of planning minimum time collision-free trajectories for a dual robot system is addressed. It is shown that this problem can be solved by first planning the minimum time trajectory for each robot without considering the existence of the other and then combining the two individual trajectories. This combination is accomplished by delaying one of the two trajectories in such a way that the time required for the coordinated motion of the two robots is minimized while avoiding collision between them. The optimality of the method is rigorously proved, the practical aspects of its realization are discussed, and example is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Hyperuniformity of generalized random organization models (2018)

Studies of random organization models of monodisperse spherical particles have shown that a hyperuniform state is achievable when the system goes through an absorbing phase transition to a critical state. Here we investigate to what extent hyperuniformity is preserved when the model is generalized to particles with a size distribution and/or nonspherical shapes. We begin by examining binary disks in two dimensions and demonstrate that their critical states are hyperuniform as two-phase media, but not hyperuniform nor multihyperuniform as point patterns formed by the particle centroids. We further confirm the generality of our findings by studying particles with a continuous size distribution. Finally, to study the effect of rotational degrees of freedom, we extend our model to noncircular particles, namely, hard rectangles with various aspect ratios, including the hard-needle limit. Although these systems exhibit only short-range orientational order, hyperuniformity is still preserved. Our analysis reveals that the redistribution of the "mass" of the particles rather than the particle centroids is central to this dynamical process. The consideration of the "active volume fraction" of generalized random organization models may help to resolve which universality class they belong to and hence may lead to a deeper theoretical understanding of absorbing-state models. Our results suggest that general particle systems subject to random organization can be a robust way to fabricate a wide class of hyperuniform states of matter by tuning the structures via different particle-size and -shape distributions. This in turn potentially enables the creation of multifunctional hyperuniform materials with desirable optical, transport, and mechanical properties.
Gonadotropin-Releasing Hormone II Stimulates Female Sexual Behavior in Marmoset Monkeys (2005)

GnRH II (pGlu-His-Trp-Ser-Try-Gly-Leu-Arg-Pro-GlyNH2), an evolutionarily conserved member of the GnRH family, stimulates reproductive behavior in a number of vertebrates. To explore a role for GnRH II in regulating primate sexual behavior, eight adult female common marmosets, each fitted with an indwelling intracerebroventricular (icv) cannula, were ovariectomized, implanted subcutaneously with empty (n = 4) or estradiol-filled (n = 4) SILASTIC brand capsules, and pair housed with an adult male mate. After icv infusion of vehicle or peptides, females were placed in an observation cage for 90 min, out of visual contact with other marmosets, before the 30-min behavioral test with their male partner. Compared with vehicle, GnRH II (1 and 10 microg) increased the total number of proceptive (sexual solicitation) behaviors (tongue flicking, proceptive stares, and frozen postures) exhibited by females toward their pair mates and specifically increased the frequency of freeze postures. Effects were maximal at 1 microg and not dependent upon estradiol supplementation. GnRH II agonists/GnRH I antagonists 135-18 (1 microg) and 132-25 (1 microg), which stimulate inositol phosphate production via the marmoset type II receptor, increased the frequency of total proceptive behavior but did not specifically stimulate freeze-posture behavior. In contrast, GnRH I, at 1 mug, did not alter the frequency of proceptive behaviors. Female receptivity (female compliance with male sexual behavior) was not altered by any of the peptides tested. These findings implicate a role for GnRH II and the cognate GnRH type II receptor in stimulating female marmoset sexual behavior.
Application of neutral d10 coinage metal complexes with an anionic bidentate ligand in delayed fluorescence-type organic light-emitting diodes (2013)

