gebhart/patrepeval huggingface dataset:
OPDA Has Key Role in Regulating Plant Susceptibility to the Root-Knot Nematode Meloidogyne hapla in Arabidopsis (2016)

Jasmonic acid (JA) is a plant hormone that plays important roles in regulating plant defenses against necrotrophic pathogens and herbivorous insects, but the role of JA in mediating the plant responses to root-knot nematodes has been unclear. Here we show that an application of either methyl jasmonate (MeJA) or the JA-mimic coronatine (COR) on <i>Arabidopsis</i> significantly reduced the number of galls caused by the root-knot nematode <i>Meloidogyne hapla</i>. Interestingly, the MeJA-induced resistance was independent of the JA-receptor COI1 (CORONATINE INSENSITIVE 1). The MeJA-treated plants accumulated the JA precursor <i>cis</i>-(+)-12-oxo-phytodienoic acid (OPDA) in addition to JA/JA-Isoleucine, indicating a positive feedback loop in JA biosynthesis. Using mutants in the JA-biosynthetic pathway, we found that plants deficient in the biosynthesis of JA and OPDA were hyper-susceptible to <i>M. hapla.</i> However, the <i>opr3</i> mutant, which cannot convert OPDA to JA, exhibited wild-type levels of nematode galling. In addition, mutants in the JA-biosynthesis and perception which lie downstream of <i>opr3</i> also displayed wild-type levels of galling. The data put OPR3 (OPDA reductase 3) as the branch point between hyper-susceptibility and wild-type like levels of disease. Overall, the data suggests that the JA precursor, OPDA, plays a role in regulating plant defense against nematodes.
Avoiding MEMS failures (2005)

As MEMS devices becomes more common, understanding their failure mechanisms has become critical. Failure mode and effect analysis provides a way of making the assessment of potential failures a systematic process.
High content 3D imaging method for quantitative characterization of organoid development and phenotype (2021)

ABSTRACT Quantitative analysis on a large number of organoids can provide meaningful information from the morphological variability observed in 3D organotypic cultures, called organoids. Yet, gathering statistics of growing organoids is currently limited by existing imaging methods and subsequent image analysis workflows that are either restricted to 2D, limited in resolution, or with a low throughput. Here, we present an automated high content imaging platform synergizing high density organoid cultures with 3D live light-sheet imaging. The platform is an add-on to a standard inverted microscope. We demonstrate our capacity to collect libraries of 3D images at a rate of 300 organoids per hour, enabling training of artificial intelligence-based algorithms to quantify the organoid morphogenetic organization at multiple scales with subcellular resolution. We validate our approach on different organotypic cell cultures (stem, primary, and cancer), and quantify the development of hundreds of neuroectoderm organoids (from human Embryonic Stem Cells) at cellular, multicellular and whole organoid scales.
Responsive liquid crystal polymer rods (2008)

In this dissertation I report on the successful fabrication of anisotropic liquid crystal polymer rods. These polymer rods demonstrated re-orientation by an applied external field. The polymer rods, 200 nm in diameter and a maximum of 60 mum in length, were produced by a template synthesis technique. A reactive liquid crystal monomer was filled into porous Anopore membranes which were used as a confining media. The liquid crystal monomer was polymerized by UV light while the liquid crystal remained in the nematic temperature range. The polymerization process permanently "freezes" the orientational order of the confined liquid crystal molecules, producing rods that are temperature independent after curing. The curing is kept in the nematic range to ensure proper orientational alignment in the pore of the membrane, where the responsive nature of the rods can be tailored by temperature, external fields, and/or surface treatments. The rods were suspended in low viscosity silicone oil and injected into indium tin oxide coated glass cells.;Both DC and AC electric fields were applied to the electro-optical glass cells, resulting in different types of rod movement. Switching times (time to change orientation from horizontal to vertical) has been observed to be as fast as 0.1 seconds and the threshold voltage has been as low as 5 volts. The switching times of the rods are mainly driven by the strength of the applied field and the molecular orientation of the rods. A model was used to describe the best case scenario of the rod structures and outlines that faster switching times are possible. Translational movement (moving vertical with the rod staying in the horizontal position) was also noted with the DC applied field. AC fields give different types of movement including rotational, vibrating, and swimming motions. The average rotational speed was found to vary linearly with the applied field strength, where the fastest speeds were at the highest field strength. Also, responsive rods were noted to move and push unresponsive rods in and out of the viewing area. The responsive rods are technologically important for possible electro-rheological fluids, magneto-rheological fluids, and components in microfluidic devices.
Network Representation Learning: Consolidation and Renewed Bearing (2019)

