gebhart/patrepeval huggingface dataset:
Targeting anaplastic lymphoma kinase in neuroblastoma (2019)

Over the last decade, anaplastic lymphoma kinase ( ALK ), a receptor tyrosine kinase ( RTK ), has been identified as a fusion partner in a diverse variety of translocation events resulting in oncogenic signaling in many different cancer types. In tumors where the full‐length ALK RTK itself is mutated, such as neuroblastoma, the picture regarding the role of ALK as an oncogenic driver is less clear. Neuroblastoma is a complex and heterogeneous tumor that arises from the neural crest derived peripheral nervous system. Although high‐risk neuroblastoma is rare, it often relapses and becomes refractory to treatment. Thus, neuroblastoma accounts for 10–15% of all childhood cancer deaths. Since most cases are in children under the age of 2, understanding the role and regulation of ALK during neural crest development is an important goal in addressing neuroblastoma tumorigenesis. An impressive array of tyrosine kinase inhibitors ( TKI s) that act to inhibit ALK have been FDA approved for use in ALK ‐driven cancers. ALK TKI s bind differently within the ATP ‐binding pocket of the ALK kinase domain and have been associated with different resistance mutations within ALK itself that arise in response to therapeutic use, particularly in ALK ‐fusion positive non‐small cell lung cancer ( NSCLC ). This patient population has highlighted the importance of considering the relevant ALK TKI to be used for a given ALK mutant variant. In this review, we discuss ALK in neuroblastoma, as well as the use of ALK TKI s and other strategies to inhibit tumor growth. Current efforts combining novel approaches and increasing our understanding of the oncogenic role of ALK in neuroblastoma are aimed at improving the efficacy of ALK TKI s as precision medicine options in the clinic.
Human health consequences of environmentally‐modulated gene expression: potential roles of ELF–EMF induced epigenetic versus mutagenic mechanisms of disease (2000)

In order to determine if there might be biological and health consequences after exposures to extremely-low frequency electromagnetic fields (ELF–EMF), either experimentally or epidemiologically, mechanistic understanding of the potential means by which any environmental agent can affect cells in a multicellular organism has to be reviewed. The goal of this limited review is to demonstrate that, while the prevailing paradigm of the environmentally-induced acute and chronic diseases involves either cell killing (cytotoxicity) or gene/chromosome mutations (genotoxicity), alteration of the expression of genetic information at the transcriptional (turning genes “on” or “off”), translational (stabilizing or de-stabilizing the genetic message), or posttranslational (altering the gene product or protein) levels has the potential to contribute to various diseases. This latter mechanism, “epigenetic” toxicity, unlike the former two which are irreversible, is characterized by threshold-like action, multiple biochemical pathways and chronic, regular exposures to be effective. Ultimately, epigenetic toxicants affect one of four potential cell states, namely alteration of cell proliferation, cell differentiation, programmed cell death (apoptosis) or adaptive responses of differentiated cells. Bioelectromagnetics 21:402–406, 2000. © 2000 Wiley-Liss, Inc.
HIGH-DENSITY MAGNETIC RECORDING PROPERTIES OF EVAPORATED Co-Ni-O THIN FILM (1989)

The Co-Ni-O thin film formed by the CVI process has a columnar structure that slants diagonally in relation to the substrate. It is known that, for the reasons described above, the film has no easy-to-magnetize direction within the plane and that there is a directionality in output reproduction. [1], [2] The orientation of the easy-to-magnetize direction of Co-Ni-O thin film has been analyzed. The head has also been studied with the objective of fully exploiting the potential capability of the recording medium. In addition, a method for reducing magnetic noise, a problem involving the recording medium itself, has been discussed.
Thymic stroma is required for the development of human T cell lineages <i>in vitro</i> (1989)

