gebhart/patrepeval huggingface dataset:
A Magnetic Bead-Integrated Chip for the Large Scale Manufacture of Normalized esiRNAs (2012)

The chemically-synthesized siRNA duplex has become a powerful and widely used tool for RNAi loss-of-function studies, but suffers from a high off-target effect problem. Recently, endoribonulease-prepared siRNA (esiRNA) has been shown to be an attractive alternative due to its lower off-target effect and cost effectiveness. However, the current manufacturing method for esiRNA is complicated, mainly in regards to purification and normalization on a large-scale level. In this study, we present a magnetic bead-integrated chip that can immobilize amplification or transcription products on beads and accomplish transcription, digestion, normalization and purification in a robust and convenient manner. This chip is equipped to manufacture ready-to-use esiRNAs on a large-scale level. Silencing specificity and efficiency of these esiRNAs were validated at the transcriptional, translational and functional levels. Manufacture of several normalized esiRNAs in a single well, including those silencing PARP1 and BRCA1, was successfully achieved, and the esiRNAs were subsequently utilized to effectively investigate their synergistic effect on cell viability. A small esiRNA library targeting 68 tyrosine kinase genes was constructed for a loss-of-function study, and four genes were identified in regulating the migration capability of Hela cells. We believe that this approach provides a more robust and cost-effective choice for manufacturing esiRNAs than current approaches, and therefore these heterogeneous RNA strands may have utility in most intensive and extensive applications.
General Backpropagation Algorithm for Training Second-order Neural Networks (2017)

The artificial neural network is a popular framework in machine learning. To empower individual neurons, we recently suggested that the current type of neurons could be upgraded to 2nd order counterparts, in which the linear operation between inputs to a neuron and the associated weights is replaced with a nonlinear quadratic operation. A single 2nd order neurons already has a strong nonlinear modeling ability, such as implementing basic fuzzy logic operations. In this paper, we develop a general backpropagation (BP) algorithm to train the network consisting of 2nd-order neurons. The numerical studies are performed to verify of the generalized BP algorithm.
Characterization of a T7-Like Lytic Bacteriophage (φSG-JL2) of <i>Salmonella enterica</i> Serovar Gallinarum Biovar Gallinarum (2008)

PhiSG-JL2 is a newly discovered lytic bacteriophage infecting Salmonella enterica serovar Gallinarum biovar Gallinarum but is nonlytic to a rough vaccine strain of serovar Gallinarum biovar Gallinarum (SG-9R), S. enterica serovar Enteritidis, S. enterica serovar Typhimurium, and S. enterica serovar Gallinarum biovar Pullorum. The phiSG-JL2 genome is 38,815 bp in length (GC content, 50.9%; 230-bp-long direct terminal repeats), and 55 putative genes may be transcribed from the same strand. Functions were assigned to 30 genes based on high amino acid similarity to known proteins. Most of the expected proteins except tail fiber (31.9%) and the overall organization of the genomes were similar to those of yersiniophage phiYeO3-12. phiSG-JL2 could be classified as a new T7-like virus and represents the first serovar Gallinarum biovar Gallinarum phage genome to be sequenced. On the basis of intraspecific ratios of nonsynonymous to synonymous nucleotide changes (Pi[a]/Pi[s]), gene 2 encoding the host RNA polymerase inhibitor displayed Darwinian positive selection. Pretreatment of chickens with phiSG-JL2 before intratracheal challenge with wild-type serovar Gallinarum biovar Gallinarum protected most birds from fowl typhoid. Therefore, phiSG-JL2 may be useful for the differentiation of serovar Gallinarum biovar Gallinarum from other Salmonella serotypes, prophylactic application in fowl typhoid control, and understanding of the vertical evolution of T7-like viruses.
Respiration and Growth Defects in Transmitochondrial Cell Lines Carrying the 11778 Mutation Associated with Leber's Hereditary Optic Neuropathy (1996)