Graphs are a natural abstraction for many problems where nodes represent entities and edges represent a relationship across entities. An important area of research that has emerged over the last decade is the use of graphs as a vehicle for non-linear dimensionality reduction in a manner akin to previous efforts based on manifold learning with uses for downstream database processing, machine learning and visualization. In this systematic yet comprehensive experimental survey, we benchmark several popular network representation learning methods operating on two key tasks: link prediction and node classification. We examine the performance of 12 unsupervised embedding methods on 15 datasets. To the best of our knowledge, the scale of our study -- both in terms of the number of methods and number of datasets -- is the largest to date. Our results reveal several key insights about work-to-date in this space. First, we find that certain baseline methods (task-specific heuristics, as well as classic manifold methods) that have often been dismissed or are not considered by previous efforts can compete on certain types of datasets if they are tuned appropriately. Second, we find that recent methods based on matrix factorization offer a small but relatively consistent advantage over alternative methods (e.g., random-walk based methods) from a qualitative standpoint. Specifically, we find that MNMF, a community preserving embedding method, is the most competitive method for the link prediction task. While NetMF is the most competitive baseline for node classification. Third, no single method completely outperforms other embedding methods on both node classification and link prediction tasks. We also present several drill-down analysis that reveals settings under which certain algorithms perform well (e.g., the role of neighborhood context on performance) -- guiding the end-user.
Basic Study on Corrosion Controlling Mechanism of Nitrite Ion and Its Effectiveness in Concrete (2014)

Lithium nitrite injection method has been employed in recent years to prevent ASR due to the presence of lithium ion. Meanwhile, in the presence of nitrite ion, lithium nitrite is also expected to inhibit steel corrosion in concrete when water, oxygen and chloride ion may ingress through ASR-induced cracks. Consequently, lithium nitrite is applied to repair concrete section either combined in patching material or being a coating material. Despite of its widespread application, quite a few problems on corrosion-inhibiting mechanism of nitrite ion have not been fully understood yet. How to evaluate the effect of nitrite ion and its related risk of macro-cell corrosion is among them. Purpose of this study is to investigate the corrosion-inhibiting mechanism of nitrite ion based on polarization tests of steel bars corroded under various kinds of corrosion conditions. A further discussion on the application of nitrite ion is present upon the test results.
QPSK phase regeneration in saturated degenerate dual-pump phase sensitive amplifiers (2011)

A novel scheme exploiting saturation effects in fiber optical parametric amplifiers using a degenerate dual-pump phase sensitive configuration is proposed and analyzed. QPSK phase regeneration is numerically demonstrated in a nonlinear interferometer structure.
Thrombin-induced release of von Willebrand factor from endothelial cells is mediated by phospholipid methylation. Prostacyclin synthesis is independent of phospholipid methylation. (1984)