Development of the T cell lineage is characterized by the homing of hematopoietic precursors to thymus, followed by their acquisition of receptors for antigen. T cell receptors are alpha beta or gamma delta heterodimers associated with CD3 (TCR-CD3). Very early T cell precursors in humans have been characterized as CD7+ 45+ cells which lack the T cell differentiation antigens CD1, CD2, CD3, CD4, and CD8. A phenotypically equivalent early thymocyte population also occurs in postnatal life, and we have previously shown that interleukin 2 (IL2) promotes the development in vitro of both the alpha beta and the gamma delta T cells from these early thymocytes. Here we have analyzed the requirements of the induction of the IL2 pathway in early thymocytes, and their developmental potential. We show that: (i) thymic stromal cells, which are present in thymocyte suspensions, are necessary to induce the IL2 pathway and the development of alpha beta or gamma delta T cell lineages from early thymocytes in vitro; and (ii) when removed from the in vivo environment, early thymocytes can develop in vitro into TCR-CD3- cells of the natural killer (NK) lineage. We conclude that CD7+ 45+, CD1-2-3-4-8- early thymocytes are multipotential progenitors that, at least, have the capacity to develop into alpha beta or gamma delta T cell and NK lineages. The analysis of the mechanisms of generation and selection of human T and NK cell diversity, not feasible in bone marrow cultures, is now possible.
Atomic Force Microscopy-Based Screening of Drug-Excipient Miscibility and Stability of Solid Dispersions (2010)

The presented results demonstrate that drug/polymer miscibility and stability of solid dispersions, with many mechanistic details, can be analyzed with Atomic Force Microscopy. The assay allows to identify well-miscible and stable combinations within hours or a few days.
Recombination-dependent replication of plasmids during bacteriophage T4 infection. (1988)

The replication of plasmids containing fragments of the T4 genome, but no phage replication origins, was analyzed as a possible model for phage secondary (recombination-dependent) replication initiation. The replication of such plasmids after T4 infection was reduced or eliminated by mutations in several phage genes (uvsY, uvsX, 46, 59, 39, and 52) that have previously been shown to be involved in secondary initiation. A series of plasmids that collectively contain about 60 kilobase pairs of the T4 genome were tested for replication after T4 infection. With the exception of those known to contain tertiary origins, every plasmid replicated in a uvsY-dependent fashion. Thus, there is no apparent requirement for an extensive nucleotide sequence in the uvsY-dependent plasmid replication. However, homology with the phage genome is required since the plasmid vector alone did not replicate after phage infection. The products of plasmid replication included long concatemeric molecules with as many as 35 tandem copies of plasmid sequence. The production of concatemers indicates that plasmid replication is an active process and not simply the result of passive replication after the integration of plasmids into the phage genome. We conclude that plasmids with homology to the T4 genome utilize the secondary initiation mechanism of the phage. This simple model system should be useful in elucidating the molecular mechanism of recombination-dependent DNA synthesis in phage T4.
Dimensioning analysis (1992)

article Free AccessDimensioning analysis: toward automatic understanding of engineering drawings Author: Dov Dori Technion-Israel Institute of Technology, Haifa, Israel Technion-Israel Institute of Technology, Haifa, IsraelView Profile Authors Info & Claims Communications of the ACMVolume 35Issue 10Oct. 1992 pp 92–103https://doi.org/10.1145/135239.135245Published:01 October 1992Publication History 26citation635DownloadsMetricsTotal Citations26Total Downloads635Last 12 Months30Last 6 weeks4 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Synthesis, characterization, and <i>in vivo</i> disposition of iodinatable polyethylene glycol derivatives: Differences <i>in vivo</i> as a function of chain length (1984)

Abstract A series of iodinatable water soluble polyethylene glycol (PEG) derivatives were prepared for use as model hydrophilic drugs. Polyethylene glycol diamine 6000 was coupled to methyl p ‐hydroxybenzimidate, and PEG 1900‐ and PEG 5000‐monomethyl ethers were coupled to tyramine and histamine. The derivatives underwent facile iodination with the chloramine‐T reaction and were stable under a wide range of conditions. The larger derivatives showed rapid renal clearance, but the 1900 MW compounds underwent significant clearance via the bile.
Role of Platelet Mitochondria: Life in a Nucleus-Free Zone (2019)

