gebhart/patrepeval huggingface dataset:
A Water Relations Analysis of Seed Germination Rates (1990)

Seed germination culminates in the initiation of embryo growth and the resumption of water uptake after imbibition. Previous applications of cell growth models to describe seed germination have focused on the inhibition of radicle growth rates at reduced water potential (Psi). An alternative approach is presented, based upon the timing of radicle emergence, to characterize the relationship of seed germination rates to Psi. Using only three parameters, a ;hydrotime constant' and the mean and standard deviation in minimum or base Psi among seeds in the population, germination time courses can be predicted at any Psi, or normalized to a common time scale equal to that of seeds germinating in water. The rate of germination of lettuce (Lactuca sativa L. cv Empire) seeds, either intact or with the endosperm envelope cut, increased linearly with embryo turgor. The endosperm presented little physical resistance to radicle growth at the time of radicle emergence, but its presence markedly delayed germination. The length of the lag period after imbibition before radicle emergence is related to the time required for weakening of the endosperm, and not to the generation of additional turgor in the embryo. The rate of endosperm weakening is sensitive to Psi or turgor.
Crawling caenorhabditis elegans spermatozoa contact the substrate only by their pseudopods and contain 2‐nm filaments (1983)

Abstract The locomotion of C. elegans spermatozoa resembles, in many respects, the crawling movements of other eukaryotic cells. However, these sperm contain surprising little actin, which plays no apparent role in this cell's motility. Electron microscopy has revealed that crawling spermatozoa retain a strict morphological polarity so that the organelle‐filled cell body is separated from the pseudopod by an array of cytoplasmic laminar membranes. When sperm crawl only the pseudopod contacts the substrate; the cell body is either pulled behind or carried on top of the rear portion of the pseudopod. Fingerlike projections which extend forward from the leading edge of the pseudopod initiate contact with the substrate. The underside of the pseudopod exhibits areas of close (40 nm separation) membrane‐substrate association with intervening areas of wide (up to 300 nm) membrane‐substrate gaps. The pseudopod cytoplasm contains 2‐nm filaments but no filamentous actin has been observed. These 2‐nm filaments were detected in thin sections of crawling cells and in negative‐stained remnants of spermatozoa disrupted by either hypotonic buffer on Triton X‐100. The filaments are found both free in the cytoplasm and closely associated with the cytoplasmic face of the plasma membrane and are usually oriented along the long axis of the cell. Neither the identity nor the function of these filaments has been established although their location and orientation suggest that they may be involved in generating propulsion.
Partitioning graphs to speedup Dijkstra's algorithm (2007)

We study an acceleration method for point-to-point shortest-path computations in large and sparse directed graphs with given nonnegative arc weights. The acceleration method is called the arc-flag approach and is based on Dijkstra's algorithm. In the arc-flag approach, we allow a preprocessing of the network data to generate additional information, which is then used to speedup shortest-path queries. In the preprocessing phase, the graph is divided into regions and information is gathered on whether an arc is on a shortest path into a given region. The arc-flag method combined with an appropriate partitioning and a bidirected search achieves an average speedup factor of more than 500 compared to the standard algorithm of Dijkstra on large networks (1 million nodes, 2.5 million arcs). This combination narrows down the search space of Dijkstra's algorithm to almost the size of the corresponding shortest path for long-distance shortest-path queries. We conduct an experimental study that evaluates which partitionings are best suited for the arc-flag method. In particular, we examine partitioning algorithms from computational geometry and a multiway arc separator partitioning. The evaluation was done on German road networks. The impact of different partitions on the speedup of the shortest path algorithm are compared. Furthermore, we present an extension of the speedup technique to multiple levels of partitions. With this multilevel variant, the same speedup factors can be achieved with smaller space requirements. It can, therefore, be seen as a compression of the precomputed data that preserves the correctness of the computed shortest paths.
Androgen deprivation promotes neuroendocrine differentiation and angiogenesis through CREB-EZH2-TSP1 pathway in prostate cancers (2018)

