gebhart/patrepeval huggingface dataset:
Interactions between RNA polymerase II, factors, and template leading to accurate transcription. (1984)

Accurate transcription by RNA polymerase II has been shown to require multiple factors in addition to the purified polymerase. In this study, we use a reconstituted transcription system, consisting of purified RNA polymerase II and three essential HeLa cell chromatographic fractions, to study events leading to transcription from the adenovirus major late promoter. A preincubation-pulse-chase protocol resolves the reaction into events occurring before and after nucleotide addition. Preincubation of template with a mixture of RNA polymerase II and factors allows formation of "activated" complexes, which are defined by the ability to rapidly commence accurate transcription when presented nucleotides. Maximal activation requires that polymerase, template, and each of the three HeLa fractions be present during preincubation. The activated complexes are template associated, as shown by their inability to exchange onto a second template added during further preincubation. Similar protocols are used to define functional intermediates leading to the activated complex. A template-associated functional complex is formed during the preincubation of template with just two of the HeLa fractions. Polymerase can associate with this intermediate complex in the absence of the third HeLa fraction. In the accompanying paper, we describe a direct analysis of initiation by "activated" complexes.
Selective recruitment of CCR6-expressing cells by increased production of MIP-3α in rheumatoid arthritis (2001)

Infiltration of various types of leucocytes has been shown to play a crucial role in the pathogenesis of rheumatoid arthritis (RA). Macrophage inflammatory protein-3 alpha (MIP-3 alpha) is a recently identified chemokine which is a selective chemoattractant for leucocytes such as memory T cells, naïve B cells and immature dendritic cells. In this study, we investigated the expression of MIP-3 alpha and its specific receptor CCR6 in the inflamed joints of patients with RA. Increased amounts of MIP-3 alpha were found by ELISA in synovial fluids (SF) of patients with RA. MIP-3 alpha was apparently detected in all synovial tissue specimens of RA patients (n = 6), but it could not be detected in that of osteoarthritis (OA) patients (n = 4). Expression of MIP-3 alpha was detected especially in the sublining layer, and infiltrating mononuclear cells in RA synovial tissue. Gene expression of MIP-3 alpha was also found in six out of 11 RA-synovial fluid cells by RT-PCR. Cultured synovial fibroblasts derived from either RA or OA patients were capable of producing MIP-3 alpha in response to IL-1 beta and TNFalpha in vitro. Furthermore, expression of CCR6 was found in infiltrating mononuclear cells in the cellular clusters and around the vessels of RA synovial tissue. These findings indicate that increased production of MIP-3 alpha may contribute to the selective recruitment of CCR6-expressing cells in RA.
A minimum interference routing algorithm for a linear lightwave network (2002)

A routing algorithm for setting up point to point connection is proposed for a linear lightwave network (LLN). The overall problem of routing is decomposed into the subproblems of physical path allocation, checking for violations of some of the special constraints (MISC (mutually independent sources combining) and color clash) of the LLN on the allocated physical path and the allocation of an appropriate channel. It is shown that the problem of finding a physical path that does not violate the MISC constraint of the LLN is NP-complete.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Use of metadata registries for searching for statistical data (2003)

The Internet has spawned an insatiable appetite for information. This appetite cannot be satisfied without useful search tools. These tools rely on metadata in order to give targeted and meaningful results to searches, and the Internet world is realising that metadata, its management, and the means to search these metadata, are an integral part of the Internet world. The EC 5th Framework project COSMOS aims to demonstrate the use of metadata in this way by building a common model for describing a statistical data set in terms of metadata, populating a metadata registry with descriptions consistent with the model, and searching the registry to find the data sets, and finally to access the data sets in the relevant repository.
SUBLINGUAL MUCOSA AS A ROUTE FOR SYSTEMIC DRUG DELIVERY (2011)

Drug delivery via the oral mucous membrane is considered to be a promising alternative to the oral route. Sublingual route is a useful when rapid onset of action is desired with better patient compliance than orally ingested tablets. In terms of permeability, the sublingual area of the oral cavity (i.e. the floor of the mouth) is more permeable than the buccal (cheek) area, which in turn is more permeable than the palatal (roof of the mouth) area. The portion of drug absorbed through the sublingual blood vessels bypasses the hepatic first‐pass metabolic processes giving acceptable bioavailability. Various techniques can be used to formulate sublingual tablets. New sublingual technologies address many pharmaceutical and patient needs, ranging from enhanced life‐cycle management to convenient dosing for paediatric, geriatric, and psychiatric patients with dysphagia. This review highlights the different sublingual dosage forms, factors affecting the sublingual absorption, advantages, various in vitro and in vivo evaluation parameters and commercially available sublingual dosage forms.
Matrix‐Assisted Laser Desorption/Ionization Time‐of‐Flight Mass Spectrometry of Oligonucleotides (2008)

