gebhart/patrepeval huggingface dataset:
NOTCH signaling specifies arterial-type definitive hemogenic endothelium from human pluripotent stem cells (2018)

NOTCH signaling is required for the arterial specification and formation of hematopoietic stem cells (HSCs) and lympho-myeloid progenitors in the embryonic aorta-gonad-mesonephros region and extraembryonic vasculature from a distinct lineage of vascular endothelial cells with hemogenic potential. However, the role of NOTCH signaling in hemogenic endothelium (HE) specification from human pluripotent stem cell (hPSC) has not been studied. Here, using a chemically defined hPSC differentiation system combined with the use of DLL1-Fc and DAPT to manipulate NOTCH, we discover that NOTCH activation in hPSC-derived immature HE progenitors leads to formation of CD144<sup>+</sup>CD43<sup>-</sup>CD73<sup>-</sup>DLL4<sup>+</sup>Runx1 + 23-GFP<sup>+</sup> arterial-type HE, which requires NOTCH signaling to undergo endothelial-to-hematopoietic transition and produce definitive lympho-myeloid and erythroid cells. These findings demonstrate that NOTCH-mediated arterialization of HE is an essential prerequisite for establishing definitive lympho-myeloid program and suggest that exploring molecular pathways that lead to arterial specification may aid in vitro approaches to enhance definitive hematopoiesis from hPSCs.
Lower extremity vein graft failure: a translational approach (2008)

Patients with the most severe manifestations of lower extremity arterial occlusive disease often require peripheral bypass surgery for limb salvage and preservation of function. Although good quality saphenous vein offers the most durable conduit for reconstruction, 5-year failure rates are 30-50% and have remained largely unchanged for the past two decades. The majority of these failures occur within the first year of implantation, which is regarded as the most biologically active time during which the vein graft adapts to the arterial environment. Although intimal hyperplasia is generally regarded as the primary culprit of vein graft failure, geometric remodeling of the healing vein graft has recently emerged as a potentially significant contributing factor. While hemodynamic forces, including an increase in shear stress and wall tension, are undoubtedly central to the magnitude and direction of vein graft remodeling, we have determined that these forces alone cannot account for the extent of variability noted in early remodeling patterns. Therefore, we hypothesize that circulating factors, such as mediators of inflammation, may modulate the vein graft response to mechanical forces. This article reviews the definition and diagnosis of vein graft failure and summarizes our current efforts to understand the mechanisms of normal and abnormal vein graft adaptation to the arterial environment.
Evidence for Two Catalytically Independent Clusters of Active Sites in a Functional Modular Polyketide Synthase (1996)

Modular polyketide synthases (PKSs), such as the 6-deoxyerythronolide B synthase (DEBS), catalyze the biosynthesis of structurally complex and medicinally important natural products. These large multifunctional enzymes are organized into "modules", where each module contains active sites homologous to those of higher eucaryotic fatty acid synthases (FASs). Like FASs, modular PKSs are known to be dimers. Here we provide functional evidence for the existence of two catalytically independent clusters of active sites within a modular PKS. In three bimodular derivatives of DEBS, the ketosynthase domain of module 1 (KS-1) or module 2 (KS-2) or the acyl carrier protein domain of module 2 (ACP-2) was inactivated via site-directed mutagenesis. As expected, the purified proteins were unable to catalyze polyketide synthesis (although the KS-1 mutant could convert a diketide thioester into the predicted triketide lactone). Remarkably however, the KS-1/KS-2 and the KS-2/ACP-2 mutant pairs could efficiently complement each other and catalyze polyketide formation. In contrast, the KS-1 and ACP-2 mutants did not complement each other. On the basis of these and other results, a model is proposed in which the individual modules of a PKS dimer form head-to-tail homodimers, thereby generating two equivalent and independent clusters of active sites for polyketide biosynthesis. Specifically, each subunit contributes half of the KS and ACP domains in each cluster. A similar complementation approach should also be useful in dissecting the organization of the remaining types of active sites within this family of multienzyme assemblies. Finally, blocked systems, such as the KS-1 mutant described here, present a new strategy for the noncompetitive conversion of unnatural substrates into polyketides by modular PKSs.
A Stereochemically Well-Defined Rhodium(III) Catalyst for Asymmetric Transfer Hydrogenation of Ketones (2005)