Mitochondrial DNA from two genetically unrelated patients carrying the mutation at position 11778 that causes Leber's hereditary optic neuropathy has been transferred with mitochondria into human mtDNA-less rho0206 cells. As analyzed in several transmitochondrial cell lines thus obtained, the mutation, which is in the gene encoding subunit ND4 of the respiratory chain NADH dehydrogenase (ND), did not affect the synthesis, size, or stability of ND4, nor its incorporation into the enzyme complex. However, NADH dehydrogenase-dependent respiration, as measured in digitonin-permeabilized cells, was specifically decreased by approximately 40% in cells carrying the mutation. This decrease, which was significant at the 99.99% confidence level, was correlated with a significantly reduced ability of the mutant cells to grow in a medium containing galactose instead of glucose, indicating a clear impairment in their oxidative phosphorylation capacity. On the contrary, no decrease in rotenone-sensitive NADH dehydrogenase activity, using a water-soluble ubiquinone analogue as electron acceptor, was detected in disrupted mitochondrial membranes. This is the first cellular model exhibiting in a foreign nuclear background mitochondrial DNA-linked biochemical defects underlying the optic neuropathy phenotype.
Improvement of the Dissolution Rate of Nitrendipine Using a New Pulse Combustion Drying Method (2007)

Solid dispersions (SDs) of nitrendipine (NTD), a poorly water-soluble drug, were prepared with the Hypulcon pulse combustion dryer system, and the physicochemical properties of particles were investigated and compared with those of particles prepared with a spray dryer. The SD particles prepared with Hypulcon using Aerosil and Tween 80 as carriers showed improved properties over those prepared with a conventional spray dryer, such as smaller particle size, tighter particle size distribution, and no agglomeration. Powder X-ray diffraction and differential scanning calorimetry evaluation showed that the drug in the NTD-Aerosil SD prepared with 5% (v/v) Tween 80 solution was dispersed in an amorphous state. Fourier transformation IR spectroscopy indicated the presence of hydrogen bonds between NTD and Aerosil. Aerosil had greater ability to improve the dissolution of NTD than Sylysia and other polymers. The highest drug supersaturation concentration was maintained continuously during the dissolution test of the NTD-Aerosil SD prepared with 5% (v/v) Tween 80 solution using Hypulcon. The good hydrophilicity and dispersibility of Aerosil, solubilization of Tween 80, and actions of shock waves and ultrasonic waves might account for the amorphization of NTD and improved dissolution rate of SDs. Pulse combustion drying with low drying costs and high thermal efficiency is a promising method for the preparation of SD particles with improved properties without using organic solvent.
Optimization of Volume & Brightness of Android Smartphone through Clustering & Reinforcement Learning (“RE-IN”) (2018)

Smartphone has become one of the most significant piece of technology that humans were able to produce in the 21st century. It has become our life companion; hence the features of the smartphones have developed in advance. But, some features may not work as expected. For instance, auto brightness changing feature is now actualized with smartphones, yet we alter the brightness according to our preference. In the same manner, considering the volume of our smartphone it doesn't change according to our preference subsequently. This research will develop a mobile application (“RE-IN”) to overcome this issue for Android smartphones. Since android smartphones allow accessing its hardware layer we can roll out improvements as we need, yet Apple doesn't permit to proceed with its hardware layer thus hard to do this for the iPhone users. By utilizing the RE-IN mobile application users may have to encounter an optimal brightness and volume on their Android smartphones agreeing the present condition of smartphone users are in. RE- IN application will keep running as a background application on an Android smartphone. When the client changes the brightness and volume as his/her preference. At that point, the reinforcement learning algorithm over the time application will distinguish how to control user's smartphone's brightness and volume relying upon the user's circumstance. When client surrounding is loaded with light, the framework will modify brightness for his/her preference. The client doesn't need to do this manually. Moreover when the client is at the too much boisterous place all of a sudden gets a call from someone; client's smartphone amplifier volume will change consequently and solaces the client's discussion. To actualize this framework it is relied upon to reinforcement learning and machine learning as the research area. By finishing the literature review, research group unable to find an Android mobile application which automates the process of volume and brightness of the Android smartphone as per user preference. After using the reinforcement learning algorithm to learn the data set then distribute the process, using client-server model and come up with a clustering algorithm(K-means algorithm) to share common attributes by considering geographical area which they live in and variables like age, gender, how they interact with the device etc. In addition, this system will identify abnormal behaviors of some particular users. RE-IN will identify the users who are keeping volume level to the highest and brightness level to its maximum and notify them in advance.
Special Feature: Epigrams on programming (1982)

