gebhart/patrepeval huggingface dataset:
The Ebola Virus VP35 Protein Is a Suppressor of RNA Silencing (2007)

RNA silencing or interference (RNAi) is a gene regulation mechanism in eukaryotes that controls cell differentiation and developmental processes via expression of microRNAs. RNAi also serves as an innate antiviral defence response in plants, nematodes, and insects. This antiviral response is triggered by virus-specific double-stranded RNA molecules (dsRNAs) that are produced during infection. To overcome antiviral RNAi responses, many plant and insect viruses encode RNA silencing suppressors (RSSs) that enable them to replicate at higher titers. Recently, several human viruses were shown to encode RSSs, suggesting that RNAi also serves as an innate defence response in mammals. Here, we demonstrate that the Ebola virus VP35 protein is a suppressor of RNAi in mammalian cells and that its RSS activity is functionally equivalent to that of the HIV-1 Tat protein. We show that VP35 can replace HIV-1 Tat and thereby support the replication of a Tat-minus HIV-1 variant. The VP35 dsRNA-binding domain is required for this RSS activity. Vaccinia virus E3L protein and influenza A virus NS1 protein are also capable of replacing the HIV-1 Tat RSS function. These findings support the hypothesis that RNAi is part of the innate antiviral response in mammalian cells. Moreover, the results indicate that RSSs play a critical role in mammalian virus replication.
Testing Extrusion Flow Stress and Friction Factor via Inverse Analysis (2011)

Accurate determination of flow stress and friction factor is the guarantee of accuracy for finite element analysis of metal extrusion. Firstly, flow stress equation parameters for materials test were initially decided in order to perform finite element analogy. Then, the simulation values and experiment values were compared and the iterative optimization algorithm was used to amend the parameters. The objective was that value error of simulation and experiment values was controlled within tolerance. Finally, accurate flow stress and friction factor were determined. In rod-rod composite extrusion experiment of pure lead,it is determined by inverse analysis that the material strength coefficient is 11.9, strain hardening exponent is 0.127,and friction factor is 0.18. The comparison of the load-stroke curve between simulation and experiment and pure lead upsetting test contribute to confirm that the measured data is accurate. The results show that inverse analysis is a precise, simple and practical method for measuring flow stress and friction factor.
Detection theory applied to high intensity focused ultrasound (HIFU) treatment evaluation (2003)

The aim of this work is to develop a HIFU treatment evaluation algorithm based on 1-D pulse/echo (P/E) ultrasound data taken during HIFU exposures. The algorithm is applicable to large treatment volumes resulting from several overlapping elementary exposures. Treatments consisted of multiple HIFU exposures with an on-time of 3 seconds each, spaced 3 mm apart, and an off-time of 6 seconds in between HIFU exposures. The HIFU was paused for approximately 70 milliseconds every 0.5 seconds, while P/E data was acquired along the beam axis, using a confocal imaging transducer. Data was collected from multiple in vitro and in vivo tissue treatments, including shams. The cumulative energy change in the P/E data was found for every HIFU exposure, as a function of depth. Subsequently, a likelihood ratio test with a fixed false alarm rate was used to derive a positive or negative lesion creation decision for that position. For false alarm rates less than 5%, positive treatment outcomes were consistently detected for better than 90% of the HIFU exposures. In addition, the algorithm outcome correlated to the applied HIFU intensity level. Lesion formation was therefore successfully detected as a function of dosage. [Work supported by NIH SBIR Grant 2 R 44 CA 83244-02.]
Efficient algorithm for mobile multicast using anycast group (2001)

The authors present a novel and efficient multicast algorithm that aims to reduce delay and communication cost for the registration between mobile nodes and mobility agents and solicitation for foreign agent services based on the mobile IP. The protocol applies anycast group technology to support multicast transmissions for both mobile nodes and home/foreign agents. Mobile hosts use anycast tunnelling to connect to the nearest available home/foreign agent where an agent is able to forward the multicast messages by selecting an anycast route to a multicast router so as to reduce the end-to-end delay. The performance analysis and experiments demonstrated that the proposed algorithm is able to enhance the performance over existing remote subscription and bidirectional tunnelling approaches regardless of the locations of mobile nodes/hosts.
Cyclic Saturation Dislocation Pattern Observation in the Vicinity of Grain Boundaries by Electron Channeling Contrast Technique (2009)