Platelets are abundant, small, anucleate circulating cells, serving many emerging pathophysiological roles beyond hemostasis; including active critical roles in thrombosis, injury response, and immunoregulation. In the absence of genomic DNA transcriptional regulation (no nucleus), platelets require strategic prepackaging of all the needed RNA and organelles from megakaryocytes, to sense stress (e.g., hyperglycemia), to protect themselves from stress (e.g., mitophagy), and to communicate a stress response to other cells (e.g., granule and microparticle release). Distinct from avian thrombocytes that have a nucleus, the absence of a nucleus allows the mammalian platelet to maintain its small size, permits morphological flexibility, and may improve speed and efficiency of protein expression in response to stress. In the absence of a nucleus, platelet lifespan of 7-10 days, is largely determined by the mitochondria. The packaging of 5-8 mitochondria is critical in aerobic respiration and yielding metabolic substrates needed for function and survival. Mitochondria damage or dysfunction, as observed with several disease processes, results in greatly attenuated platelet survival and increased risk for thrombovascular events. Here we provide insights into the emerging roles of platelets despite the lack of a nucleus, and the key role played by mitochondria in platelet function and survival both in health and disease.
Reactivity of Yttrium Quinoline–Imine–Phenoxide Complexes Towards Inter‐ and Intramolecular Alkyl Nucleophilic Attacks (2008)

Abstract Yttrium(III) chloride complexes [YCl 2 (NNO H )] ( 1 H ) and [YCl 2 (NNO Me )] ( 1 Me ) {NNO H = 2‐ tert ‐butyl‐6‐(quinolin‐8‐yliminomethyl)phenoxide; NNO Me = 2‐ tert ‐butyl‐6‐[(2‐methylquinolin‐8‐ylimino)methyl]phenoxide} were synthesized by treating a thf solution of YCl 3 at room temperature with the NNO H ‐H and NNO Me ‐H ligands {NNO H ‐H = 2‐ tert ‐butyl‐6‐(quinolin‐8‐yliminomethyl)phenol; NNO Me ‐H = 2‐ tert ‐butyl‐6‐[(2‐methylquinolin‐8‐ylimino)methyl]phenol}, which were previously deprotonated with potassium tert ‐butoxide or thallium ethoxide. Surprisingly, reaction of 1 H with the Grignard reagent MeMgBr to prepare the corresponding dialkyl derivative led to the formation of the tetranuclear magnesium dimer [Mg 2 BrCl{NN(Me)O H }(thf)] 2 {NN(Me)O H =2‐ tert ‐butyl‐6‐[1‐(quinolin‐8‐ylamido)ethyl]phenoxide} ( 2 ), whose structure was determined by single‐crystal X‐ray diffraction. By reacting the neutral ligand NNO H ‐H withY(CH 2 SiMe 3 ) 3 · 2thf in toluene at low temperature the alkyl complex [Y(CH 2 SiMe 3 ){NN(CH 2 SiMe 3 )O}(thf)] {NN(CH 2 SiMe 3 )O = 2‐ tert ‐butyl‐6‐[1‐(quinolin‐8‐ylamido)‐2‐trimethylsilanylethyl]phenoxide} ( 3 ) was isolated. The supposed reaction mechanism leading to the formation of 3 was simulated by using the PM6 Hamiltonian. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008)
Regulation of cognitive activity and early communication development in young autistic, mentally retarded, and young normal children (2001)

Based on the Piagetian framework, this study examined regulation of cognitive activity and developmental communication profiles and their interrelationship in groups of autistic, mentally retarded, and normal children of comparable overall, verbal, and oculo-manual developmental ages (from 6 to 24 months). Regulation of activity was assessed with both an object permanence test and an original behavior grid, and development of communication skills with the Guidetti-Tourrette scales (French adaptation of the Seibert-Hogan scales). The results showed evidence of certain types of dysregulation of cognitive activity and a general delay in communication ability in autistic children compared to the other two groups. Moreover, although the intensity of some of these disorders decreased in relation to the developmental levels of social interaction and joint attention in normal children, they were related to both high and low levels of development of social interaction only in autistic children. These findings raise the hypothesis of a relationship between a disorder of disengaging from an activity and developmental levels of social interaction noted at two transitory periods of early development (12 and 24 months) only in children with autism. Developmental and neuropsychological interpretations of this particular pattern are proposed.
Combating small molecule environmental contaminants: detection and sequestration using functional nucleic acids (2022)

