gebhart/patrepeval huggingface dataset:
The TOPLESS Interactome: A Framework for Gene Repression in Arabidopsis     (2011)

Transcription factors activate or repress target gene expression or switch between activation and repression. In animals and yeast, Groucho/Tup1 corepressor proteins are recruited by diverse transcription factors to induce context-specific transcriptional repression. Two groups of Groucho/Tup1-like corepressors have been described in plants. LEUNIG and LEUNIG_HOMOLOG constitute one group and TOPLESS (TPL) and the four TPL-related (TPR) corepressors form the other. To discover the processes in which TPL and the TPR corepressors operate, high-throughput yeast two-hybrid approaches were used to identify interacting proteins. We found that TPL/TPR corepressors predominantly interact directly with specific transcription factors, many of which were previously implicated in transcriptional repression. The interacting transcription factors reveal that the TPL/TPR family has been coopted multiple times to modulate gene expression in diverse processes, including hormone signaling, stress responses, and the control of flowering time, for which we also show biological validation. The interaction data suggest novel mechanisms for the involvement of TPL/TPR corepressors in auxin and jasmonic acid signaling. A number of short repression domain (RD) sequences have previously been identified in Arabidopsis (Arabidopsis thaliana) transcription factors. All known RD sequences were enriched among the TPL/TPR interactors, and novel TPL-RD interactions were identified. We show that the presence of RD sequences is essential for TPL/TPR recruitment. These data provide a framework for TPL/TPR-dependent transcriptional repression. They allow for predictions about new repressive transcription factors, corepressor interactions, and repression mechanisms and identify a wide range of plant processes that utilize TPL/TPR-mediated gene repression.
A General and Practical Access to Chiral Quinoxalinones with Low Copper‐Catalyst Loading (2010)

Abstract A general, straightforward, and practical access to multi‐substituted chiral quinoxalin‐2‐ones has been achieved based on the copper(I) chloride‐dimethylethylenediamine (DMEDA) catalyst system. With the use of 1 mol% copper(I) chloride, structurally diverse quinoxalin‐2‐ones were generated with high optical purity from readily available starting materials, 2‐haloanilines and α‐amino acids, in a one‐pot manner.
Java Enterprise design patterns (2001)

Acknowledgments About the Author Chapter 1 Introduction to Software Patterns Description of Patterns Pattern Name Synopsis Context Forces Solution Consequences Implementation Known Uses Code Example Related Patterns A Very Brief History of Patterns Organization of This Book. Chapter 2 Overview of UML Class Diagram Collaboration Diagram Statechart Diagram Deployment Diagram Chapter 3 The Software Life Cycle Chapter 4 Transaction Patterns Acid Transaction Composite Transaction Two Phase Commit Audit Trail Chapter 5 Distributed Architecture Patterns Shared Object Object Request Broker Object Replication Redundant Independent Objects Prompt Repair Mobile Agent Demilitarized Zone Process Pairs Chapter 6 Distributed Computing Patterns Object Identifier Registry Protection Proxy Publish-Subscribe Retransmission Mailbox Heavyweight/Lightweight Heartbeat Connection Multiplexing Chapter 7 Concurrency Patterns Session Object Lock File Static Locking Order Optimistic Concurrency Thread Pool Ephemeral Cache Item Transaction State Stack. Chapter 8 Temporal Patterns Time Server Versioned Object Temporal Property Chapter 9 Database Patterns Persistence Layer CRUD Stale Object Type Conversion Is Dirty Lazy Retrieval Appendix A Persistence Framework Bibliography Index.
Use of Cement Kiln Dust for the Stabilization of Soils (2004)