The cyclic saturation dislocation patterns within grains and in the vicinity of low-angle grain boundaries in fatigued copper crystal were successfully observed by electron channeling contrast technique in SEM. The results show that the dislocation patterns within grains consisted of typical two-phase structure, i.e. persistent slip bands (PSB) and veins. With increasing plastic strain amplitude (gamma(pl) greater than or equal to 1.7 x 10(-3)), large amount of PSBs and regular dislocation walls were observed. The dislocation walls and PSBs could cross through the low-angle grain boundaries continuously except that the dislocation-free zone (DFZs) appeared at some local regions. Combining with the cyclic stress-strain response and dislocation patterns, the effect of low-angle grain boundaries on cyclic deformation behavior was discussed.
N-carboethoxypiperidine, a Convenient Reagent for the Preparation of Symmetrical Ketones from Organolithiums (1995)

Dedicated ro Prof RnlfHuisgen on rhe occasion of his 75th birthdaya -N-Carboethoxypiperidine on reaction with organolithium reagents, RLi, followed by acidic work-up gave excellent yields of the corresponding symmetrical ketones, R2CO.
Characterization of Hydrogen Permeation Through Zinc‐Nickel Alloys under Corroding Conditions: Mathematical Model and Experimental Study (1998)

A mathematical model was developed for the characterization of hydrogen permeation into metals and alloys under corroding conditions. The model requires a knowledge of the corrosion rate of the given metal or alloy in solutions of various concentrations. It provides quantitative values of rate constants of the hydrogen discharge, recombination, and adsorption reactions. This model can serve as a diagnostic criterion for determining the effectiveness of various metals and alloys as hydrogen permeation inhibitors and can be used for evaluation of hydrogen entry inhibition efficiency. Experiments were carried out to study the effectiveness of thin layers of electrodeposited Zn‐Ni alloys to inhibit hydrogen permeation into iron. The experimental permeation data obtained for Zn‐Ni‐coated iron were analyzed using the model and the results were compared with the hydrogen permeation characteristics of bare iron.
Extreme Learning Machine for Multilayer Perceptron (2015)

Extreme learning machine (ELM) is an emerging learning algorithm for the generalized single hidden layer feedforward neural networks, of which the hidden node parameters are randomly generated and the output weights are analytically computed. However, due to its shallow architecture, feature learning using ELM may not be effective for natural signals (e.g., images/videos), even with a large number of hidden nodes. To address this issue, in this paper, a new ELM-based hierarchical learning framework is proposed for multilayer perceptron. The proposed architecture is divided into two main components: 1) self-taught feature extraction followed by supervised feature classification and 2) they are bridged by random initialized hidden weights. The novelties of this paper are as follows: 1) unsupervised multilayer encoding is conducted for feature extraction, and an ELM-based sparse autoencoder is developed via l1 constraint. By doing so, it achieves more compact and meaningful feature representations than the original ELM; 2) by exploiting the advantages of ELM random feature mapping, the hierarchically encoded outputs are randomly projected before final decision making, which leads to a better generalization with faster learning speed; and 3) unlike the greedy layerwise training of deep learning (DL), the hidden layers of the proposed framework are trained in a forward manner. Once the previous layer is established, the weights of the current layer are fixed without fine-tuning. Therefore, it has much better learning efficiency than the DL. Extensive experiments on various widely used classification data sets show that the proposed algorithm achieves better and faster convergence than the existing state-of-the-art hierarchical learning methods. Furthermore, multiple applications in computer vision further confirm the generality and capability of the proposed learning scheme.
Vasodilator Therapy of Cardiac Failure (1977)