MALDI-MS is one of the most useful techniques available for determining biomolecule mass. It offers high mass accuracy, good sensitivity, simplicity, and speed. Because singly charged ions of oligonucleotides are typically observed, MALDI-MS spectra are easy to interpret. This unit presents protocols for sample preparation and purification, matrix preparation, and matrix/analyte sample preparation. It provides an introduction to the instrumentation and its calibration, and a discussion of some of the useful applications of MALDI-MS analysis in the study of oligonucleotides. This technique is typically used for 120-mer or smaller oligonucleotides.
Comparison and evaluation of data mining techniques with algorithmic models in software cost estimation (2012)

Software Cost Estimation (SCE) is one of important topics in producing software in recent decades. Real estimation requires cost and effort factors in producing software by using of algorithmic or Artificial Intelligent (AI) techniques. Boehm developed the Constructive Cost Model (COCOMO) that is one of the algorithmic SCE models. Also, these models contain three increasingly basic, intermediate and detailed forms, i.e. basic COCOMO is suitable for quick, early, rough order of among the estimates of required effort in producing software, but its accuracy is limited due to its loss of factors to account for difference between cost drivers. Intermediate COCOMO assumes these project attributes into account. In addition detailed COCOMO accounts for individual project phases used. The COCOMO algorithmic techniques families have used since 1981. In recent years, some techniques emerged by using intelligent techniques to solve and estimate the effort required in producing software. In this paper, different data mining techniques to estimate software costs are presented and then the results of each technique are evaluated and compared. However, NASA's projects to train and test each of these techniques are applied. Then, data set to train and test the data mining techniques improve the estimation accuracy of the models in many cases. We show the comparison between COCOMO model and data mining techniques here. The results indicate that these methods result in many benefit answers. Also we show the comparison of the estimation accuracy of COCOMO model with data mining techniques. Data mining techniques improve the estimation accuracy of the models in many cases. So the estimated effort more improvement in this models.
Alcoholytic deblocking of N‐terminally acetylated peptides and proteins for sequence analysis (1996)

N-terminal acetylation of polypeptides is a common feature preventing direct Edman degradation. We describe a method for the removal of the acetyl group, with only a low extent of internal peptide bond cleavage, also in large proteins, by treatment at room temperature with trifluoroacetic acid and methanol. The alcohol is essential for selective deacetylation, and it is proposed that the deblocking mechanism consists of an acid-catalyzed nucleophilic substitution involving methanol. The extent of deacetylation is limited, but the initial yield in the sequence analysis can be up to 10%. Deblocking of samples spotted or blotted onto sequencer filters is equally possible as the use of isolated samples from column separations. Deblocking on sequencer filters is also possible directly after negative results on initial sequencer attempts with samples proving to be blocked.
Intertemporal and interspatial comparisons of income : the meaning of relative prices (1993)

The conceptual issues confronting compilers of price indices have not changed much over the years. They include the intractability of basic index-number problems, the practical difficulties of sampling and matching prices, and the uncertainties about the appropriate weighting scheme for comparing events in specific locales over time and across locales. The author considers inconsistencies in some measures of time-to-time and place-to-place comparisons of income. He argues for a method that harmonizes price work across generally recognized national price compilations, such as consumer price indices (CPSs), the International Comparison Programme (ICP), and national accounting. Modern economies tend to be more open, so relative prices should be more similar, but it is increasingly apparent that price levels and trends can differ considerably even within a nation - particularly those encompassing economically heterogeneous areas. The global ICP exercise has provided useful insights into the issues involved. At the same time, international comparisons of the type ICP aims to facilitate are now seen as being more sensitive than expected to changes in relative prices. ICP has given little attention to this issue, but there is a rich literature on the subject with respect to CPS. The common ground for the two logics is essentially national accounts, broadly defined. Through conceptual and practical work done by the World Bank on the topic, the author suggests that harmonizing the various methods is essential to a proper interpretation of the market signals that prices send to economic agents. He also explains how a better synthesis reduces the overall cost of collecting relevant information and disseminating it to users.
Arthroscopic rotator cuff repair: suture anchor properties, modes of failure and technical considerations (2011)