[reaction: see text] A rhodium(III) catalyst for asymmetric transfer hydrogenation of ketones has been designed. The incorporation of a tethering group between the diamino group and the cyclopentadienyl unit provides extra stereochemical rigidity. The catalyst is capable of enantioselective reduction of a range of ketones in excellent ee using formic acid/triethylamine as both the solvent and the reducing agent.
Recombinant HMG1 Protein Produced in Pichia pastoris : A Nonviral Gene Delivery Agent (1997)

This paper describes the production of a recombinant protein from the expression system based on the methylotrophic yeast Pichia pastoris. Efficient production of rat high-mobility-group 1 (HMG1) protein was obtained using the system. Two forms of HMG1 were secreted into the culture medium: a 24.5-kDa species corresponding to the native HMG1 and a 32-kDa glycosylated derivative. Non-glycosylated recombinant HMG1 was purified easily and shown to possess the same DNA-binding properties as HMG1 purified from calf thymus. Plasmid DNA complexed to the recombinant HMG1 is taken up by a variety of mammalian cells in culture. Transient expression of a luciferase reporter gene was observed. Under selective conditions, stable expression of a neomycin gene was established as a result of integration into the genome. HMG1-mediated gene delivery was as efficient as calcium phosphate-mediated transfection but without associated cell damage. In addition, stable transfectants obtained after selection for G418 resistance usually integrated only one copy of the transfected DNA in contrast to the high unpredictable number obtained by the calcium phosphate method. HMG1 transfection complexes were not toxic to cultured cells, even at high concentrations.
ISC, a Novel Group of Bacterial and Archaeal DNA Transposons That Encode Cas9 Homologs (2015)

Cas9 endonucleases, the effectors of type II CRISPR-Cas systems, represent the new generation of genome-engineering tools. Here, we describe in detail a novel family of transposable elements that encode the likely ancestors of Cas9 and outline the evolutionary scenario connecting different varieties of these transposons and Cas9.
Bone marrow angiogenesis and mast cell density increase simultaneously with progression of human multiple myeloma (1999)

Immunohistochemical, cytochemical and ultrastructural data showing vivid angiogenesis and numerous mast cells (MCs) in the bone marrow of 24 patients with active multiple myeloma (MM) compared with 34 patients with non-active MM and 22 patients with monoclonal gammopathy of undetermined significance (MGUS) led us to hypothesize that angiogenesis parallels progression of MM, and that MCs participate in its induction via angiogenic factors in their secretory granules.
Dendronized fluorosurfactant for highly stable water-in-fluorinated oil emulsions with minimal inter-droplet transfer of small molecules (2019)

Fluorosurfactant-stabilized microfluidic droplets are widely used as pico- to nanoliter volume reactors in chemistry and biology. However, current surfactants cannot completely prevent inter-droplet transfer of small organic molecules encapsulated or produced inside the droplets. In addition, the microdroplets typically coalesce at temperatures higher than 80 °C. Therefore, the use of droplet-based platforms for ultrahigh-throughput combination drug screening and polymerase chain reaction (PCR)-based rare mutation detection has been limited. Here, we provide insights into designing surfactants that form robust microdroplets with improved stability and resistance to inter-droplet transfer. We used a panel of dendritic oligo-glycerol-based surfactants to demonstrate that a high degree of inter- and intramolecular hydrogen bonding, as well as the dendritic architecture, contribute to high droplet stability in PCR thermal cycling and minimize inter-droplet transfer of the water-soluble fluorescent dye sodium fluorescein salt and the drug doxycycline.
A Delaunay-Based Method for Surface Approximation (1983)