Acute Myocardial InfarctionVasodilator therapy has been advocated for two purposes in patients with acute myocardial infarction: improvement in pump function; and reduction in myocardial ischemia.Pump FunctionLeft ventricular dysfunction in acute myocardial infarction is characterized by a high left ventricular diastolic pressure and a low stroke volume.32 Since the left ventricle usually is not much dilated despite the high filling pressure some of the rise in pressure has been attributed to a reduction in diastolic compliance.33 Clinical signs of left ventricular failure often coexist with the hemodynamic derangement, but sometimes the lungs are clear and the heart sounds . . .
Downtime Analysis of Virtual Machine Live Migration (2011)

Virtual machine environments like VMware, XEN, KVM, and Hyper-V support live migration of guest operating systems, which is used in data centers to provide uninterrupted service during maintenance or to move computation away from failure-prone hosts. The duration of migration, as well as the virtual machine downtime during this process are essential when assessing if service availability agreements might be violated. We present the result of an experimental study that analyzed virtual machine live migration downtime and duration. We show that total migration time as well as downtime are dominated by specific memory utilization patterns inside the virtualized guest. We experienced that downtime involved by live migration can vary by a factor of more than 23, which can have significant impact on service availability. Keywords-virtual machine, live migration, downtime I. INTRODUCTION
Developmentally Regulated N-terminal Variants of the Nuclear Receptor Hepatocyte Nuclear Factor 4α Mediate Multiple Interactions through Coactivator and Corepressor-Histone Deacetylase Complexes (2002)

To understand the mechanisms governing the regulation of nuclear receptor (NR) function, we compared the parameters of activation and repression of two isoforms of the orphan receptor hepatocyte nuclear factor (HNF) 4alpha. HNF4alpha7 and HNF4alpha1 differ only in their N-terminal domains, and their expression in the liver is regulated developmentally. We show that the N-terminal activation function (AF)-1 of HNF4alpha1 possesses significant activity that can be enhanced through interaction with glucocorticoid receptor-interacting protein 1 (GRIP-1) and cAMP response element-binding protein-binding protein (CBP). In striking contrast, HNF4alpha7 possesses no measurable AF-1, implying major functional differences between the isoforms. Indeed, although HNF4alpha1 and HNF4alpha7 are able to interact via AF-2 with GRIP-1, p300, and silencing mediator for retinoid and thyroid receptors (SMRT), only HNF4alpha1 interacts in a synergistic fashion with GRIP-1 and p300. Although both isoforms interact physically and functionally with SMRT, the repression of HNF4alpha7 is less robust than that of HNF4alpha1, which may be caused by an increased ability of the latter to recruit histone deacetylase (HDAC) activity to target promoters. Moreover, association of SMRT with HDACs enhanced recruitment of HNF4alpha1 but not of HNF4alpha7. These observations suggest that NR isoform-specific association with SMRT could affect activity of the SMRT complex, implying that selection of HDAC partners is a novel point of regulation for NR activity. Possible physiological consequences of the multiple interactions with these coregulators are discussed.
A Novel Signaling Network Essential for Regulating Pseudomonas aeruginosa Biofilm Development (2009)

The important human pathogen Pseudomonas aeruginosa has been linked to numerous biofilm-related chronic infections. Here, we demonstrate that biofilm formation following the transition to the surface attached lifestyle is regulated by three previously undescribed two-component systems: BfiSR (PA4196-4197) harboring an RpoD-like domain, an OmpR-like BfmSR (PA4101-4102), and MifSR (PA5511-5512) belonging to the family of NtrC-like transcriptional regulators. These two-component systems become sequentially phosphorylated during biofilm formation. Inactivation of bfiS, bfmR, and mifR arrested biofilm formation at the transition to the irreversible attachment, maturation-1 and -2 stages, respectively, as indicated by analyses of biofilm architecture, and protein and phosphoprotein patterns. Moreover, discontinuation of bfiS, bfmR, and mifR expression in established biofilms resulted in the collapse of biofilms to an earlier developmental stage, indicating a requirement for these regulatory systems for the development and maintenance of normal biofilm architecture. Interestingly, inactivation did not affect planktonic growth, motility, polysaccharide production, or initial attachment. Further, we demonstrate the interdependency of this two-component systems network with GacS (PA0928), which was found to play a dual role in biofilm formation. This work describes a novel signal transduction network regulating committed biofilm developmental steps following attachment, in which phosphorelays and two sigma factor-dependent response regulators appear to be key components of the regulatory machinery that coordinates gene expression during P. aeruginosa biofilm development in response to environmental cues.
Molecular Dynamics Simulations of Human Cystatin C and Its L68Q Varient to Investigate the Domain Swapping Mechanism (2007)

