gebhart/patrepeval huggingface dataset:
Mechanics of the Nucleus (2011)

The nucleus is the distinguishing feature of eukaryotic cells. Until recently, it was often considered simply as a unique compartment containing the genetic information of the cell and associated machinery, without much attention to its structure and mechanical properties. This article provides compelling examples that illustrate how specific nuclear structures are associated with important cellular functions, and how defects in nuclear mechanics can cause a multitude of human diseases. During differentiation, embryonic stem cells modify their nuclear envelope composition and chromatin structure, resulting in stiffer nuclei that reflect decreased transcriptional plasticity. In contrast, neutrophils have evolved characteristic lobulated nuclei that increase their physical plasticity, enabling passage through narrow tissue spaces in their response to inflammation. Research on diverse cell types further demonstrates how induced nuclear deformations during cellular compression or stretch can modulate cellular function. Pathological examples of disturbed nuclear mechanics include the many diseases caused by mutations in the nuclear envelope proteins lamin A/C and associated proteins, as well as cancer cells that are often characterized by abnormal nuclear morphology. In this article, we will focus on determining the functional relationship between nuclear mechanics and cellular (dys-)function, describing the molecular changes associated with physiological and pathological examples, the resulting defects in nuclear mechanics, and the effects on cellular function. New insights into the close relationship between nuclear mechanics and cellular organization and function will yield a better understanding of normal biology and will offer new clues into therapeutic approaches to the various diseases associated with defective nuclear mechanics.
Fusion proteins containing a minimal G Pl-attachment signal are apically expressed in transfected MDCK cells (1991)

We have shown that addition of the C-terminal 37 amino acids of decay-accelerating factor (DAF) to secretory proteins leads to glycosyl-phosphatidyl-inositol (GPI) anchoring and apical surface expression in MDCK cells. Theoretically, transferred apical sorting information may reside in the glycolipid-anchor moiety or the DAF sequence (9 amino acids) that remains after signal cleavage and GPI attachment. We show here that removal of eight of these nine remaining amino acids, thereby creating a minimal GPI-attachment signal, results in apical expression of GPI-anchored human growth hormone. These data argue that the apical sorting information conveyed by the C terminus of DAF is related to its ability to direct GPI attachment, rather than to a specific sequence that remains in the fusion protein.
Cardioprotective effects of cyclosporine A in an <i>in vivo </i>model of myocardial ischemia and reperfusion (2007)

CsA reduced the cardiac damage associated with ischemia-reperfusion injury of the heart. The cardioprotective effects of CsA might be associated with the protection of mitochondria and the inhibition of caspase-3 activity. It also suggests that the MPTP might play an important role in cardiomyocytes death after ischemia-reperfusion injury.
A Study on the Possible Causes of China’s Trade Deficits with South Korea after Their Establishment of Diplomatic Relations (2009)

The trend of globalization since the early 1990s has had a profound impact on trade relations between China and South Korea. It affected these two countries in positive ways, and brought Sino-Korean trade to its highest level since the establishment of diplomatic relations on August 24, 1992. Sino-Korean trade, as the scale of its growth and development accelerated, was also exposed to and encountered various problems. Among those problems, the most important and urgent problem to be solved was that in Sino-Korea trade, the deficit on the China side has continued to increase. This paper focuses on analyzing the causes of this problem.
Plasma-treated PET surfaces improve the biocompatibility of human endothelial cells (2000)

Failures of small internal diameter vascular grafts have been caused by the lack of a stable endothelial lining to form on their artificial surfaces. Polymer surfaces can be optimized by means of proper treatment to allow a homogeneous and uniform coverage in artificial prosthesis applications. Several solutions were studied to improve cell attachment and growth on artificial materials. In the present study, polyethyleneterephthalate (PET) surfaces were treated by plasma processes with oxygen and ammonia and also in the presence of a gas mixture to verify the effect of functional groups grafting onto the endothelial cell growth. Related surface chemical modifications were investigated by X-ray photoelectron spectroscopy (XPS). Then using cytotoxicity and cytocompatibility tests, the biocompatibility of the modified PET surfaces was assessed by studying the behavior of human umbilical vein endothelial cells (HUVEC). The results showed that plasma-treated PET samples have no toxic effect on HUVEC. The cytocompatibility tests revealed an increase in cell growth with incubation time and the presence of well-spread and flattened cells (SEM analyses). Thus it is reported that plasma treatments can improve PET biocompatibility to HUVEC.
Role of Glutathione S-Transferase Omega Gene Polymorphisms in Breast-Cancer Risk (2009)