article Free Access Share on Special Feature: Epigrams on programming Author: Alan J. Perlis Yale Univ. Yale Univ.View Profile Authors Info & Claims ACM SIGPLAN NoticesVolume 17Issue 9September 1982 pp 7–13https://doi.org/10.1145/947955.1083808Online:01 September 1982Publication History 88citation1,419DownloadsMetricsTotal Citations88Total Downloads1,419Last 12 Months131Last 6 weeks18 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
A Putative Nucleoporin 96 Is Required for Both Basal Defense and Constitutive Resistance Responses Mediated by<i>suppressor of npr1-1</i>,<i>constitutive 1</i>  (2005)

The Arabidopsis thaliana suppressor of npr1-1, constitutive 1 (snc1) mutant contains a gain-of-function mutation in a Toll Interleukin1 receptor-nucleotide binding-Leu-rich repeat-type resistance gene (R-gene), which leads to constitutive activation of disease resistance response against pathogens. In a screen for suppressors of snc1, a recessive mutation, designated mos3 (for modifier of snc1,3), was found to suppress the constitutive pathogenesis-related gene expression and resistance to virulent Pseudomonas syringae maculicola ES4326 and Peronospora parasitica Noco2 in snc1. In addition, mos3 is also compromised in resistance mediated by Resistance to Peronospora parasitica 4 (RPP4), Resistance to Pseudomonas syringae pv maculicola (RPM1), and Resistance to Pseudomonas syringae 4 (RPS4). Single mutant mos3 plants exhibited enhanced disease susceptibility to P. s. pv maculicola ES4326, suggesting that MOS3 is required for basal resistance to pathogens as well. mos3-1 was identified by map-based cloning, and it encodes a protein with high sequence similarity to human nucleoporin 96. Localization of the MOS3-green fluorescent protein fusion to the nuclear envelope further indicates that MOS3 may encode a nucleoporin, suggesting that nuclear and cytoplasmic trafficking plays an important role in both R-gene-mediated and basal disease resistance.
The calorically restricted low-fat nutrient-dense diet in Biosphere 2 significantly lowers blood glucose, total leukocyte count, cholesterol, and blood pressure in humans. (1992)

Biosphere 2 is a 3.15-acre space containing an ecosystem that is energetically open (sunlight, electric power, and heat) but materially closed, with air, water, and organic material being recycled. Since September 1991, eight subjects (four women and four men) have been sealed inside, living on food crops grown within. Their diet, low in calories (average, 1780 kcal/day; 1 kcal = 4.184 kJ), low in fat (10% of calories), and nutrient-dense, conforms to that which in numerous animal experiments has promoted health, retarded aging, and extended maximum life span. We report here medical data on the eight subjects, comparing preclosure data with data through 6 months of closure. Significant changes included: (i) weight, 74 to 62 kg (men) and 61 to 54 kg (women); (ii) mean systolic/diastolic blood pressure (eight subjects), 109/74 to 89/58 mmHg (1 mmHg = 133 Pa); (iii) total serum cholesterol, from 191 +/- 11 to 123 +/- 9 mg/dl (mean +/- SD; 36% mean reduction), and high density lipoprotein, from 62 +/- 8 to 38 +/- 5 (risk ratio unchanged); (iv) triglyceride, 139 to 96 mg/dl (men) and 78 to 114 mg/dl (women); (v) fasting glucose, 92 to 74 mg/dl; (vi) leukocyte count, 6.7 to 4.7 x 10(9) cells per liter. We conclude that drastic reductions in cholesterol and blood pressure may be instituted in normal individuals in Western countries by application of a carefully chosen diet and that a low-calorie nutrient-dense regime shows physiologic features in humans similar to those in other animal species.
Chemical Vapor Deposition of Gallium Sulfide Thin Films (2000)