Rotator cuff injury and tears are a common source of shoulder pain, particularly among the elderly. Arthroscopic repair has now become the mainstay in the treatment of significant injuries that have failed conservative therapy. Compared with the traditional open technique, arthroscopic repair offers patients smaller incisions and less soft-tissue trauma, which result in improved postoperative pain and rehabilitation. The advances that have made arthroscopic repairs a reality includes improvement in arthroscopic rotator cuff instrumentation, particularly suture anchors. Suture anchors are used to reattach the torn rotator cuff tissue back onto the bone. Current rotator cuff anchors vary by design, anchor composition and suture materials. A treating physician should be aware of the advantages and limitations of these implants, which may influence the choice of one anchor over another. In addition to anchor variables, other factors that may affect the success of the repair include the local environment and surgical technique. In this article, various aspects of anchor design will be discussed. In addition, a concise review of technical considerations will also be discussed.
Horizontal radials enhance oil production from a thermal project (1992)

Ultrashort radius horizontal radials have enhanced oil production from a cyclic thermal project conducted by the U.S. Department of Energy (DOE). The project demonstrated that this innovative drilling and completion system is applicable in thermal operations in heavy oil reservoirs. This paper reports that the radials improved the production stability in both the well with radials and offset wells. Production rate increased by two to four times. Gravity override was minimized or eliminated. Furthermore, the radials provided access to new reserves previously precluded from the vertical well due to reservoir heterogeneity or low reservoir energy. Their penetration beyond near well bore damage enhanced the oil production rate. The essentially flat production within the limitations of the heat input to the reservoir indicated stability.
Design of compactors for signature-analyzers in built-in self-test (2002)

Originally developed decades ago, logic built-in self-test (BIST) evolved and is now increasingly being adopted to cope with rapid growth in design size and complexity. Compared to deterministic pattern test, logic BIST requires many more test patterns, and therefore, increased test time unless many more internal scan chains can be shifted in parallel. To match this large number of scan chains, the width of the signature analyzer would have to be enlarged, which would result in large area overhead and signature storage space. Instead, a combinational space-compactor is inserted between the scan chain outputs and the signature analyzer inputs. However, the compactor may deteriorate the ability to test and diagnose the design. This paper analyzes how compactors affect test and diagnosis and shows that compactors can be designed to actually improve the testability of certain faults, while providing full diagnosis capability. Algorithms that allow automated design of optimal compactors are presented and results are discussed.
Competitive Binding of Cations to Duplex DNA Revealed through Molecular Dynamics Simulations (2012)

The concept of "ion atmosphere" is prevalent in both theoretical and experimental studies of nucleic acid systems, yet the spatial arrangement and the composition of ions in the ion atmosphere remain elusive, in particular when several ionic species (e.g., Na(+), K(+), and Mg(2+)) compete to neutralize the charge of a nucleic acid polyanion. Complementing the experimental study of Bai and co-workers (J. Am. Chem. Soc.2007, 129, 14981), here we characterize ion atmosphere around double-stranded DNA through all-atom molecular dynamics simulations. We demonstrate that our improved parametrization of the all-atom model can quantitatively reproduce the experimental ion-count data. Our simulations determine the size of the ion atmosphere, the concentration profiles of ionic species competing to neutralize the DNA charge, and the sites of the cations' preferential binding at the surface of double-stranded DNA. We find that the effective size of the ion atmosphere depends on both the bulk concentration and valence of ions: increasing either reduces the size of the atmosphere. Near DNA, the concentration of Mg(2+) is strongly enhanced compared to monovalent cations. Within the DNA grooves, the relative concentrations of cations depend on their bulk values. Nevertheless, the total charge of competing cations buried in the DNA grooves is constant and compensates for about ~30% of the total DNA charge.
Silicon on insulator material technology (1995)

A silicon on insulator material technology based on wafer bonding is described, in which a heat treatment induces an in-depth microslicing of one of the two bonded wafers previously implanted with hydrogen. The basic phenomena, and the first physical and electrical characterisations are discussed briefly.
Toward a Reactant Library in Template-Directed Solid-State Organic Synthesis:  Reactivity Involving a Monofunctional Reactant Based on a Stilbazole (2002)

Cocrystallization of 4-chlorostilbazole (4-Cl-sbz) with either resorcinol (res) or 4-ethylresorcinol (4-Et-res) yields three-component molecular assemblies, (res)·2(4-Cl-sbz) and (4-Et-res)·2(4-Cl-sbz), held together by two O−H···N hydrogen bonds. The olefins of each assembly conform to the distance criterion of Schmidt for [2+2] photoreaction. In the former, the olefins lie antiparallel, whereas in the latter, the olefins lie parallel. Both solids are photoactive, leading to the regiocontrolled solid-state synthesis of rctt-1,2-bis(4-pyridyl)-3,4-bis(4-chlorophenyl)cyclobutane (4-Cl-dpcb) in near or quantitative yield. The photoactivity of (res)·2(4-Cl-sbz) is attributed to the reactant undergoing a pedal-like change in conformation prior to cyclobutane formation. The ability to change the diol to achieve olefin alignment is expected to provide additional synthetic flexibility to this template approach.
Peptide−Nucleic Acid-Modified Ion-Sensitive Field-Effect Transistor-Based Biosensor for Direct Detection of DNA Hybridization (2006)