The results of the study suggest that GSTO1 and GSTO2 variants are not associated with breast cancer risk, but that wild-type GSTO1 (A140/A140) is likely among cases at an advanced stage.
Overview of spent fuel burnup measurements (1991)

The purpose of this paper is to provide a summary of the principal factors that influence burnup measurement accuracy, and the manner in which different combinations of these factors in any particular application influence the achievable accuracy in that application. The principal focus of the paper is on the passive measurement of various burnup indicators. This paper also provides a general background for four subsequent papers which discuss burnup measurement in two particular applications: for burnup credit in spent fuel shipping casks; and for safeguards purposes. This paper provides a basis for comparing these two applications in terms that directly relate to the measurement process.
Jacobson et al. 2018 Cell Host Microbe 16S rRNA gene sequencing data (2018)

These are the raw DNA sequencing files and corresponding metadata for the 16S rRNA sequencing analyzed in Jacobson et al. 2018
Genetically modified enterotoxigenic <i>Escherichia coli</i> vaccines induce mucosal immune responses without inflammation (2007)

Genetically modified ETEC vaccines are safe and induce significant mucosal IgA responses to important colonisation factors. Mucosal IgA responses were clearly seen in WGLF, which is useful for evaluating oral vaccines.
Phase I/IIa Clinical Trial of Therapeutic Angiogenesis Using Hepatocyte Growth Factor Gene Transfer to Treat Critical Limb Ischemia (2010)

Intramuscular injection of naked HGF plasmid is safe and feasible and can achieve successful improvement of ischemic limbs as sole therapy.
Internet starter kit for Macintosh (1993)

System requirements for computer disk: Macintosh computer; System 7.0 or higher; high-density floppy disk drive; modem
Towards peptide formation inside the channels of a new divinylaniline-bridged periodic mesoporous organosilica (2010)

The first synthesis of a new highly ordered divinylaniline-bridged periodic mesoporous organosilica (PMO) with crystal-like pore walls and further chemical modification of the amino groups on the inner surface of the product by a peptide formation reaction with a chiral amino acid are reported.
NDRG2 is a new HIF-1 Target Gene Necessary for Hypoxia-Induced Apoptosis in A549 Cells (2008)

The NDRG2 gene belongs to a family of N-Myc downstream-regulated genes (NDRGs) and is expressed in many normal tissues. NDRG2 gene expression has been shown to be regulated in the stress response of certain cells. However, its function is not yet fully understood. Many studies have demonstrated that hypoxia, one of the stress responses, induced apoptosis in several cell types. In the current study, we investigated NDRG2 involvement in hypoxia response and found that NDRG2 expression was markedly up-regulated in several tumor cell lines exposed to hypoxic conditions or similar stresses at the mRNA and protein level. We also observed that the expression of NDRG2 was regulated by Hypoxia-inducible factor 1 (HIF-1) in tumor cells under hypoxia. Three hypoxia-responsive elements (HREs) in the NDRG2 promoter were identified. HRE1 could directly bind Hif-1 in vivo. Importantly, we found that silencing or enforcing the expression of NDRG2 could strongly inhibit or increase apoptosis. In addition, our data also showed that Ndrg2 was able to be translocated from the cytoplasm to the nucleus, and the segment from 101 to 178 amino acids of Ndrg2 is responsible for its translocation. Taken together, this study suggests that NDRG2 is a Hif-1 target gene and closely related with hypoxia-induced apoptosis in A549 cells.
Interleukin 1B gene polymorphism is associated with baseline C-reactive protein levels in healthy individuals. (2004)