The compound [Ga(S-i-Pr)2(μ-S-i-Pr)]2, a thermally stable solid with a low melting point, was used as a single-source precursor to gallium sulfide films in a low-pressure chemical vapor deposition process. Film depositions were carried out at substrate temperatures in the range 350−610 °C. The films were determined to have a Ga2S3 stoichiometry by Rutherford backscattering and energy-dispersive X-ray spectrometries. X-ray diffraction studies showed that the films deposited on glass, silicon, and YSZ (111) substrates were composed of γ-Ga2S3, α-Ga2S3, and highly oriented γ-Ga2S3, respectively.
Combining Artificial Intelligence, Ontology, and Frequency-based Approaches to Recommend Activities in Scientific Workflows (2018)

The number of activities provided by scientific workflow management systems is large, which requires scientists to know many of them to take advantage of the reusability of these systems. To minimize this problem, the literature presents some techniques to recommend activities during the scientific workflow construction. In this paper we specified and developed a hybrid activity recommendation system considering information on frequency, input and outputs of activities and ontological annotations. Additionally, this paper presents a modeling of activities recommendation as a classification problem, tested using 5 classifiers; 5 regressors; and a composite approach which uses a Support Vector Machine (SVM) classifier, combining the results of other classifiers and regressors to recommend; and Rotation Forest, an ensemble of classifiers. The proposed technique was compared to related techniques and to classifiers and regressors, using 10-fold-cross-validation, achieving a Mean Reciprocal Rank (MRR) at least 70% greater than those obtained by classical techniques.
Thermal protection performance of survival suits in ice-water. (1984)

Five models of dry and insulative survival suits for cold-water immersion were studies for their thermal protection while worn by subjects floating in ice-water at 1 degree C for 6 h. Rectal temperature, extremity skin temperatures, and heart rate were monitored. No significant differences occurred in the thermal or heart rate responses of the subjects wearing the five models of suits. The immersion induced only mild hypothermia; the overall amount of rectal cooling during the 6-h period was 0.80 degree C, or a rate of 0.13 degree C/h. Extremity temperatures fell within the first 2 h to levels that induced strong sensation of cold and moderate shivering. The results show that dry and insulative survival suits can provide excellent protection against fatal levels of hypothermia resulting from ice-water immersion. Predicted survival time, given the very low cooling rate observed, exceeds 1 d if drowning can be avoided.
Prevention of lymphadenopathy in MRL-<i>lpr/lpr</i> mice by blocking peripheral lymph node homing with Mel-14 in vivo. (1988)

MRL-lpr/lpr mice develop massive lymphadenopathy and autoimmunity. There is evidence that both migration and local proliferation contribute to the accumulation of Ly-2-, L3T4-, 6B2+ T cells in the peripheral lymph node (PLN). Mel-14 is an antibody which binds to the lymphocyte lymph node homing receptor (gp90Mel-14) and can block migration of lymphocytes to the PLN. Treatment of mice from birth to 11 wk of age with Mel-14 and another rat IgG2a mAb, 6B2, resulted in reduction (10- to 20-fold) in lymphadenopathy. Mel-14, but not 6B2, preferentially reduced the percentages of Thy-1+, 6B2+ lymphocytes in the lymph node. Treatment with a third antibody, anti-Ly-1, had no effect on lymphadenopathy. Mel-14 treatment resulted in diversion of the Ly-2-, L3T4-, 6B2+, gp90Mel-14 cells to the spleen and consequently induced marked splenomegaly. Thymocytes from MRL-lpr/lpr and MRL-+/+ mice were analyzed by two-color flow cytometry analysis after depletion of Ly-2+ and L3T4+ T cells. There was no difference in the percent of Ly-2-, L3T4-, 6B2+, gp90Mel-14 positive thymocytes comparing these two strains. Mel-14 treatment did not alter Ig levels or autoantibody production. These studies suggest Mel-14 reduced lymphadenopathy by interfering with homing to PLN, whereas 6B2 may have interfered with marrow production of precursor cells or killed 6B2+ cells after they exited the marrow. The data are consistent with the idea that lymphadenopathy occurs in MRL-lpr/lpr mice due to increased homing gp90-Mel-14 T cells to the PLN and that gp90Mel-14 is a necessary receptor for the abnormal 6B2+ T cells.
Computing planar sections of surfaces of revolution with revolute quadric decomposition (2004)