The biochemical events that lead to thrombin-stimulated release of von Willebrand factor and prostacyclin synthesis in cultured endothelial cells are examined. Treatment of human umbilical vein endothelial cells with thrombin results in an instantaneous increase in phospholipid methylation which can be blocked by 3-deazaadenosine, a methyltransferase inhibitor. 3-Deazaadenosine also blocks the thrombin-induced Ca2+ influx into endothelial cells and the release of von Willebrand factor, indicating that these processes are coupled. The phorbol ester 4 beta-phorbol 12-myristate 13-acetate (PMA) and the Ca2+ ionophore A23187 both bypass the phospholipid methylation and directly stimulate Ca2+ influx and von Willebrand factor release. In contrast to the stimulus-induced von Willebrand factor release, the thrombin-induced prostacyclin synthesis cannot be blocked by 3-deazaadenosine. Similarly, incubation of endothelial cells with EDTA has no influence on the thrombin-induced prostacyclin synthesis, and PMA has no stimulatory effect on prostacyclin synthesis. These observations indicate that thrombin induces different metabolic responses in endothelial cells: phospholipid methylation followed by a Ca2+ influx, which subsequently leads to release of von Willebrand factor, and liberation of arachidonic acid from phospholipids for prostacyclin formation, which is independent of phospholipid methylation and Ca2+ influx.
Secure lazy provisioning of virtual desktops to a portable storage device (2012)

It is the software and data stored on a 'personal computer' that makes it personal. These contents can be conveniently stored as a disk image on a server and made available on the users' personal storage as and when required through lazy provisioning. We describe a desktop virtualization system that allows users to securely execute virtual machines on untrusted physical machines. This system is enabled through a portable personal device which contains a bootloader in tamper-proof storage. The hypervisor and the virtual machines are securely provisioning from a trusted server. Blocks are cached on the local storage of the portable device after their first access through a copy-on-read driver. We show that a desktop OS can be started promptly using the system and that the subsequent user experience is close to that for a conventional machine.
An On-chip Homodyne Detector for Measuring Quantum States (2017)

Here we present the first quantum homodyne detector on a silicon chip. We demonstrate all of the characteristics required for detection of quantum states: high speed, signal-to-noise ratio, and common-mode rejection ratio.
Smart sensors and calibration standards for high precision metrology (2015)

The paper summarize the PTB activities in the field of silicon sensors for dimensional metrology especially roughness measurements and silicon calibration standards developed during the past ten years. A focus lies in the development of 2D silicon microprobes which enable roughness measurements in nozzles as small as 100 &mu;m in diameter. Moreover these microprobes offer the potential for very fast tactile measurements up to 15 mm/s due to their tiny mass and therefore small dynamic forces. When developing high precision tactile sensors care has to be taken, not to scratch the often soft surfaces. Small probing forces and well defined tip radii have to be used to avoid surface destruction. Thus probing force metrology and methods to determine the radius and form of probing tips have been developed. Silicon is the preferred material for the calibration of topography measuring instruments due to its excellent mechanical and thermal stability and due to the fabrication and structuring possibilities of silicon microtechnology. Depth setting standards, probing force setting standards, tip radius and tip form standards, reference springs and soft material testing artefacts will be presented.
ChemInform Abstract: Dihydroazamacrosphelides: Synthesis and Apoptosis Inducing Activities. (2012)

Abstract Compounds (II) and (VII) induce apoptosis on lymphoma cells although the activity is rather moderate.
Optimal Primaries (2013)

We analyze a model of US presidential primary elections for a given party. There are two candidates, one of whom is a higher quality candidate. Voters reside in m different states and receive noisy private information about the identity of the superior candidate. States vote in some order, and this order is chosen by a social planner. We provide conditions under which the ordering of the states that maximizes the probability that the higher quality candidate is elected is for states to vote in order from smallest to largest populations and most accurate private information to least accurate private information.
The Classroom and Teaching (2006)

This section offers a look at modeling of the 21st century knowledge era schools. These schools require adaptable space, flexible time, Internet access, student-teacher collaboration and teachers as role models.
Vitamin C inhibits p53‐induced senescence by preventing ROS generation and p38 MAPKinase activation (2008)