The incidence of aggressive neuroendocrine prostate cancers (NEPC) related to androgen-deprivation therapy (ADT) is rising. NEPC is still poorly understood, such as its neuroendocrine differentiation (NED) and angiogenic phenotypes. Here we reveal that NED and angiogenesis are molecularly connected through EZH2 (enhancer of zeste homolog 2). NED and angiogenesis are both regulated by ADT-activated CREB (cAMP response element-binding protein) that in turn enhances EZH2 activity. We also uncover anti-angiogenic factor TSP1 (thrombospondin-1, THBS1) as a direct target of EZH2 epigenetic repression. TSP1 is downregulated in advanced prostate cancer patient samples and negatively correlates with NE markers and EZH2. Furthermore, castration activates the CREB/EZH2 axis, concordantly affecting TSP1, angiogenesis and NE phenotypes in tumor xenografts. Notably, repressing CREB inhibits the CREB/EZH2 axis, tumor growth, NED, and angiogenesis in vivo. Taken together, we elucidate a new critical pathway, consisting of CREB/EZH2/TSP1, underlying ADT-enhanced NED and angiogenesis during prostate cancer progression.
Part 4A. Morphological and biochemical markers (1998)

Rochefort, H; Laurent, V; Farnoud, R; Liaudet, E; Rey, J-M; Lemamy, G; Derocq, D; Rougeot, C; Roger, P; Petitjean, C; Proux, L; Garcia, MAuthor Information
Online Regularization by Denoising with Applications to Phase Retrieval (2019)

Regularization by denoising (RED) is a powerful framework for solving imaging inverse problems. Most RED algorithms are iterative batch procedures, which limits their applicability to very large datasets. In this paper, we address this limitation by introducing a novel online RED (On-RED) algorithm, which processes a small subset of the data at a time. We establish the theoretical convergence of On-RED in convex settings and empirically discuss its effectiveness in non-convex ones by illustrating its applicability to phase retrieval. Our results suggest that On-RED is an effective alternative to the traditional RED algorithms when dealing with large datasets.
Outcomes of Shoulder Arthroplasty in Olmsted County, Minnesota (2006)

Most studies on shoulder arthroplasty include a diverse group of patients presenting to a tertiary care center. Little information is available regarding outcomes in a community setting. We reviewed 98 residents (110 shoulders) of Olmsted County, Minnesota who had shoulder arthroplasties from 1976 to 2000. There were 65 total shoulder arthroplasties and 45 humeral head replacements. The most common indications were osteoarthritis for total shoulder arthroplasties (48/65) and acute fracture for hemiarthroplasties (27/45). The Neer ratings were excellent or satisfactory in 92% of total shoulder arthroplasties and 56% of hemiarthroplasties. The 10-year survival rate was 96%. The mean postoperative active forward elevation was greater in patients who had a total shoulder arthroplasty (132 degrees) compared with a hemiarthroplasty (113 degrees), as was external rotation (total shoulder arthroplasties = 58 degrees, humeral head replacements = 38 degrees). The outcomes for total shoulder arthroplasty and hemiarthroplasty compared favorably with outcomes reported in the literature. There was a high rate of satisfactory or excellent results after total shoulder arthroplasty for osteoarthritis. Hemiarthroplasty offered less satisfactory results, most likely related to the use of this procedure for trauma. This information will assist the community surgeon in counseling patients and weighing the risks and benefits of a shoulder arthroplasty.
The SeaView security model (1990)

A multilevel database is intended to provide the security needed for database systems that contain data at a variety of classifications and serve a set of users having different clearances. A formal security model for such a system is described. The model is formulated in two layers, one corresponding to a reference monitor that enforces mandatory security, and the second an extension of the standard relational model defining multilevel relations and formalizing policies for labeling new and derived data, data consistency, and discretionary security. The model also defines application-independent properties for entity integrity, referential integrity, and polyinstantiation integrity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Lipid biomarkers for algal resistance to viral infection in the ocean (2023)