Stabilization of soils is an effective method for improving soil properties and pavement system performance. Cement kiln dust (CKD) represents an alternative to the traditional stabilization agents of lime, cement, and Class C fly ash. As with the other additives, cement kiln dust can be expected to vary in effectiveness depending on the soil type. A total of eight different soils with classifications of CH, CL, ML, SM, and SP were subjected to a series of durability tests, including freeze-thaw, wet-dry, and leach testing, to evaluate the relative performance of CKD as a stabilization agent. Results were compared with previous findings for the same soils stabilized with lime, cement, and fly ash. Atterberg limits and strength tests were conducted before and after selected durability tests. Relative values of soil stiffness were also tracked over a 28-day curing period using the soil stiffness gauge to evaluate ongoing reactions. The results provide guidance on which soil types can be expected to have significant improvements in performance with the addition of CKD.
Container Architecture for Detection and Prevention of Intrusions using virtualization technique (2013)

Network Intrusion Detection Systems (IDSs) which are based on sophisticated algorithms rather than current signature-base detections are in demand. Web services have moved to a multi-tiered design wherein the webserver runs the application front-end logic and data are outsourced to a database or file server in order to enable communication and the management of personal information from anywhere. The proposed system is Container based Intrusion Detection System, an IDS system that models the network behavior of user sessions across both the front-end webserver and the back-end database. This system used to detect attacks in multi-tiered web services. Our approach can create normality models of isolated user sessions that include both the web front-end (HTTP) and back-end (File or SQL) network transactions. For websites that do not permit content modification from users, there is a direct causal relationship between the requests received by the front-end webserver and those generated for the database back end. Virtualization is used to isolate objects and enhance security performance. Lightweight containers can have considerable performance advantages over full virtualization containers.
The acid-sensitive potassium channel TASK-1 in rat cardiac muscle (2007)

Our results suggest that in rat cardiomyocytes I(TASK) makes a substantial contribution to the outward current flowing in the plateau range of potentials and that this current component can be inhibited via alpha1A-adrenergic receptors.
Small offset-voltage In/sub 0.49/Ga/sub 0.51/P/GaAs double-barrier bipolar transistor (1992)

In/sub 0.49/Ga/sub 0.51/P/GaAs double-barrier bipolar transistors (DBBTs) grown by gas-source molecular beam epitaxy (GSMBE) have been fabricated and measured. This structure has two InGaP barrier layers (100 AA in thickness): one is inserted between the emitter-base (e-b) junction and the other between the base-collector (b-c) junction. An offset voltage of 26 mV and a differential current gain of 120 at room temperature were obtained with a heavily doped p/sup +/ (2*10/sup 19/ cm/sup -3/) base (500 AA in thickness). The small offset voltage was attributed to the similar structure of the e-b and b-c junctions and to the suppression of the hole injection current into the collector by the InGaP hole barrier at the b-c junction.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The α and β Subunit of the Nascent Polypeptide-associated Complex Have Distinct Functions (2000)

Nascent polypeptide-associated complex (NAC) is probably the first cytosolic protein to contact nascent polypeptide chains emerging from ribosomes. In this way NAC prevents inappropriate interactions with other factors. Eventually other factors involved in targeting and folding, like the Signal Recognition Particle or cytosolic chaperones, must gain access to the nascent chain. All NAC preparations to date consist of two copurifying polypeptides. Here we rigorously show that these two polypeptides, termed alpha- and betaNAC, form a very stable complex in vivo and in vitro and that a functional complex can be reconstituted from the individual subunits. A dissection of the contributions of the individual subunits to NACs function revealed that both subunits are in direct contact with nascent polypeptide chains on the ribosome and that both contribute to the prevention of inappropriate interactions. However, betaNAC alone directly binds to the ribosome and is sufficient to prevent ribosome binding to the endoplasmic reticulum membrane.
On the road to OC-768 [optical carrier] (2001)

Optical fiber promises higher data rates, but first it must get around a few hurdles presented by physics. Optical networking's capacity is increasing in response to Web surfing, images attached to e-mail, and the development of remote-collaboration applications. All these applications consume significant amounts of bandwidth. Optical networking uses two basic methods to increase an optical fiber's transmission capacity. First, you can increase data transmission rates. Second, you can couple multiple wavelengths onto a single fiber. An obvious outgrowth of these two basic methods is to combine them by transmitting more quickly on individual wavelengths and packing more wavelengths onto a common optical fiber. In November 2000, Global Crossing teamed up with Lucent Technologies to upgrade a 70km fiber network in Belgium to a 40Gbps operating rate for an approximately one-week OC-768 field trial. Although the field trial produced promising results, an actual upgrade of the existing optical infrastructure might not occur for several years. This pessimism comes from several factors, most of which relate to physics The most significant problem arises from a simple fact of physics: As the data rate increases, pulses become narrower. Although the field trial indicated OC-768 can operate over modern optical fiber, the jury is still out on the effect of multiple wavelengths, each operating at 40 Gbps.
Expression of LGI1 Impairs Proliferation and Survival of HeLa Cells (2009)