We previously reported that tumor cells expressing p53 increase intracellular levels of reactive oxygen species (ROS). In this study, we describe the inhibitory effect of L‐ascorbate (Vitamin C) on replicative senescence induced by a transient p53 over‐expression system using adenovirus vector in EJ human bladder carcinoma cells, lacking a functional p53. As a result, L‐ascorbate was found to inhibit p53‐induced senescence in human bladder cancer EJ cells. Moreover, the senescence‐like phenotype (SLP) induced by p53, which is morphological changes, and irreversible cell cycle arrest, was not observed in L‐ascorbate‐treated EJ cells. On the contrary, ascorbic acid did not significantly affect normal cell proliferation. We investigated the molecular mechanisms of the inhibitory effect of L‐ascorbate on the development of replicative senescence in EJ cells. We found that L‐ascorbate inhibit this p53‐induced ROS generation. Moreover, p38 kinase activated during p53‐induced senescence was not observed in L‐ascorbate‐treated EJ cells. Consistently, a chemical inhibitor of p38 kinase, SB203580 was found to inhibit p53‐induced senescence. Therefore, L‐ascorbate inhibits p53‐induced senescence by preventing ROS generation, which in turn leads to the activation of p38 MAPKinase. These results reveal the inhibitory mechanism of L‐ascorbate on cellular senescence.
Genealogical trees on the web (2008)

This paper presents an extensive study about the evolution of textual content on the Web, which shows how some new pages are created from scratch while others are created using already existing content. We show that a significant fraction of the Web is a byproduct of the latter case. We introduce the concept of Web genealogical tree, in which every page in a Web snapshot is classified into a component. We study in detail these components, characterizing the copies and identifying the relation between a source of content and a search engine, by comparing page relevance measures, documents returned by real queries performed in the past, and click-through data. We observe that sources of copies are more frequently returned by queries and more clicked than other documents.
Monolithic GaAs/AlGaAs <i>pin</i> MESFET photoreceiver using a single molecular beam epitaxy growth step (1993)

A monolithic pin/MESFET photoreceiver in the GaAs/AlGaAs system was investigated. The structure used a single epitaxial growth step in which the pin photodiode was grown on top of the MESFET. The photoreceivers exhibited flatband gains as high as 17 dB and bandwidths as high as 2.0 GHz.
Few shot clustering for indoor occupancy detection with extremely low-quality images from battery free cameras (2020)

Reliable detection of human occupancy in indoor environments is critical for various energy efficiency, security, and safety applications. We consider this challenge of occupancy detection using extremely low-quality, privacy-preserving images from low power image sensors. We propose a combined few shot learning and clustering algorithm to address this challenge that has very low commissioning and maintenance cost. While the few shot learning concept enables us to commission our system with a few labeled examples, the clustering step serves the purpose of online adaptation to changing imaging environment over time. Apart from validating and comparing our algorithm on benchmark datasets, we also demonstrate performance of our algorithm on streaming images collected from real homes using our novel battery free camera hardware.
The Effect of Contrast Material on Radiation Dose at CT: Part II. A Systematic Evaluation across 58 Patient Models (2017)

Purpose To estimate the radiation dose as a result of contrast medium administration in a typical abdominal computed tomographic (CT) examination across a library of contrast material-enhanced computational patient models. Materials and Methods In part II of this study, first, the technique described in part I of this study was applied to enhance the extended cardiac-torso models with patient-specific iodine-time profiles reflecting the administration of contrast material. Second, the patient models were deployed to assess the patient-specific organ dose as a function of time in a typical abdominal CT examination using Monte Carlo simulation. In this hypothesis-generating study, organ dose refers to the total energy deposited in the unit mass of the tissue inclusive of iodine. Third, a study was performed as a strategy to anticipate the biologically relevant dose (absorbed dose to tissue) in highly perfused organs such as the liver and kidney. The time-varying organ-dose increment values relative to those for unenhanced CT examinations were reported. Results The results from the patient models subjected to the injection protocol indicated up to a total 53%, 30%, 35%, 54%, 27%, 18%, 17%, and 24% increase in radiation dose delivered to the heart, spleen, liver, kidneys, stomach, colon, small intestine, and pancreas, respectively. The biologically relevant dose increase with respect to the dose at an unenhanced CT examination was in the range of 0%-18% increase for the liver and 27% for the kidney across 58 patient models. Conclusion The administration of contrast medium increases the total radiation dose. However, radiation dose, while relevant to be included in estimating the risk associated with contrast-enhanced CT, may still not fully characterize the total biologic effects. Therefore, given the fact that many CT diagnostic decisions would be impossible without the use of iodine, this study suggests the need to consider the effect of iodinated contrast material on the organ doses to patients undergoing CT studies when designing CT protocols. <sup>©</sup> RSNA, 2017 Online supplemental material is available for this article.
Computational drugs repositioning identifies inhibitors of oncogenic PI3K/AKT/P70S6K-dependent pathways among FDA-approved compounds (2016)