A series of heteroleptic coinage metal(I) complexes [Cu(PP)(PS)] 1, [Ag(PP)(PS)] 2, and [Au(PP)(PS)] 3 [PP = 1,2-bis(diphenylphosphino)benzene and PS− = 2-diphenylphosphinobenzenethiolate] were synthesized. X-ray crystallography demonstrated that 1–3 possessed tetrahedral structures containing two types of bidentate ligands, PP and PS−. Photophysical studies and time-dependent density functional theory calculations indicated that the emission from 1–3 in the solid state at room temperature originated from thermally activated delayed fluorescence (TADF). The thiolate ligand with strong electron-donating character (PS−) reduced the contribution from metal orbitals to the highest occupied molecular orbitals of the complexes, decreasing the metal-to-ligand charge-transfer character of the excited states of 1–3. The origin of TADF in 1–3 was attributed to ligand-to-ligand charge-transfer on the basis of molecular orbital calculations. Au(I) complex 3 was unstable in solution because of a rapid ligand exchange reaction, and Ag(I) complex 2 showed limited solubility in organic solvents. Cu(I) complex 1, which exhibited efficient green TADF with a maximum emission wavelength of 521 nm and a quantum yield of 0.52 in the solid state, was used to fabricate TADF-type organic light-emitting diodes via a wet process.
Influence of crystallinity on the morphology of poly(ethylene oxide) containing diblock copolymers (1997)

Abstract Low‐molecular‐weight poly(ethylene oxide)‐polyalkane (PEO‐PA) diblock copolymers have been examined between the order‐disorder transition and PEO melting temperature using small‐angle neutron scattering (SANS), differential scanning calorimetry (DSC), and dynamic mechanical spectroscopy (DMS). Crystallization imposes layered ordering with polymer stems oriented perpendicular, or tilted, relative to the microdomain interface, thereby disrupting conventional amorphous microdomain morphologies. This effect can be used to switch the high symmetry bicontinuous ordered G phase to lower symmetry cylinders or lamellae.
Occurrence and Abatement of Volatile Sulfur Compounds during Biogas Production (2004)

Volatile sulfur compounds (VSCs) in biogas originating from a biogas production plant and from a municipal sewage water treatment plant were identified. Samples were taken at various stages of the biogas-producing process, including upgrading the gas to vehicle-fuel quality. Solid-phase microextraction was used for preconcentration of the VSCs, which were subsequently analyzed using gas chromatography in combination with mass spectrometry. Other volatile organic compounds present also were identified. The most commonly occurring VSCs in the biogas were hydrogen sulfide, carbonyl sulfide, methanethiol, dimethyl sulfide, and dimethyl disulfide, and hydrogen sulfide was not always the most abundant sulfur (S) compound. Besides VSCs, oxygenated organic compounds were commonly present (e.g., ketones, alcohols, and esters). The effect of adding iron chloride to the biogas reactor on the occurrence of VSCs also was investigated. It was found that additions of 500-g/m3 substrate gave an optimal removal of VSCs. Also, the use of a prefermentation step could reduce the amount of VSCs formed in the biogas process. Moreover, in the carbon dioxide scrubber used for upgrading the gas, VSCs were removed efficiently, leaving traces (ppbv levels). The scrubber also removed other organic compounds.
A MicroRNA Expression Signature for Cervical Cancer Prognosis (2010)

Invasive cervical cancer is a leading cause of cancer death in women worldwide, resulting in about 300,000 deaths each year. The clinical outcomes of cervical cancer vary significantly and are difficult to predict. Thus, a method to reliably predict disease outcome would be important for individualized therapy by identifying patients with high risk of treatment failures before therapy. In this study, we have identified a microRNA (miRNA)-based signature for the prediction of cervical cancer survival. miRNAs are a newly identified family of small noncoding RNAs that are extensively involved in human cancers. Using an established PCR-based miRNA assay to analyze 102 cervical cancer samples, we identified miR-200a and miR-9 as two miRNAs that could predict patient survival. A logistic regression model was developed based on these two miRNAs and the prognostic value of the model was subsequently validated with independent cervical cancers. Furthermore, functional studies were done to characterize the effect of miRNAs in cervical cancer cells. Our results suggest that both miR-200a and miR-9 could play important regulatory roles in cervical cancer control. In particular, miR-200a is likely to affect the metastatic potential of cervical cancer cells by coordinate suppression of multiple genes controlling cell motility.
Homogeneous and Heterogeneous Polymerization of \varepsilon-Caprolactone by Neodymium Alkoxides Prepared In Situ (2001)

International audience
Near‐field scanning optical microscopy in liquid for high resolution single molecule detection on dendritic cells (2004)