This paper describes a method for constructing a surface representation model from a given set of data points.A Triangulated Irregular. Network has been chosen as data structure, thus representing the surface as a set of contiguous non -overlapping and irregurarly shaped triangular facets.The proposed method makes use of a Delaunay triangular grid adapted to non-convex domains. Using only representative subsets of the given set of points, the method allows the construction of approximating surfaces which rest within a predefined tolerance.
Grassmannian beamforming for multiple-input multiple-output wireless systems (2003)

Transmit beamforming and receive combining are simple methods for exploiting the significant diversity that is available in multiple-input multiple-output (MIMO) wireless systems. Unfortunately, optimal performance requires either complete channel knowledge or knowledge of the optimal beamforming vector; both are hard to realize. In this article, a quantized maximum signal-to-noise ratio (SNR) beamforming technique is proposed where the receiver only sends the label of the best beamforming vector in a predetermined codebook to the transmitter. By using the distribution of the optimal beamforming vector in independent and identically distributed Rayleigh fading matrix channels, the codebook design problem is solved and related to the problem of Grassmannian line packing. The proposed design criterion is flexible enough to allow for side constraints on the codebook vectors. Bounds on the codebook size are derived to guarantee full diversity order. Results on the density of Grassmannian line packings are derived and used to develop bounds on the codebook size given a capacity or SNR loss. Monte Carlo simulations are presented that compare the probability of error for different quantization strategies.
Bayesian blind marginal separation of convolutively mixed discrete sources (2002)

We formulate the discrete source separation problem in a Bayesian framework. We show that it is possible to integrate analytically the so called nuisance parameters, leading to an analytic expression of the marginal posterior distribution of the symbols conditional upon the observations. We present two algorithms, a deterministic algorithm and stochastic algorithm, that allow one to optimize the marginal posterior distribution. We present simulation results and draw some conclusions.
Morphometric analysis and classification of the facial phenotype associated with fetal alcohol syndrome in 5‐ and 12‐year‐old children (2009)

Landmark-based morphometric analysis holds promise for quantitative assessment of craniofacial dysmorphology. We describe an application of facial shape analysis to characterize the facial anomalies associated with fetal alcohol syndrome (FAS) in a mixed ancestry population. Generalized Procrustes analysis, regression and discriminant function analysis were applied to stereo-photogrammetrically derived 3D coordinates of landmarks taken from 34 subjects (n = 17 FAS and n = 17 normal controls). Four shape analyses were carried out, namely a comparison of the FAS and control facial shapes at age 5, and one at age 12; a comparison of the FAS facial shapes at ages 5 and 12; and a comparison of control facial shapes at ages 5 and 12. The first two analyses showed that the FAS face is characterized by small palpebral fissures, a thin upper lip, and midfacial hypoplasia. Classification of subjects as having FAS using leave-one-out cross-validation showed that the 5-year-old group could be classified with 95.46% accuracy and the 12-year-olds with 80.13% accuracy. The third and fourth analyses revealed that the differences in facial shape between FAS individuals in different age groups were more pronounced than for control individuals, supporting the notion that FAS facial anomalies diminish with age. Geometric morphometric analysis of stereo-photogrammetrically derived 3D facial landmarks allows visualization of the facial anomalies associated with FAS, as well as classification of facial shapes.
Automated and Integrated System for High-Throughput DNA Genotyping Directly from Blood (1999)

An automated and integrated system for DNA typing directly from blood samples has been developed. The multiplexed eight-array system is based on capillary microfluidics and capillary array electrophoresis. Three short-tandem-repeat loci, vWA, THO1, and TPOX, are coamplified simultaneously in a fused-silica capillary by a hot-air thermocycler. Blood is directly used as the sample for polymerase chain reaction (PCR) without any pretreatment. Modifications of standard protocols are necessary for direct PCR from blood. A programmable syringe pump plus a set of multiplexed liquid nitrogen freeze/thaw switching valves are employed for liquid handling in the fluid distribution network. The system fully integrates sample loading, PCR, addition of an absolute standard, on-line injection of sample and standards, separation and detection. The genotypes from blood samples can be clearly identified in eight parallel channels when the electropherograms are compared with that of the standard allelic ladder by itself. Regeneration and cleaning of the entire system prior to subsequent runs are also integrated into the instrument. The instrumentation is compatible with future expansion to hundreds of capillaries to achieve even higher throughput.
Assessing Probability of Ancestry Using Simple Sequence Repeat Profiles: Applications to Maize Hybrids and Inbreds (2002)