The discovery of inhibitors for oncogenic signalling pathways remains a key focus in modern oncology, based on personalized and targeted therapeutics. Computational drug repurposing via the analysis of FDA-approved drug network is becoming a very effective approach to identify therapeutic opportunities in cancer and other human diseases. Given that gene expression signatures can be associated with specific oncogenic mutations, we tested whether a "reverse" oncogene-specific signature might assist in the computational repositioning of inhibitors of oncogenic pathways. As a proof of principle, we focused on oncogenic PI3K-dependent signalling, a molecular pathway frequently driving cancer progression as well as raising resistance to anticancer-targeted therapies. We show that implementation of "reverse" oncogenic PI3K-dependent transcriptional signatures combined with interrogation of drug networks identified inhibitors of PI3K-dependent signalling among FDA-approved compounds. This led to repositioning of Niclosamide (Niclo) and Pyrvinium Pamoate (PP), two anthelmintic drugs, as inhibitors of oncogenic PI3K-dependent signalling. Niclo inhibited phosphorylation of P70S6K, while PP inhibited phosphorylation of AKT and P70S6K, which are downstream targets of PI3K. Anthelmintics inhibited oncogenic PI3K-dependent gene expression and showed a cytostatic effect in vitro and in mouse mammary gland. Lastly, PP inhibited the growth of breast cancer cells harbouring PI3K mutations. Our data indicate that drug repositioning by network analysis of oncogene-specific transcriptional signatures is an efficient strategy for identifying oncogenic pathway inhibitors among FDA-approved compounds. We propose that PP and Niclo should be further investigated as potential therapeutics for the treatment of tumors or diseases carrying the constitutive activation of the PI3K/P70S6K signalling axis.
Homeobox genes in the functioning of plant meristems (1995)

The maize homebox gene knotted1 (kn1) is expressed in vegetative and floral meristems and is down-regulated at the site of primordia formation. kn1-related genes from maize and other species also show meristem-specific expression and offer additional tools for studying the activities of shoot meristems. Members of this gene family are expressed early in embryogenesis, providing molecular markers for meristem initiation. Ectopic expression of either kn1 or a related Arabidopsis gene, KNAT1, causes dramatic alterations in Arabidopsis and tobacco leaf morphology. Most significantly, meristems form on the leaf, producing small shoots. We discuss whether the phenotypes can be interpreted as changes in positional information or timing of determination.
Task-Aware Feature Generation for Zero-Shot Compositional Learning (2019)

Visual concepts (e.g., red apple, big elephant) are often semantically compositional and each element of the compositions can be reused to construct novel concepts (e.g., red elephant). Compositional feature synthesis, which generates image feature distributions exploiting the semantic compositionality, is a promising approach to sample-efficient model generalization. In this work, we propose a task-aware feature generation (TFG) framework for compositional learning, which generates features of novel visual concepts by transferring knowledge from previously seen concepts. These synthetic features are then used to train a classifier to recognize novel concepts in a zero-shot manner. Our novel TFG design injects task-conditioned noise layer-by-layer, producing task-relevant variation at each level. We find the proposed generator design improves classification accuracy and sample efficiency. Our model establishes a new state of the art on three zero-shot compositional learning (ZSCL) benchmarks, outperforming the previous discriminative models by a large margin. Our model improves the performance of the prior arts by over 2x in the generalized ZSCL setting.