Clustering of cell surface receptors into micro-domains in the plasma membrane is an important mechanism for regulating cellular functions. Unfortunately, these domains are often too small to be resolved with conventional optical microscopy. Near-field scanning optical microscopy (NSOM) is a relatively new technique that combines ultra high optical resolution, down to 70 nm, with single molecule detection sensitivity. As such, the technique holds great potential for direct visualisation of domains at the cell surface. Yet, NSOM operation under liquid conditions is far from trivial. In this contribution, we show that the performance of NSOM can be extended to measurements in liquid environments using a diving bell concept. For the first time, individual fluorescent molecules on the membrane of cells in solution are imaged with a spatial resolution of 90 nm. Furthermore, using this technique we have been able to directly visualise nanometric sized domains of the C-type lectin DC-SIGN on the membrane of dendritic cells, both in air and in liquid.
Options strategy for technology companies (2014)

Product innovation in the technology ecosystem can be enhanced through proper management of the supply chain. While there are several strategies that technology investors favor for profitability during the earning cycles, one of the strategies utilized quite often is the short strangle. A short strangle is an effective strategy with a theoretically unlimited risk. For example, Google's recent earnings sent its share price up sharply by 13.8%, breaking the $1,000 barrier for the first time and increasing the company's value by nearly $40 billion within a day. Such variations can be very costly for an investor who trades around earnings using short strangles. The aim of this paper is to debunk this myth and demonstrate how a short strangle can be traded safely as long as certain requirements are met. We will employ two companies in the technology sector to illustrate how our criteria can help in making better trading decisions. Since the volatility crush is the key determinant for profitability, we modeled the crush between the implied volatility of the front and next earliest expiration using Bayesian statistics. The accuracy of the Bayesian model is quantified using the Google stock as an example and it is shown that the method is reasonably accurate even with sharp changes in volatility trends.
Development of an Inspector Satellite Propulsion Module Using Photostructurable Glass/Ceramic Materials (2004)

A 1-kg class miniature satellite can provide close-in support assistance to a conventional host satellite. The Co-Orbital Satellite Assistant (COSA) is a satellite inspector with a weeklong mission. COSA maneuvering requirements for LEO and GEO applications have velocity increments of less than a meter per second. Perturbation forces such as air drag and solar pressure typically drive 'V requirements an order-of-magnitude higher. With the exception of deorbit or disposal, a cold gas thruster system is appropriate for a COSA in LEO or GEO. We are currently fabricating a second-generation laboratory-class propulsion module out of a photostructurable glass ceramic material that meets the propulsion requirements for a LEO COSA mission. It uses eight thrusters and is designed to demonstrate station-keeping and leader-follower operation on an air table.
Exocrine and Endocrine Interactions in Cystic Fibrosis: A Potential Key to Understanding Insulin Secretion in Health and Disease? (2016)

The study of β-cell function in vivo has been hampered by the relative inaccessibility of the pancreas as well as the hybrid exocrine/endocrine nature of the organ. This has limited the ability to correlate structure with function, although some efforts have been made in this regard (1,2). Moreover, there are no tests available that can easily, accurately, and reproducibly measure β-cell secretion in a way that might be clinically relevant or influence therapeutic decisions for individual patients (3). The issue is further compounded by the conflation of β-cell function with β-cell mass, where the former can be taken to represent response to a “physiological” challenge and the latter is represented by the (presumed) maximal response to a “supra-physiological” challenge (4). How these relate to the numbers of functional islets or to islet “health” and integrity remains unknown, despite numerous efforts to image β-cell mass in vivo. Unfortunately in a time when an echocardiogram is routinely used for the assessment of cardiac structure and function, diabetologists are stuck with the equivalent of Laennec’s stethoscope.

The response to a meal is affected by multiple factors (Fig. 1), including gastric accommodation, gastric trituration of complex food, intraluminal digestion, and subsequent absorption (5–8). In addition, the prevailing degree of insulin action will also alter β-cell secretion; indeed for glucose tolerance to be maintained, β-cell function must be able to compensate for impaired insulin action (4). This concept is embodied in the disposition index, which describes the hyperbolic relationship between the two parameters (9) (Fig. 1). Examination of insulin secretion in disease states where these parameters are directly or indirectly affected by the disease process …
Photopolymers for non‐linear optics: Design and synthesis of a polymer containing styrene‐terminated tolane chromophores and its stabilization in an oriented configuration by photocrosslinking (1995)