Small molecule contaminants pose a significant threat to the environment and human health. While regulations are in place for allowed limits in many countries, detection and remediation of contaminants in more resource-limited settings and everyday environmental sources remains a challenge. Functional nucleic acids, including aptamers and DNA enzymes, have emerged as powerful options for addressing this challenge due to their ability to non-covalently interact with small molecule targets. The goal of this perspective is to outline recent efforts toward the selection of aptamers for small molecules and describe their subsequent implementation for environmental applications. Finally, we provide an outlook that addresses barriers that hinder these technologies from being widely adopted in field friendly settings and propose a path forward toward addressing these challenges.
Follicular stem cell marker PHLDA1 (TDAG51) is superior to cytokeratin‐20 in differentiating between trichoepithelioma and basal cell carcinoma in small biopsy specimens (2011)

Our results suggest that PHLDA1 represents a practical and easily used tool that can be applied to the differentiation of trichoepithelioma and basal cell carcinoma in small biopsy specimens. Rather than searching for CK20-positive Merkel cells, assessing PHLDA1 expression allows the differential diagnosis between trichoepithelioma and basal cell carcinoma to be solved at scanning magnification.
An integrated DSP-based architecture for FLIR optical scanning mirror calibration and control (1994)

A galvanometric optical scanner in a FLIR (forward looking infrared) system is controlled so as to adhere to a highly linear scan pattern using a DSP-based control architecture. Position sensor scale factor accuracy is calibrated with ten optical feedback loop, position-based FLIR imaging pulses are produced, and diagnostic self-test procedures are run, all with the same DSP used for position control.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Suppression of tumor growth via IGFBP3 depletion as a potential treatment in glioma (2019)

Our findings suggest IGFBP3 predicts poor outcome of glioma patients and is a potential therapeutic target for which depletion of its expression suppresses tumor growth through inducing apoptosis and accumulation of DNA damage in glioma cells.
Inductive query by examples (IQBE): a machine learning approach (1994)

This paper presents an incremental, inductive learning approach to query-by-examples for information retrieval (IR) and database management systems (DBMS). After briefly reviewing conventional information retrieval techniques and the prevailing database query paradigms, we introduce the ID5R algorithm, previously developed by Utgoff (1989), for "intelligent" and system-supported query processing.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
3D shape recovery from single image by using texture information (2008)

In this papaer, we propose a three-dimension shape recovery method that works with a single image without prior information about an image, a camera or a scene. Three-dimension shape recovery can be produced from the depth map that is generated from the convolution between the 2D planar image and the texture gradient image. The experimental results have been presented demonstrating the 3D image’s surfaces and the comparisons of cross-section images between the 3D model from the digitizer and our proposed method.
Tissue Engineering of Articular Cartilage with Biomimetic Zones (2009)

Articular cartilage damage is a persistent and increasing problem with the aging population, and treatments to achieve biological repair or restoration remain a challenge. Cartilage tissue engineering approaches have been investigated for over 20 years, but have yet to achieve the consistency and effectiveness for widespread clinical use. One of the potential reasons for this is that the engineered tissues do not have or establish the normal zonal organization of cells and extracellular matrix that appears critical for normal tissue function. A number of approaches are being taken currently to engineer tissue that more closely mimics the organization of native articular cartilage. This review focuses on the zonal organization of native articular cartilage, strategies being used to develop such organization, the reorganization that occurs after culture or implantation, and future prospects for the tissue engineering of articular cartilage with biomimetic zones.
High-precision shortest distance estimation for large-scale social networks (2016)