Marine viruses play a key role in regulating phytoplankton populations, greatly affecting the biogeochemical cycling of major nutrients in the ocean. Resistance to viral infection has been reported for various phytoplankton species under laboratory conditions. Nevertheless, the occurrence of resistant cells in natural populations is underexplored due to the lack of sensitive tools to detect these rare phenotypes. Consequently, our current understanding of the ecological importance of resistance and its underlying mechanisms is limited. Here, we sought to identify lipid biomarkers for the resistance of the bloom-forming alga <i>Emiliania huxleyi</i> to its specific virus, <i>E. huxleyi</i> virus (EhV). By applying an untargeted lipidomics approach, we identified a group of glycosphingolipid (GSL) biomarkers that characterize resistant <i>E. huxleyi</i> strains and were thus termed resistance-specific GSLs (resGSLs). Further, we detected these lipid biomarkers in <i>E. huxleyi</i> isolates collected from induced <i>E. huxleyi</i> blooms and in samples collected during an open-ocean <i>E. huxleyi</i> bloom, indicating that resistant cells predominantly occur during the demise phase of the bloom. Last, we show that the GSL composition of <i>E. huxleyi</i> cultures that recover following infection and gain resistance to the virus resembles that of resistant strains. These findings highlight the metabolic plasticity and coevolution of the GSL biosynthetic pathway and underscore its central part in this host-virus arms race.
Exploration of the versatility of ring opening metathesis polymerization: an approach for gaining access to low density polymeric aerogels (2012)

We report the preparation of low density polymeric aerogels using the ring opening metathesis polymerization (ROMP) approach to copolymerize dicyclopentadiene (DCPD) with norbornene-based monomers (NB-R) employing a first generation Grubbs' ruthenium-based catalyst. The ROMP approach offers an attractive synthetic method that enables the fabrication of low-density (0.02–0.05 g cm−3), uniform thickness aerogel coatings on non-planar substrates. First, we explore the effect of crosslinking in the polymer backbone on the uniformity of the gel coatings formed under shear by either adding a multi-norbornene based crosslinker (NBn-R) to increase, or linear NB-R comonomers to decrease, the degree of crosslinking, respectively. We observed that adding linear monomers dramatically improved the uniformity of the gel films which we attribute to cross-linking induced changes in the rheological properties at the gel point. Second, the copolymerization of DCPD and NB-R with a different pendant group also causes a significant change in the morphology of the PDCPD-based aerogels by modifying the lengths of the strands in the fibrous polymer network. The effect of NB-R addition on the pore structure of the aerogels is discussed in the context of a molecular and interparticle crosslinking model. Finally, (bis)iodo-norbornene was synthesized to demonstrate the feasibility to fabricate functionalized aerogels by using our copolymerization approach. Our results highlight the potential of the ROMP-based copolymerization approach as a facile and versatile route to functionalized low density polymeric aerogels.
Anti-Inflammatory Effects of Methanol Extract of Codium fragile in Lipopolysaccharide-Stimulated RAW 264.7 Cells (2011)

The methanol extract of Codium fragile (MECF) has been reported to possess bioactive properties such as antidegranulation in eosinophils, as well as anti-edema, antibacterial, and antiviral activities. However, little is known about the molecular effects of MECF on lipopolysaccharide (LPS)-induced inflammation. Therefore, we investigated whether MECF affects the expression of inflammatory mediators in LPS-stimulated RAW 264.7 cells. To evaluate the anti-inflammatory effects of MECF, the cells were pretreated with MECF for 1 hour and then cultured with LPS for 24 hours. Our results indicate that MECF significantly attenuated secretion of LPS-induced inflammatory mediators nitric oxide (NO), prostaglandin E(2) (PGE(2)), and tumor necrosis factor (TNF)-α in RAW 264.7 cells. Additionally, LPS-induced mRNA and protein expression of inducible NO synthase (iNOS), cyclooxygenase (COX)-2, and TNF-α was decreased by pretreatment with MECF. These data indicate that MECF attenuates the expression of these inflammatory mediators at the transcriptional level. Therefore, we also investigated the effects of MECF on nuclear factor-κB (NF-κB) activity, which may be an important transcriptional factor for regulating the expression of iNOS, COX-2, and TNF-α mRNA. Our results showed that MECF reduced LPS-induced NF-κB activity via the suppression of nuclear translocation of the p50 and p65 NF-κB subunits and degradation of inhibitor of κB. In conclusion, we propose that MECF treatment down-regulates the expression and secretion of LPS-induced inflammatory mediators by inhibiting NF-κB activity.
2013 ESC Guidelines on cardiac pacing and cardiac resynchronization therapy (2013)