Abstract A new photocrosslinkable polymer designed for application in second harmonic generation has been prepared and tested for frequency doubling of IR lasers. The polymer is based on a colorless polyurethane with pendant tolane nonlinear optical chromophores that carry a polymerizable styrene moiety at their extremities. Photocrosslinking is achieved by irradiation of films containing a small amount of a bleachable radical photoinitiator. The effect of photoinduced radical crosslinking on the mobility of the chromophores has been studied by recording the intensity of the frequency doubled light, generated by a poled sample, with increasing temperature. As expected, photocrosslinking leads to NLO materials with highly stable chromophore orientation.
Methods and Tools for Wavelet-Based Scalable Multiview Video Coding (2011)

A wavelet-based multiview video coding scheme is presented in this paper. It uses a 4-D wavelet transform, which is composed of a 1-D temporal wavelet transform, namely motion compensated temporal filtering, a 1-D view-directional wavelet transform, namely disparity compensated view filtering and a 2-D spatial wavelet transform. Since the presented framework can make use of the inherent scalability properties of the wavelet transforms involved, it allows full scalability of the coded bitstream in the temporal, view, spatial, and quality dimensions. Coding performance close to the H.264/advanced video coding based standard multiview video codec is shown. Enhancements of the view transform, in order to better account for brightness and color variations across views are introduced. Additionally, the use of a signal adaptive anisotropic wavelet packet (WP) transform as a generalization of WP transforms for the spatial decomposition is proposed. Both enhancements lead to a decrease of bit rate of up to 11% compared with the baseline version of the codec.
Abstract PR05: Familial cancer patient specific iPSCs based study of a potential oncogenic factor, sFRP2, in osteosarcoma (2018)

Abstract Osteosarcoma (OS), despite being a serious pediatric cancer with the lowest survival rate, is not well studied due to its rare occurrence. For this reason, studying OS in a patient-specific manner is more challenging. In an attempt to establish a method to study OS in a patient-specific manner, we previously generated Li-Fraumeni syndrome (LFS---a germline P53 mutation disease) patient specific iPSCs, and demonstrated that the LFS-iPSC derived mesenchymal stem cells (MSCs) and osteoblasts (OBs) can recapitulate tumorigenic phenotypes in vitro and in vivo (Lee, Kim, et al., Cell 2015). Taking advantage of this new platform, we focused on finding potential therapeutic targets. We found SFRP2 (secreted frizzled related protein 2) to be highly expressed in LFS iPSC-derived MSCs and OBs by global RNA-seq gene expression analysis. Using global transcript profiling of ectopic overexpression (OE) of sFRP2 in wild-type MSCs, we discovered that sFRP2 regulates osteoblast differentiation, cell adhesion, cell proliferation, and apoptosis-related gene sets. Further functional assays revealed that sFRP2 OE contributes to the generation of abnormal osteoblast cells, which are the cause of OS, by suppressing osteogenic alkaline phosphatase activity, mineralization, and osteogenic BMP and WNT signaling. Furthermore, ectopic OE of sFRP2 is associated with LFS mediated tumorigenesis. sFRP2 OE in MSCs and OBs facilitates cell proliferation through cell cycle alteration and increases anchorage independency. In in ovo and in vivo xenograft assays (subcutaneous and intratibial injections), the tumor size is significantly increased in sFRP2 OE group and decreased in knockdown sFRP2 group. Interestingly, we also found that sFRP2 OE augments angiogenesis in vitro and in vivo, suggesting sFRP2 has a role as a paracrine factor. In the future, we will analyze sFRP2 expression levels in human OS tissue samples to determine whether sFRP2 OE has clinical relevance. Conclusively, this study demonstrates that P53 mutation-mediated osteosarcoma exerts oncogenicity through sFRP2 overexpression and that targeting of sFRP2 is a potential therapeutic strategy for OS treatment. This abstract is also being presented as Poster A22. Citation Format: Huen Suk Kim, Ye X. Yuan, Jeffrey M. Bernitz, Andreia Gomes, Christopher Schaniel, Dung-Fang Lee, Ihor R. Lemischka. Familial cancer patient specific iPSCs based study of a potential oncogenic factor, sFRP2, in osteosarcoma [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr PR05.