Over the past decades, many large-scale social network systems, such as Facebook and Twitter, have been deployed in different countries. How to efficiently analyze the topological characteristics of large-scale social networks has been a challenging problem in the research community. One of the critical topological characteristics is the shortest distance between two nodes in a network. The existing shortest distance algorithms, such as Breadth First Search (BFS), work well with small networks. For a network with billions of nodes, calculating the pairwise shortest distances with these algorithms requires an overlong period of time. In this paper, we present a high-precision ShOrtest Distance Approximation (SODA) scheme, which utilizes a small set of pre-calculated distances to estimate the shortest distance between each pair of nodes in large-scale social networks. Compared with the existing shortest distance estimation schemes for social networks, SODA leads to high estimation accuracy since it utilizes a novel optimization method, Robust Discrete Matrix Decomposition (RDMD), to eliminate the impact of significant errors/outliers and generate the coordinates of the nodes in a network simultaneously. In addition, SODA differentiates the asymmetric distances in directed graphs. Consequently, SODA works well with both directed and undirected social networks. Finally, SODA only involves convex optimization. Therefore, SODA is highly competitive in terms of computation complexity. Our experimental results indicate that SODA outperforms the state-of-the-art shortest distance estimation schemes in terms of estimation accuracy and running time.
Scalable and fault-tolerant network-on-chip design usingthe quartered recursive diagonal torus topology (2008)

Network-on-a-chip (NoC) is an effective approach to connect and manage the communication between the variety of design elements and intellectual property blocks required in large and complex system-on-chips. In this paper, we propose a new NoC architecture, referred as the Quartered Recursive Diagonal Torus (QRDT), which is constructed by overlaying diagonal torus. Due to its small diameter and rich routing recourses, QRDT is determined to be well suitable to construct highly scalable NoCs.
Mixed-Signal Neuromorphic Inference Accelerators: Recent Results and Future Prospects (2018)

Recent advances in dense, continuous-state nonvolatile memories have enabled extremely fast, compact, and energy-efficient analog and mixed-signal circuits. Such circuits are perfectly suited, in particular, for hardware implementations of the inference operation in advanced neuromorphic networks, which requires massive amounts of dot-product operations with low-to-medium precision. In this paper, we first review typical implementations of such mixed-signal circuits. We then describe some recent experimental demonstrations of prototype mixed-signal neuromorphic networks by our team, in particular, a mixed-signal inference accelerator with unprecedented speed and energy efficiency. The paper is concluded by outlining some urgently needed work, in particular the development of high-performance general-purpose inference accelerators, and discussing our preliminary results in this direction.
Anodic Aluminium Oxide Membranes Used for the Growth of Carbon Nanotubes (2009)

The suitability of anodic aluminum oxide (AAO) membranes as template supported on Si substrates for obtaining organized iron catalyst for carbon nanotube (CNT) growth has been investigated. The iron catalyst was confined in the holes of the AAO membrane. CVD synthesis with ethylene as carbon source led to a variety of carbon structures (nanotubes, helices, bamboo-like, etc). In absence of AAO membrane the catalyst was homogeneously distributed on the Si surface producing a high density of micron-length CNTs.
The language of Webkinz: Early childhood literacy in an online virtual world (2010)

In recent years there has been an explosion of virtual worlds intended for early childhood populations; however, because the majority of research on games and such worlds has focused on adults and adolescents, we know very little about these spaces. This article attempts to address this gap by providing a qualitative content analysis of the affordances that Webkinz World an online environment that as of March 2010 had over 3 million unique site visitors per month, offers for children’s literacy and language development. Analyses suggest that the site provides unique opportunities for immersion in literacy-rich contexts and academically-oriented practices that may enhance those that are readily available in many children’s daily lives. However, looking beyond the discrete linguistic and technical aspects of learning in Webkinz World reveals a designed culture with limitations on learning and a constrained set of literacies and social messages that warrant further critical exploration.
Convenient Synthesis of Tributylsilyl Methacrylate (2007)

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