Determination of parentage is fundamental to the study of biology and to applications such as the identification of pedigrees. Limitations to studies of parentage have stemmed from the use of an insufficient number of hypervariable loci and mismatches of alleles that can be caused by mutation or by laboratory error and that can generate false exclusions. Furthermore, most studies of parentage have been limited to comparisons of small numbers of specific parent-progeny triplets thereby precluding large-scale surveys of candidates where there may be no prior knowledge of parentage. We present an algorithm that can determine probability of parentage in circumstances where there is no prior knowledge of pedigree and that is robust in the face of missing data or mistyped data. We present data from 54 maize hybrids and 586 maize inbreds that were profiled using 195 SSR loci including simulations of additional levels of missing and mistyped data to demonstrate the utility and flexibility of this algorithm.
Insulator-based dielectrophoresis with β-galactosidase in nanostructured devices (2014)

Insulator-based dielectrophoresis (iDEP) has been explored as a powerful analytical technique in recent years. Unlike with larger entities such as cells, bacteria or organelles, the mechanism of iDEP transport of proteins remains little explored. In this work, we extended the pool of proteins investigated with iDEP in nanostructured devices with β-galactosidase. Our work indicates that β-galactosidase shows concentration due to negative DEP which we compare to DEP response of immunoglobulin G (IgG) encapsulated in micelles also showing negative DEP. Experimental observations are further compared with numerical simulations to elucidate the influence of electrokinetic transport and the magnitude of DEP mobility. Numerical simulations suggest that the DEP mobility calculated using the classical model underestimates the actual contribution of DEP on the experimentally monitored concentration effect of proteins. Moreover, we observed a unique voltage dependent β-galactosidase concentration which we attribute to an additional factor influencing the protein concentration at the nanoconstrictions, namely ion concentration polarization. Our work aids in understanding factors influencing protein iDEP transport which is required for the future development of protein preconcentration or separation methods based on iDEP.
Designing Touch Screen Numeric Keypads: Effects of Finger Size, Key Size, and Key Spacing (1997)

Designing numeric keypads for point-of-sale devices to optimize keying speed and accuracy while efficiently utilizing touch screen real estate is a challenge. Existing design guidelines for touch screens are applicable to only specific classes of devices and fail to consider user variables such as finger size. The present study investigated keying speed and error rates for various keypad configurations in a simulated retail keying task. Finger sizes were taken into account. Results support the use of compressed (2 mm or less) interkey spacing in keypad designs. No significant effects of key size were found. Gender differences in keying speed and accuracy were explained by finger size differences between males and females. Implications for the design of touch screen user interfaces in point-of-sale applications are discussed.
The chemokine receptors CXCR3 and CCR5 mark subsets of T cells associated with certain inflammatory reactions. (1998)

T cells infiltrating inflammatory sites are usually of the activated/memory type. The precise mechanism for the positioning of these cells within tissues is unclear. Adhesion molecules certainly play a role; however, the intricate control of cell migration appears to be mediated by numerous chemokines and their receptors. Particularly important chemokines for activated/memory T cells are the CXCR3 ligands IP-10 and Mig and the CCR5 ligands RANTES, macrophage inflammatory protein-1alpha, and macrophage inflammatory protein-1beta. We raised anti-CXCR3 mAbs and were able to detect high levels of CXCR3 expression on activated T cells. Surprisingly, a proportion of circulating blood T cells, B cells, and natural killer cells also expressed CXCR3. CCR5 showed a similar expression pattern as CXCR3, but was expressed on fewer circulating T cells. Blood T cells expressing CXCR3 (and CCR5) were mostly CD45RO+, and generally expressed high levels of beta1 integrins. This phenotype resembled that of T cells infiltrating inflammatory lesions. Immunostaining of T cells in rheumatoid arthritis synovial fluid confirmed that virtually all such T cells expressed CXCR3 and approximately 80% expressed CCR5, representing high enrichment over levels of CXCR3+ and CCR5+ T cells in blood, 35 and 15%, respectively. Analysis by immunohistochemistry of various inflamed tissues gave comparable findings in that virtually all T cells within the lesions expressed CXCR3, particularly in perivascular regions, whereas far fewer T cells within normal lymph nodes expressed CXCR3 or CCR5. These results demonstrate that the chemokine receptor CXCR3 and CCR5 are markers for T cells associated with certain inflammatory reactions, particularly TH-1 type reactions. Moreover, CXCR3 and CCR5 appear to identify subsets of T cells in blood with a predilection for homing to these sites.
Physics and applications of aligned carbon nanotubes (2011)