C-reactive protein (CRP) is a sensitive marker of inflammation induced by both IL-6 and IL-1. Thus, genetic variation in these genes could be associated with the variety in C-reactive protein levels, and therefore with the severity of the entire inflammatory response. Even a subtle elevation in baseline CRP levels in healthy individuals has been found to significantly increase the risk for cardiovascular diseases. Therefore, to find out the possible role of pro-inflammatory cytokines in CRP baseline regulation we conducted a study of 338 healthy blood donors whose CRP levels were determined and whose single nucleotide polymorphisms of IL1A(C/T)-889, IL1B(C/T)-511, IL1B(C/T) + 3954, IL6(G/C)-174 and ILRN (a VNTR) both genotyped and haplotyped. The data revealed an association between CRP levels and the IL1B + 3954 genotype. Also, the bilocus haplotype IL1B-511*1/IL1B + 3954*2 was more frequent in subjects with below median CRP levels (< 0.72 mg/l), and composite genotype analysis of IL1B-511/IL1B + 3954 supported this finding. Our findings suggest that in healthy people, basal CRP levels are regulated by IL1B but not by IL6 genetics.
Imaging Expression of the Human Somatostatin Receptor Subtype-2 Reporter Gene with <sup>68</sup>Ga-DOTATOC (2010)

68Ga-DOTATOC is an excellent specific ligand for this hSSTr2 reporter system and for hSSTr2 reporter gene PET. Because DOTATOC has undergone extensive clinical testing, this human reporter system has the potential for translation to human studies.
Kinetic Mechanism of Quinone Oxidoreductase 2 and Its Inhibition by the Antimalarial Quinolines (2004)

Quinone oxidoreductase 2 (QR2) purified from human red blood cells was recently shown to be a potential target of the quinoline antimalarial compounds [Graves et al., (2002) Mol. Pharmacol. 62, 1364]. QR2 catalyzes the two-electron reduction of menadione via the oxidation of N-alkylated or N-ribosylated nicotinamides. To investigate the mechanism and consequences of inhibition of QR2 by the quinolines further, we have used steady-state and transient-state kinetics to define the mechanism of QR2. Importantly, we have shown that QR2 when isolated from an overproducing strain of E. coli is kinetically equivalent to the enzyme from the native human red blood cell source. We observe ping-pong kinetics consistent with one substrate/inhibitor binding site that shows selectivity for the oxidation state of the FAD cofactor, suggesting that selective inhibition of the liver versus red blood cell forms of malaria may be possible. The reductant N-methyldihydronicotinamide and the inhibitor primaquine bind exclusively to the oxidized enzyme. In contrast, the inhibitors quinacrine and chloroquine bind exclusively to the reduced enzyme. The quinone substrate menadione, on the other hand, binds nonspecifically to both forms of the enzyme. Single-turnover kinetics of the reductive half-reaction are chemically and kinetically competent and confirm the inhibitor selectivity seen in the steady-state experiments. Our studies shed light on the possible in vivo potency of the quinolines and provide a foundation for future studies aimed at creating more potent QR2 inhibitors and at understanding the physiological significance of QR2.
Stress-engineered spatially selective self-assembly of strained InAs quantum dots on nonplanar patterned GaAs(001) substrates (1998)

The lattice-mismatch stress-induced two-dimensional-to-three-dimensional morphology change is combined with interfacet adatom migration to selectively assemble parallel chains of InAs islands on top of [11̄0] oriented stripe mesas of sub-100-nm widths on GaAs(001) substrates. On such mesa stripes, prepared in situ via size-reducing epitaxy, deposition of InAs amounts subcritical for island formation on planar GaAs (001) is shown to allow self-assembly of three, two, and single chains of InAs three-dimensional island quantum dots selectively on the stripe mesa tops for widths decreasing from 100 nm down to 30 nm.
SDFog: A Software Defined Computing Architecture for QoS Aware Service Orchestration over Edge Devices (2016)

Cloud computing revolutionized the information technology (IT) industry by offering dynamic and infinite scaling, on-demand resources and utility-oriented usage. However, recent changes in user traffic and requirements have exposed the shortcomings of cloud computing, particularly the inability to deliver real-time responses and handle massive surge in data volumes. Fog computing, that brings back partial computation load from the cloud to the edge devices, is envisioned to be the next big change in computing, and has the potential to address these challenges. Being a highly distributed, loosely coupled and still in the emerging phase, standardization, quality-of-service management and dynamic adaptability are the key challenges faced by fog computing research fraternity today. This article aims to address these issues by proposing a service-oriented middleware that leverages the convergence of cloud and fog computing along with software defined networking (SDN) and network function virtualization (NFV) to achieve the aforementioned goals. The proposed system, called "Software Defined Fog" (SDFog), abstracts connected entities as services and allows applications to orchestrate these services with end-to-end QoS requirements. A use-case showing the necessity of such a middleware has been presented to show the efficacy of the SDN-based QoS control over the Fog. This article aims at developing an integrated system to realize the software-defined control over fog infrastructure.
Study of gate contact over active area (2014)