Here, we report the development of a peptide-nucleic acid (PNA)-modified ion-sensitive field-effect transistor (IS-FET)-based biosensor that takes advantage of the change in the surface potential upon hybridization of a negatively charged DNA. PNA was immobilized on a silicon nitride gate insulator by an addition reaction between a maleimide group introduced on the gate surface, the succinimide group of N-(6-maleimidocaproyloxy) succinimide, and the thiol group of the terminal cysteine in PNA. The surface was characterized after each step of the reaction by X-ray photoelectron spectroscopy analysis, and the kinetic analysis of the hybridization events was assessed by surface plasmon resonance. In addition, we measured the -potential before and after PNA-DNA hybridization in the presence of counterions to investigate the change in surface charge density at the surface-solution interface within the order of the Debye length. On the basis of the zeta-potential, the surface charge density, DeltaQ, calculated using the Grahame equation was approximately 4.0 x 10(-3) C/m2 and the estimated number of hybridized molecules was at least 1.7 x 10(11)/cm2. The I-V characteristics revealed that the PNA-DNA duplexes induce a positive shift in the threshold voltage, VT, and a decrease in the saturated drain current, ID. These results demonstrate that direct detection of DNA hybridization should be possible using a PNA-modified IS-FET-based biosensor. PNA is particularly advantageous for this system because it enables highly specific and selective binding at low ionic strength.
An Adaptive Algorithm for Motion Compensated Color Image Coding (1987)

This paper presents an adaptive algorithm for motion compensated color image coding. The algorithm can be used for video teleconferencing or broadcast signals. Activity segmentation is used to reduce the bit rate and a variable stage search is conducted to save computations. The adaptive algorithm is compared with the nonadaptive algorithm and it is shown that with approximately 60 percent savings in computing the motion vector and 33 percent additional compression, the performance of the adaptive algorithm is similar to the nonadaptive algorithm. The adaptive algorithm results also show improvement of up to 1 bit/pel over interframe DPCM coding with nonuniform quantization. The test pictures used for this study were recorded directly from broadcast video in color.
Multiple, heart-cross-reactive epitopes of streptococcal M proteins. (1985)

We present evidence that a highly purified pepsin extract of type 5 streptococcal M protein (pep M5) contains at least three epitopes that are cross-reactive with sarcolemmal membrane proteins of human myocardium. The tissue-cross-reactive determinants of pep M5 are also partially shared with pep M6 and pep M19. Three rabbits immunized with a single 300 micrograms dose of pep M5 developed significant levels of heart-cross-reactive antibodies, as determined by indirect immunofluorescence tests. All three sera also contained antibodies that cross-reacted with pep M6 and pep M19. The heart tissue--specific antibodies that were eluted from sarcolemmal membranes opsonized types 5, 6, and 19 streptococci, indicating that they were directed against protective M protein epitopes on the surface of virulent organisms. Immunofluorescence inhibition tests, using purified M proteins as soluble inhibitors of heart-cross-reactive antibodies, revealed the number and M protein serotype distribution of the tissue-cross-reactive epitopes. Immunoblot analyses demonstrated the sarcolemmal membrane proteins containing the various cross-reactive antigenic determinants.
Interaction-aware Multi-agent Tracking and Probabilistic Behavior Prediction via Adversarial Learning (2019)

In order to enable high-quality decision making and motion planning of intelligent systems such as robotics and autonomous vehicles, accurate probabilistic predictions for surrounding interactive objects is a crucial prerequisite. Although many research studies have been devoted to making predictions on a single entity, it remains an open challenge to forecast future behaviors for multiple interactive agents simultaneously. In this work, we take advantage of the Generative Adversarial Network (GAN) due to its capability of distribution learning and propose a generic multi-agent probabilistic prediction and tracking framework which takes the interactions among multiple entities into account, in which all the entities are treated as a whole. However, since GAN is very hard to train, we make an empirical research and present the relationship between training performance and hyperparameter values with a numerical case study. The results imply that the proposed model can capture both the mean, variance and multi-modalities of the groundtruth distribution. Moreover, we apply the proposed approach to a real-world task of vehicle behavior prediction to demonstrate its effectiveness and accuracy. The results illustrate that the proposed model trained by adversarial learning can achieve a better prediction performance than other state-of-the-art models trained by traditional supervised learning which maximizes the data likelihood. The well-trained model can also be utilized as an implicit proposal distribution for particle filtered based Bayesian state estimation.