Human cystatin C variant (L68Q), one of the amyloidgenic proteins, has been shown to form dimeric structure spontaneously via domain swapping and easily cause amyloid deposits in the brains of patients suffering from Alzheimer's disease or hereditary cystatin C amyloid angiopathy. The monomeric L68Q and wild-type (wt) HCCs share similar structural feature consisting of a core with a five-stranded anti-parallel beta-sheet (beta-region) wrapped around a central helix. In this study, various molecular dynamics simulations were conducted to investigate the conformational fluctuations of the monomeric L68Q and wt HCCs at various combinations of temperature (300 and 500K) and pH (2 and 7) to gain insights into the domain swapping mechanism. The results show that elevated temperature accelerates the disruption of the hydrophobic core and acidic condition promotes the destruction of three salt bridges between beta2 and beta3 in both HCCs. The results also indicate that the interior hydrophobic core of the L68Q variant is relatively unstable, leading to domain swapping more readily comparing to wt HCC under conditions favoring this process. However, these two monomeric HCCs adopt the same mechanism of domain swapping as follows: (i) first, the interior hydrophobic core is disrupted; (ii) subsequently, the central helix departs from the beta-region; (iii) then, the beta2-L1-beta3 hairpin structure unfolds following the so-called "zip-up" mechanism; and (iv) finally, the open form HCC is generated.
D‐penicillamine versus zinc sulfate as first‐line therapy for Wilson's disease (2014)

DPA and ZS are effective in the majority of WD patients. Neither therapy appears to be clearly superior. Therefore ZS may be considered a reasonable alternative to DPA as a first-line therapy.
Madrid "ciudad única" (II). La explosión urbana en la región madrileña y sus efectos colaterales (2011)

Indice La explosion urbana: analisis de la distribucion espacial de la poblacion, el empleo y la vivienda. Lectura de la explosion urbana en terminos de distancias. El desbordamiento regional y el efecto frontera. En las provincias limitrofes con Madrid. Los efectos colaterales de la explosion urbana: una aproximacion a la evaluacion del modelo desde la optica de la sostenibilidad. Bibliografia. Resumen En el numero de la revista anterior, se analizaron las grandes transformaciones estructurales que explican el dinamismo economico, demografico e inmobiliario que ha experimentado la region urbana madrilena en la ultima decada, haciendo hincapie en la evolucion de las actividades productivas, las dinamicas sociales e inmobiliarias y el despliegue de infraestructuras. Se examinan a continuacion, enunciadas como explosion urbana, las pautas espaciales del crecimiento y su distribucion sobre el territorio, atendiendo a las dinamicas de dispersion y descentralizacion de la poblacion, el empleo y la vivienda por toda la region urbana madrilena y al inicio del desbordamiento de estos procesos mas alla de los limites administrativos, hacia las comunidades fronterizas. Finalmente, se realiza una aproximacion desde el punto de vista de la sostenibilidad, a traves de una serie de indicadores (consumo de materiales, energia, suelo, etc.) que permiten introducir nuevos criterios valorativos de las dinamicas economicas y territoriales que se han descrito. A la luz de esta aproximacion, se vislumbran serias dudas que cuestionan las supuestas virtudes –practicamente indiscutidas y socialmente aplaudidas– del modelo de crecimiento madrileno. Abstract In the previous number of this publication, there was an analysis the enormous structural transformations explaining the economic, demographic and building dynamism that the urban region of Madrid have suffered during the last decade, emphasizing the evolution of the productive activities, the social and building dynamics and the infrastructure deployment. Next, stated as 'urban explosion', the growth spacial patterns were analysed, as well as its layout on the land, taking into account the population, employment and housing dispersion and decentralization dynamics which take place all along the urban region of Madrid, and which are about to exceed these processes beyond the administrative limits, towards the neighbouring communities. To conclude, there is an approach from the sustainability perspective through a series of indicators (material goods, energy and soil consumption, among others) that allow to insert new criteria that value the economic and territorial dynamics hereabove mentioned. Under this approach, we can discern important doubts questioning the alleged virtues –practically undisputed and socially praised– of the growth model in Madrid.
Plant‐to‐Plant Variability in Corn Production (2005)