Ever since the discovery of carbon nanotubes (CNTs) by Iijima in 1991, there have been extensive research efforts on their synthesis, physics, electronics, chemistry, and applications due to the fact that CNTs were predicted to have extraordinary physical, mechanical, chemical, optical, and electronic properties. Among the various forms of CNTs, single-walled and multi-walled, random and aligned, semiconducting and metallic, aligned CNTs are especially important since fundamental physics studies and many important applications will not be possible without alignment. Even though there have been significant endeavors on growing CNTs in an aligned configuration since their discovery, little success had been realized before our first report on growing individually aligned CNTs on various substrates by plasma-enhanced chemical vapor deposition (PECVD) [Science 282 (1998) 1105–1108]. Our report spearheaded a new field on growth, characterization, physics, and applications of aligned CNTs. Up to now, there have been thousands of scientific publications on synthesizing, studying, and utilizing aligned CNTs in various aspects. In this communication, we review the current status of aligned CNTs, the physics for their alignment, their applications in field emission, optical antennas, subwavelength light transmission in CNT-based nanocoax structures, nanocoax arrays for novel solar cell structures, etc. The focus of this review is to examine various aligned CNT systems, either as an individual or as an array, either the orientation is vertical, parallel, or at other angles to the substrate horizon, either the CNT core structures are mostly hollow channels or are composed of complex compartments. Major fabrication methods are illustrated in detail, particularly the most widely used PECVD growth technique on which various device integration schemes are based, followed by applications whereas current limitations and challenges will also be discussed to lay down the foundation for future developments.
The Cellular Labile Iron Pool and Intracellular Ferritin in K562 Cells (1999)

The labile iron pool (LIP) harbors the metabolically active and regulatory forms of cellular iron. We assessed the role of intracellular ferritin in the maintenance of intracellular LIP levels. Treating K562 cells with the permeant chelator isonicotinoyl salicylaldehyde hydrazone reduced the LIP from 0.8 to 0.2 μmol/L, as monitored by the metalo-sensing probe calcein. When cells were reincubated in serum-free and chelator-free medium, the LIP partially recovered in a complex pattern. The first component of the LIP to reappear was relatively small and occurred within 1 hour, whereas the second was larger and relatively slow to occur, paralleling the decline in intracellular ferritin level (t½= 8 hours). Protease inhibitors such as leupeptin suppressed both the changes in ferritin levels and cellular LIP recovery after chelation. The changes in the LIP were also inversely reflected in the activity of iron regulatory protein (IRP). The 2 ferritin subunits, H and L, behaved qualitatively similarly in response to long-term treatments with the iron chelator deferoxamine, although L-ferritin declined more rapidly, resulting in a 4-fold higher H/L-ferritin ratio. The decline in L-ferritin, but not H-ferritin, was partially attenuated by the lysosomotrophic agent, chloroquine; on the other hand, antiproteases inhibited the degradation of both subunits to the same extent. These findings indicate that, after acute LIP depletion with fast-acting chelators, iron can be mobilized into the LIP from intracellular sources. The underlying mechanisms can be kinetically analyzed into components associated with fast release from accessible cellular sources and slow release from cytosolic ferritin via proteolysis. Because these iron forms are known to be redox-active, our studies are important for understanding the biological effects of cellular iron chelation.