In this paper, analog and digital low-voltage MOSFETs having the gate contact over Shallow Trench Isolation (reference layout) or over active area (innovative layout) are studied. Using electrical parameters measurements, Linear Ramp Voltage Stress and Hot Carrier Injection stress, we demonstrate that moving the gate contact over active area does not degrade the performances and reliability of studied devices whatever the device area or oxide thickness (down to 2.1nm), and hence, could be a relevant solution in order to reduce the CMOS device area.
Proximity Tracking on Time-Evolving Bipartite Graphs (2008)

Given an author-conference network that evolves over time, which are the conferences that a given author is most closely related with, and how do they change over time? Large time-evolving bipartite graphs appear in many settings, such as social networks, co-citations, market-basket analysis, and collaborative filtering. Our goal is to monitor (i) the centrality of an individual node (e.g., who are the most important authors?); and (ii) the proximity of two nodes or sets of nodes (e.g., who are the most important authors with respect to a particular conference?) Moreover, we want to do this efficiently and incrementally, and to provide “any-time” answers. We propose pTrack and cTrack, which are based on random walk with restart, and use powerful matrix tools. Experiments on real data show that our methods are effective and efficient: the mining results agree with intuition; and we achieve up to 15∼176 times speed-up, without any quality loss.
Phase III Randomized Trial of Bisphosphonates as Adjuvant Therapy in Breast Cancer: S0307 (2019)

We found no evidence of differences in efficacy by type of bisphosphonate, either in overall analysis or subgroups. Despite an increased rate of osteonecrosis of the jaw with zoledronic acid, overall toxicity grade differed little across arms. Given that patients expressed preference for oral formulation, efforts to make oral agents available in the United States should be considered.
Synthesis, Characterization and Properties of Novel Poly(urethane‐imide) Networks as Electrical Insulators with Improved Thermal Stability (2006)

Abstract Summary: A new series of thermoplastic poly(urethane‐imide)s (TPUI1‐4) containing hydroxyl groups in the backbone was synthesized from the reaction of epoxy‐terminated polyurethane prepolymers (EPU1‐4) and an imide containing diacid (DIDA) chain extender under optimized reaction conditions. EPU1‐4 was prepared through end‐functionalization of NCO‐terminated polyurethanes based on polyester polyol (CAPA) and hexamethylene diisocyanate with glycidol. A blocked isocyanate (BIC) was made from the reaction of trimethylol propane (TMP), toluene diisocyanate (TDI) and N ‐methylaniline (NMA). Polymer networks were prepared from the reaction of librated isocyanate groups of BIC with hydroxyl groups of TPUIs. The starting materials and polymers were characterized by conventional spectroscopic methods and the physical, thermal and electrical properties of crosslinked networks were studied. Investigation of the recorded properties for these samples showed considerable improvement in thermal and electrical properties in comparison to common polyurethanes. Synthetic route for preparation of TPUIs. magnified image Synthetic route for preparation of TPUIs.
PHOTOSENSITIZED OXIDATION IN THE OCULAR LENS: EVIDENCE FOR PHOTOSENSITIZERS ENDOGENOUS TO THE HUMAN LENS (1981)

Abstract— Numerous investigators have attempted to associate near UV light exposure with various changes which occur to lens crystallins during aging and cataractogenesis. Recently we have shown in vitro that singlet oxygen mediated oxidation of lens crystallins produces effects very similar to those documented for crystallins from old or cataractous lenses and suggested that near UV photodynamic effects may play a major role in vivo in aging in the human lens. In the present work we demonstrate that certain oxidation products of tryptophan which have been identified in human lens can act as near UV photosensitizers, producing singlet oxygen. The insoluble protein fraction from human cataracts is shown to have the capacity to act as a photosensitizer. An age‐related increase in photosensitizing capacity is also demonstrated in the soluble crystallins from human lens. These findings are discussed with respect to development of pigmented nuclear cataracts.
Optimizing datacenter power with memory system levers for guaranteed quality-of-service (2012)