Corn ( Zea mays L.) grain yields are known to vary from plant to plant, but the extent of this variability across a range of environments has not been evaluated. This study was initiated to evaluate by‐plant corn grain yield variability over a range of production environments and to establish the relationships among mean grain yield, standard deviation, coefficient of variation, and yield range. A total of forty‐six 8‐ to 30‐m corn transects were harvested by plant in Argentina, Mexico, Iowa, Nebraska, Ohio, Virginia, and Oklahoma from 2002 to 2004. By‐plant corn grain yields were determined, and the average individual plant yields were calculated. Over all sites in all countries and states, plant‐to‐plant variation in corn grain yield averaged 2765 kg ha −1 (44.1 bu ac −1 ). At the sites with the highest average corn grain yield (11478 and 14383 kg ha −1 , Parana Argentina, and Phillips, NE), average plant‐to‐plant variation in yield was 4211 kg ha −1 (67 bu ac −1 ) and 2926 kg ha −1 (47 bu ac −1 ), respectively. As average grain yields increased, so did the standard deviation of the yields obtained within each row. Furthermore, the yield range (maximum corn grain yield minus the minimum corn grain yield per row) was found to increase with increasing yield level. Regardless of yield level, plant‐to‐plant variability in corn grain yield can be expected and averaged more than 2765 kg ha −1 over sites and years. Averaging yield over distances >0.5 m removed the extreme by‐plant variability, and thus, the scale for treating other factors affecting yield should be less than 0.5 m. Methods that homogenize corn plant stands and emergence may decrease plant‐to‐plant variation and could lead to increased grain yields.
A Local Algorithm for Product Return Prediction in E-Commerce (2018)

With the rapid growth of e-tail, the cost to handle returned online orders also increases significantly and has become a major challenge in the e-commerce industry. Accurate prediction of product returns allows e-tailers to prevent problematic transactions in advance. However, the limited existing work for modeling customer online shopping behaviors and predicting their return actions fail to integrate the rich information in the product purchase and return history (e.g., return history, purchase-no-return behavior, and customer/product similarity). Furthermore, the large-scale data sets involved in this problem, typically consisting of millions of customers and tens of thousands of products, also render existing methods inefficient and ineffective at predicting the product returns. To address these problems, in this paper, we propose to use a weighted hybrid graph to represent the rich information in the product purchase and return history, in order to predict product returns. The proposed graph consists of both customer nodes and product nodes, undirected edges reflecting customer return history and customer/product similarity based on their attributes, as well as directed edges discriminating purchase-no-return and no-purchase actions. Based on this representation, we study a random-walk-based local algorithm for predicting product return propensity for each customer, whose computational complexity depends only on the size of the output cluster rather than the entire graph. Such a property makes the proposed local algorithm particularly suitable for processing the large-scale data sets to predict product returns. To test the performance of the proposed techniques, we evaluate the graph model and algorithm on multiple e-commerce data sets, showing improved performance over state-of-the-art methods.