The LGI1 gene was suggested to function as tumor suppressor for its ability to reduce malignant features of glioblastoma cells. In support to this proposal were the findings that overexpression of LGI1 in neuroblastoma cells inhibited proliferation and induced apoptosis. In this study we performed stable LGI1 expression in HeLa cells to examine whether the noxious effect of LGI1 might be extended to cancer cells of diverse origin. HeLa cell clones stably expressing LGI1 exhibited a significant impairment of proliferation and a consistent increase of cell death when compared with control cells lacking expression of LGI1. Expression of LGI1 increased the activity of apoptosis effectors caspase-3/7; furthermore it downregulated the antiapoptotic BCL2 gene and upregulated the proapoptotic BAX gene expression, suggesting that the cause of HeLa cells death might be an increased susceptibility to apoptosis induced by LGI1. The results suggested that LGI1 is capable to restrain growth and survival of adenocarcinoma cells such as HeLa.
Specific and heritable gene editing in <i>Arabidopsis</i> (2014)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Newly emerged African swine fever virus strain Belgium/Etalle/wb/2018: Complete genomic sequence and comparative analysis with reference p72 genotype II strains (2019)

In a new example of pathogens hopscotching the globe, African swine fever virus hit north-western Europe's wildlife in summer 2018, marking a further spread of a disease that had invaded Central and Eastern Europe recently. The complete genomic sequence of the Belgium/Etalle/wb/2018 virus is reported, with the hope it will provide a valuable tool for tracing geographical spread and biologic evolution of the virus.
Density of <i>Demodex folliculorum</i> in Patients Receiving Epidermal Growth Factor Receptor Inhibitors (2011)

EGFRI patients have an increased susceptibility to DF colonization or infection, respectively. Our results support the recent concept that EGFRI may induce an impairment of antimicrobial defense mechanisms.
Microassembly combining pick-and-place and water mist (2010)

This paper reports a novel and versatile hybrid microassembly technique that applies water mist on the surface of microparts to assist alignment of microchips. This technique combines the traditional robotic pick-and-place technique and self-assembly technique. Two different approaches are studied: 1) mist-last where a 200μm × 200μm × 70μm SU-8 chip is placed roughly on another chip of the same size using a microgripper and then water mist is delivered to achieve self-alignment; 2) mist-first where water mist is delivered before the releasing of a chip near the target. The second approach is further studied to examine the maximum tolerance of placement error and placement of chips on hydrophilic/hydrophobic patterns. The experimental results indicate the proposed technique is reliable and versatile for stacking and assembling microchips. a 200μm × 200μm × 70μm SU-8 chip was assembled on the top of another SU-8 chip of the same dimensions, where the success rate can reach 75% with bias as high as 180μm. Microparts of size 200μm × 200μm × 70μm can be successfully assembled on hydrophilic/hydrophobic patterns.
On the Code and Soft Capacity of the UMTS FDD Downlink and the Capacity Increase by using a Secondary Scrambling Code (2006)

The downlink capacity of a UMTS FDD network is limited by the number of available channelization codes (code capacity) and by the available NodeB transmit power (soft capacity). The channelization codes of one sector are taken from an OVSF tree such that the number of codes per spreading factor is equal to the spreading factor itself. In the case that the codes of the OVSF tree are already exploited and the required transmit power is still clearly below its maximum, it is possible to establish another OVSF tree by using a secondary scrambling code. In this paper we develop a Monte Carlo simulation model for comparing the code capacity with the soft capacity of a UMTS network with sectorization, soft and softer handover. Several factors of influence like the orthogonality factor, the user activity, or the codes and power that are reserved for the HSDPA are investigated. Additionally, the capacity increase by using a second OVSF tree with the secondary scrambling code is studied
Tetrathiafulvalene-Calix[4]pyrroles:  Synthesis, Anion Binding, and Electrochemical Properties (2006)