Co-location of applications is a proven technique to improve hardware utilization. Recent advances in virtualization have made co-location of independent applications on shared hardware a common scenario in datacenters. Co-location, while maintaining Quality-of-Service (QoS) for each application is a complex problem that is fast gaining relevance for these datacenters. The problem is exacerbated by the need for effective resource utilization at datacenter scales. In this work, we show that the memory system is a primary bottleneck in many workloads and is a more effective focal point when enforcing QoS. We examine four different memory system levers to enforce QoS: two that have been previously proposed, and two novel levers. We compare the effectiveness of each lever in minimizing power and resource needs, while enforcing QoS guarantees. We also evaluate the effectiveness of combining various levers and show that this combined approach can yield power reductions of up to 28%.
Reactivity of aryl and heteroaryl azides with vinylsilane and alkynylsilane. Formation of C-silylated 1,2,3-triazolines and 1,2,3-triazoles (1991)

The reactions of the silylated dipolarophiles trimethyl(vinyl)silane, trimethoxy(vinyl)silane and (trimethylsilyl)acetylene, with some para-substituted phenyl azides, 2-azidobenzo[b]thiophene (2-BTA) and 3-azidobenzo[b]thiophene (3-BTA) have been examined. At room temperature these reactions give the respective 1-substituted 4-silylated-1,2,3-triazoline. However, only the reactions of 4-nitrophenyl and 4-cyanophenyl azide occur smoothly, furnishing triazolines in high yields; similar reactions with phenyl, 4-tolyl, 4-methoxyphenyl and 4-chlorophenyl azide are slower, affording mixtures of a 3-(N-arylamino)methyl-3,5-bis(trimethylsilyl)-1-pyrazoline, arising from the primary triazoline adduct through ring-opening to diazo compounds 2, and the corresponding 1-aryl-2-(trimethylsilyl)aziridine, resulting from nitrogen extrusion from the same elusive triazoline. On the other hand reactions of 2-BTA and 3-BTA involve rapid extrusion of nitrogen to afford exclusively the corresponding 1-(benzo(b)thienyl)-2-silylated aziridine.Results suggest that all these azides generally undergo 1,3-dipolar cycloadditions to terminally silylated alkenes to give triazoline adducts with the same geometrical orientation and whose thermal behaviour was found to be strongly dependent on the activating or deactivating effects exerted by N-1 substituents.Suitable support for electronic and steric factors acting in the same direction in the orientations of the former cyclo-ANAE adducts has been provided by the observation that the same aryl azides, 2-BTA and 3-BTA exhibit analogous 1,3-dipolar cycloadditions with (trimethylsilyl) acetylene from which stable 1-aryl(or heteroaryl)-4-trimethylsilyl-1,2,3-triazoles are obtained in quantitative yields.
Clinical Studies of Antisense Oligonucleotides for Cancer Therapy (2004)

Until now, the clinical demise of cancer has relied on surgical resection and the inhibition of tumor cell proliferation using ionizing radiation or chemotherapeutic drugs designed to perturb DNA synthesis or the mitotic event. The development of cytotoxic agents has resulted in improvements in the treatment of leukemia, lymphoma, testicular cancer, and many other solid tumor types (). Hormone-based drugs have also been useful for breast and prostate cancers (). Although much success has been achieved, cytotoxic modalities walk the therapeutic tightrope of toxicities to normal tissues vs cancer cells, and drug resistance is generally present de novo or develops with treatment. Over the last decade or so, more attention has been focused on different therapeutic approaches. These include the development of monoclonal antibodies (MAbs) to specifically target cancer cells, and small molecule-inhibitors of cell-signaling pathways that have been linked to oncogenesis or maintenance of the malignant phenotype. For example, the former approach has seen the development and licensing of Herceptin® (trastuzumab; Genentech/Roche), a humanized MAb that targets erbB2/HER2, a receptor tyrosine kinase that is overexpressed in some 30% of breast cancers and has shown promising clinical activity when used in combination with other drugs for the treatment of metastatic breast cancer (, , ). Promising small-molecule inhibitors of cell-signaling pathways include Gleevec™ (STI571, imitanib mesylate; Novartis) and Iressa™ (ZD1839, gefitinib; AstraZeneca).