The ESC Guidelines represent the views of the ESC and were arrived at after careful consideration of the available evidence at the time they were written. Health professionals are encouraged to take them fully into account when exercising their clinical judgement. The guidelines do not, however, override the individual responsibility of health professionals to make appropriate decisions in the circumstances of the individual patients, in consultation with that patient and, where appropriate and necessary, the patient's guardian or carer. It is also the health professional's responsibility to verify the rules and regulations applicable to drugs and devices at the time of prescription.
Enhancement of superconducting transition temperature in FeSe electric-double-layer transistor with multivalent ionic liquids (2018)

Electric-double-layer transistors (EDLTs), which consist of ionic liquids (IL) as gate dielectrics, have attracted keen interest owing to dramatic modulation of physical properties by high-density carrier accumulation and tuning. In this study, EDLTs based on the superconducting ultrathin FeSe film with multivalent ILs exhibit a great potential for improvement of physical properties at the interface charge accumulation layer. The superior superconducting property found in high-Tc FeSe-EDLT with divalent IL sheds new light on the importance of interface engineering via appropriate selection of ILs.
First realization of the piezoelectronic stress-based transduction device (2015)

We present the first realization of a monolithically integrated piezoelectronic transistor (PET), a new transduction-based computer switch which could potentially operate conventional computer logic at 1/50 the power requirements of current Si-based transistors (Chen 2014 Proc. IEEE ICICDT pp 1-4; Mamaluy et al 2014 Proc. IWCE pp 1-2). In PET operation, an input gate voltage expands a piezoelectric element (PE), transducing the input into a pressure pulse which compresses a piezoresistive element (PR). The PR resistance goes down, transducing the signal back to voltage and turning the switch 'on'. This transduction physics, in principle, allows fast, low-voltage operation. In this work, we address the processing challenges of integrating chemically incompatible PR and PE materials together within a surrounding cage against which the PR can be compressed. This proof-of-concept demonstration of a fully integrated, stand-alone PET device is a key step in the development path toward a fast, low-power very large scale integration technology.
Which diameter and angle rule provides optimal flow patterns in a coronary bifurcation (2012)

The branching angle and diameter ratio in epicardial coronary artery bifurcations are two important determinants of atherogenesis. Murray's cubed diameter law and bifurcation angle have been assumed to yield optimal flows through a bifurcation. In contrast, we have recently shown a 7/3 diameter law (HK diameter model), based on minimum energy hypothesis in an entire tree structure. Here, we derive a bifurcation angle rule corresponding to the HK diameter model and critically evaluate the streamline flow through HK and Murray-type bifurcations. The bifurcations from coronary casts were found to obey the HK diameter model and angle rule much more than Murray's model. A finite element model was used to investigate flow patterns for coronary artery bifurcations of various types. The inlet velocity and pressure boundary conditions were measured by ComboWire. Y-bifurcation of Murray type decreased wall shear stress-WSS (10%-40%) and created an increased oscillatory shear index-OSI in atherosclerosis-prone regions as compared with HK-type bifurcations. The HK-type bifurcations were found to have more optimal flow patterns (i.e., higher WSS and lower OSI) than Murray-type bifurcations which have been traditionally believed to be optimized. This study has implications for changes in bifurcation angles and diameters in percutaneous coronary intervention.
Broadband dipolar recoupling for magnetization transfer in solid-state NMR correlation spectroscopy (2008)