The syntheses of monotetrathiafulvalene-calix[4]pyrrole 5 and bistetrathiafulvalene-calix[4]pyrrole 6, prepared from the acid-catalyzed condensation of monopyrrolo[3,4-d]tetrathiafulvalene (MPTTF, 7) with acetone in the presence of tripyrrane 8 and dipyrromethane 9, respectively, are described. Compound 5 and the previously reported tetrathiafulvalene-calix[4]pyrrole 4 both adopt a 1,3-alternative conformation in the solid state, as determined from X-ray crystallographic analysis. The anion binding properties of the tetrathiafulvalene-calix[4]pyrroles 5 and 6, as well as those of the parent meso-octamethylcalix[4]pyrrole (1), were investigated in acetone using (1)H NMR spectroscopic and isothermal titration calorimetry (ITC) techniques and, within the error limits of the methods, were generally found to give concordant results. On the basis of the results of the ITC studies carried out in 1,2-dichloroethane, increasing the number of tetrathiafulvalene units annulated to the calix[4]pyrrole system serves to enhance the anion binding affinities substantially but at the price of lowered selectivity. Cyclic voltammetry (CV) studies, carried out in 1,2-dichloroethane, provided evidence of an anion-dependent electrochemical response with Cl(-) and Br(-) ions. This response was particularly dramatic in the case of the monotetrathiafulvalene-calix[4]pyrrole 5, with a DeltaE(max) of -145 mV being seen after the addition of approximately 1 equiv of Cl(-) ion.
Selective cortical neuronal damage after middle cerebral artery occlusion in rats. (1989)

We studied histopathologic changes in cerebral cortex of 20 rats after middle cerebral artery occlusion by using the Fink-Heimer suppressive silver impregnation method and conventional stains. At 6 hours after occlusion, Fink-Heimer-stained sections revealed abundant coarsely granular, intensely argyrophilic neurons in the ischemic cortex. These distinctive argyrophilic neurons could be clearly differentiated from neurons that suffered postmortem changes; argyrophilic neurons were present in all layers of the lateral parietal cortex but in only the superficial cortical layers II and III in the parasagittal area of the frontoparietal cortex and the temporo-occipital area. At 24 hours after occlusion as the ischemic region progressed to pannecrosis, argyrophilic neurons were still evident in peri-infarct regions, with more prominent neuritic silver deposits but no changes in number or spatial distribution. Over 2-7 days, the argyrophilic neurons gradually disappeared while many fine silver-impregnated degenerating terminals appeared in the peri-infarct regions. At 3-6 weeks after occlusion, no more argyrophilic neurons were seen in the cortex although degenerating axons were still present in the deep white matter. Our results indicate selective neuronal damage in the superficial cortical layers and massive axonal degeneration in the cerebrum surrounding infarcts. The neuronal damage does not appear to progress beyond 6 hours after middle cerebral artery occlusion. The Fink-Heimer method has many advantages over existing conventional stains for documenting selective neuronal damage in focal cerebral ischemia.
An analytical delay model for RLC interconnects (1996)

We develop an analytical delay model based on first and second moments to incorporate inductance effects into the delay estimate for interconnection lines. Delay estimates using our analytical model are within 15% of SPICE-computed delay across a wide range of interconnect parameter values. We also extend our delay model for estimation of source-sink delays in arbitrary interconnect trees. For the small tree topology considered, we observe improvements of at least 18% in the accuracy of delay estimates when compared to the Elmore model (which is independent of inductance), even though our estimates are as easy to compute as the Elmore delay. The speedup of delay estimation via our analytical model is several orders of magnitude when compared to a simulation methodology such as SPICE.
Pharmacologic antidotes to experimental doxorubicin skin toxicity: a suggested role for beta-adrenergic compounds. (1982)