Computing the planar sections of objects is a fundamental operation in solid modeling. Subdivision method is commonly used for solving such intersection problems. In this paper, a revolute quadric decomposition is proposed for surfaces of revolution, which are subdivided into a set of coaxial revolute quadrics along the generatrix. This reduces the intersection problem of a plane and a surface of revolution to the intersection problem of a plane and a revolute quadric, which has robust, accurate and efficient geometric solution. Further, the intersection curves can be represented with a group of G (G. Baciu et al., 2001) conic arcs. A new concept, valid intersection interval (VII), is introduced and a new technique, cylindrical bounding shell clipping, is proposed for efficient intersection detection for a plane and a surface of revolution. Finally, a tracing algorithm is presented for recognizing singular points and closed loops of intersection curves. Implemented examples show the robustness and effectiveness of the proposed algorithm.
Benchmarking Apache Accumulo BigData Distributed Table Store Using Its Continuous Test Suite (2013)

In this paper, we present results of benchmarking Apache Accumulo distributed table store using the continuous tests suite included in its open source distribution. The continuous test suite contains tests that build and traverse a very large linked list, implemented via a simple table-row indexing mechanism. This underlying design provides insight for developing applications dealing with complex relationship among data sets as typically found in graph analytics applications. The benchmark study investigated sustained continuous mode stress testing and identified optimum configurations for very high-throughput data ingest, sequential and random query operations. Apache Accumulo also has the unique feature of cell level data access security, and the benchmark evaluates the processing overhead for this feature. We also tested high-speed table data verification and validation. These benchmark tests were run on a large cluster optimized for large-scale analytics and we present the performance figures for Apache Accumulo found in the study.
Photo-Crosslinking of Copolymeric Methacrylates Bearing Stilbene Chromophores (2012)

Radical polymerization of methyl methacrylate (2) as major component and the methacrylates 1a or 1b, which contain an (E)-stilbene unit fixed by a tether to the ester group, yield easily soluble copolymers 3a, b. Whereas the dominant photoreactions in solution are (E)⇄Z) isomerizations and intra-chain [2π +2π] cycloadditions, cast films of 3a, b give an inter-chain photo-crosslinking on irradiation. Compared to homopolymers, the copolymers are not only better soluble and more easily processible, their films show less undesired light scattering. The cross-linked material is completely insoluble in organic solvents. Thus, it represents the basis for negative photoresists and the corresponding imaging techniques.
In situ formation of phosphate barriers in soil (2023)

Reactive barriers and methods for making reactive barriers in situ in soil for sequestering soil ontaminants including actinides and heavy metals. The barrier includes phosphate, and techniques are disclosed for forming specifically apatite barriers. The method includes injecting dilute reagents into soil in proximity to a contamination plume or source such as a waste drum to achieve complete or partial encapsulation of the waste. Controlled temperature and pH facilitates rapid formation of apatite, for example, where dilute aqueous calcium chloride and dilute aqueous sodium phosphate are the selected reagents. Mixing of reagents to form precipitate is mediated and enhanced through movement of reagents in soil as a result of phenomena including capillary action, movement of groundwater, soil washing and reagent injection pressure.
Lenalidomide for the treatment of relapsed and refractory multiple myeloma (2012)

Lenalidomide is an amino-substituted derivative of thalidomide with direct antiproliferative and cytotoxic effects on the myeloma tumor cell, as well as antiangiogenic activity and immunomodulatory effects. Together with the introduction of bortezomib and thalidomide, lenalidomide has significantly improved the survival of patients with relapsed and refractory myeloma. The most common adverse events associated with lenalidomide include fatigue, skin rash, thrombocytopenia, and neutropenia. In addition, when lenalidomide is combined with dexamethasone or other conventional cytotoxic agents, there is an increase in the incidence of venous thromboembolic events. There is now evidence that continued treatment with lenalidomide has a significant impact on survival by improving the depth and duration of response. This highlights the value of adverse event management and appropriate dose adjustments to prevent toxicity, and of allowing continued treatment until disease progression. In this review, we will discuss the different lenalidomide-based treatment regimens for patients with relapsed/refractory myeloma. This is accompanied by recommendations of how to manage and prevent adverse events associated with lenalidomide-based therapy.