International audience
TP53INP1 overexpression in prostate cancer correlates with poor prognostic factors and is predictive of biological cancer relapse (2011)

TP53INP1 overexpression in PC seems to be a worse prognostic factor, particularly predictive of biological cancer relapse. Results in vitro suggest that TP53INP1 could be considered as a relevant target for potential specific therapy.
Abstract 4529: Self-assembled lipid-polymer hybrid nanoparticles for the sustained delivery of siRNA and the treatment of drug-resistant cancers. (2013)

Abstract RNA interference (RNAi), which can selectively knockdown target genes, has shown great potential in the treatment of various diseases including cancer. Thus far, numerous nanoparticle (NP) platforms such as lipoplex and polyplex have been developed to facilitate the safe and effective delivery of small interfering RNA (siRNA), which represents a major hurdle for the clinical applications of RNAi. Nevertheless, these NP systems lack the sustained siRNA release property, and thus can only induce transient gene silencing due to the short lifetime of siRNA. Therefore, the delivery of siRNA using controlled-release NPs would be necessary for achieving sustained gene silencing. Herein, we will present a novel NP platform for safe and effective siRNA delivery in a sustained manner, which can be developed through the self-assembly of biodegradable and biocompatible polymers and lipids. The lipid-polymer hybrid NPs show excellent in vitro knockdown efficacy at low doses of siRNA, and promising in vivo results for delivering siRNA to xenograft tumors. More importantly, these NPs can control the temporal release of siRNA, with the half-release time of ∼ 9 days, for sustained silencing of target gene expression. Results demonstrate that the luciferase expression is still less than 25% at day 7 when the lucifrease-expressed HeLa cells were transfected with the NPs containing 40 pmol anti-luciferase siRNA. As a comparison, the luciferase expression is largely recovered (∼ 80%) at day 7, after transfection with lipo2000-siRNA complexes. Furthermore, this NP platform has been applied to deliver anti-drug resistance siRNA (e.g., anti-PHB1) and chemotherapeutic drugs (e.g., taxanes) for the effective treatment of drug resistant cancers. We believe that the lipid-polymer hybrid NP platform with the property of sustained siRNA release could hold potential in both fundamental studies and clinical applications. Citation Format: Jinjun Shi, Yingjie Xu, Xiaoyang Xu, Alexander Votruba, Xi Zhu, Eric Pridgen, Zeyu Xiao, Robert Langer, Bruce R. Zetter, Omid C. Farokhzad. Self-assembled lipid-polymer hybrid nanoparticles for the sustained delivery of siRNA and the treatment of drug-resistant cancers. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4529. doi:10.1158/1538-7445.AM2013-4529
Development of the High Strain Composite Deployable Vector Sensor Payload for the AERO and VISTA Cubesat Missions (2023)

View Video Presentation: https://doi.org/10.2514/6.2023-2695.vid The Auroral Emissions Radio Observer (AERO) and Vector Interferometry Space Technology using AERO (VISTA) CubeSat missions will use two identical 6U CubeSats developed to measure HF auroral emissions from Low Earth Orbit for NASA's Space Mission Directorate (SMD) for Heliophysics. Each CubeSat employs a unique antenna, called a Vector Sensor Antenna (VSA), to measure all six electromagnetic degrees of freedom of incoming HF radiation via a combination of loop, dipole and monopole antennas. The VSA payload stows into a 13.7 cm by 8.7 cm by 11.5 cm volume within the 6U spacecraft, and through a series of deployments, makes a 4 m by 4 m by 2.3 m antenna array. The relatively large antenna element deployment from such a small initial volume is achieved using fiberglass composite tape springs which unroll to form the antenna elements. These tape springs fall into a class of structural elements called High Strain Composites (HCS), which are becoming more commonly used in space missions. This paper describes the development, testing and integration of the AERO-VISTA VSA payload second generation prototype.