Doxorubicin (ADM) skin toxicity is a serious complication of inadvertent perivenous drug infiltrations. In an attempt to attempt to identify possible antidotes, nine diverse pharmacologic agents were injected intradermally into the hair-free dorsum of BALB/c mice following an intradermal ADM dose of either 0.05 or 0.5 mg. Seven of the compounds were ineffective in reducing ADM-induced ulceration; the compounds included lidocaine, cimetidine, diphenhydramine, sodium heparin, hyaluronidase, N-acetylcysteine, and alpha-diphenhydramine, sodium heparin, hyaluronidase, N-acetylcysteine, and alpha-tocopherol. The latter five compounds actually increased ulceration induced by ADM (0.5 mg), especially N-acetylcysteine, which tripled the total toxic effect. Two opposing beta-adrenergic compounds, the antagonist propranolol and the agonist isoproterenol, reduced skin ulceration resulting from experimental treatment with intradermal ADM. A role for the beta-adrenergic receptor in mediating ADM-induced skin ulceration is suggested.
Chemokines in hematopoiesis (2008)

Chemokine-chemokine receptor interactions are important to hematopoiesis and immune cell function, two highly interactive processes. Recent studies have clarified the role of chemokines and their receptors in regulating hematopoiesis, and agents modulating chemokines are being evaluated in preclinical and clinical studies. Examples of such efforts include inhibition of CD26 for enhanced homing and engraftment of hematopoietic stem and progenitor cells, and the use of the SDF-1/CXCL12-CXCR4 antagonist, AMD3100 for mobilization of hematopoietic stem and progenitor cells and their use for stem cell transplantation.
Effects of indigo naturalis on colonic mucosal injuries and inflammation in rats with dextran sodium sulphate-induced ulcerative colitis (2017)

The effects of indigo naturalis (IN), which is a traditional Chinese herbal formulation, have been clinically demonstrated in treating refractory ulcerative colitis (UC). The present study aimed to verify the effects and mechanisms of IN in experimental UC rats. A total of 48 male Sprague-Dawley rats were randomly divided into six groups: Chow, model, high-dose IN, medium-dose IN, low-dose IN and mesalazine (a bowel-specific aminosalicylate drug) groups. The models were administered 3.5% dextran sodium sulphate solution for 7 days. The treatment groups were administered IN or mesalazine and then sacrificed and sampled on day 8. Disease activity index (DAI), histological damage score (HDS) and myeloperoxidase (MPO) activity were used to evaluate the severity of UC. Colon and serum cytokines were detected using liquid-phase chip technology and the expression of occludin protein in colonic mucosa was assessed by immunohistochemistry and western blot analysis. The results indicated that the oral administration of IN may reduce DAI, HDS and MPO activity. IN also reduced the expression of inflammatory cytokines and increased the expression of colonic mucosal repair-related cytokines and occludin protein. These results highlight the potential of IN as a therapeutic agent for treating UC through its action of inflammation control and colonic mucosal damage repair.
Identification of a subdomain of CENP-B that is necessary and sufficient for localization to the human centromere. (1992)

We have combined in vivo and in vitro approaches to investigate the function of CENP-B, a major protein of human centromeric heterochromatin. Expression of epitope-tagged deletion derivatives of CENP-B in HeLa cells revealed that a single domain less than 158 residues from the amino terminus of the protein is sufficient to localize CENP-B to centromeres. Centromere localization was abolished if as few as 28 amino acids were removed from the amino terminus of CENP-B. The centromere localization signal of CENP-B can function in an autonomous fashion, relocating a fused bacterial enzyme to centromeres. The centromere localization domain of CENP-B specifically binds in vitro to a subset of alpha-satellite DNA monomers. These results suggest that the primary mechanism for localization of CENP-B to centromeres involves the recognition of a DNA sequence found at centromeres. Analysis of the distribution of this sequence in alpha-satellite DNA suggests that CENP-B binding may have profound effects on chromatin structure at centromeres.