gebhart/patrepeval huggingface dataset:
Nucleotide Sequence of a Pollen-Specific cDNA from Helianthus annuus L. Encoding a Highly Basic Protein (1994)

Pollen, as the male gametophyte, plays a vital role in the reproduction of flowering plants. Mature pollen grains contain mRNAs that are the products of approximately 20,000 different genes, of which up to 4000 may be pollen specific (Mascarenhas, 1990). In recent years, severa1 pollen-specific genes have been isolated from different plants. Some of these genes encode proteins showing amino acid homology to known hydrolytic enzymes, such as polygalacturonase (Allen and Lonsdale, 1993), pectin esterase (Albani et al., 1991), and pectate lyase (Wing et al., 1989). A11 of these genes are expressed after microspore mitosis and their transcripts accumulate considerably in mature pollen. So far, no sequence homology to known proteins has been detected in the other pollen-specific genes studied to date (Hanson et al., 1989). We report here the molecular characterization of another pollen-specific cDNA clone, SF16, from sunflower (Helianthus unnuus L.) (Table I). This gene is present in a single copy in the sunflower genome, expressed late in pollen development, and has no homology to other published sequences. In the original series of northem experiments (not including RNA from pollen), this clone was found to hybridize preferentially to RNA from pistils (Herdenberger et al., 1990); more recent and detailed expression studies revealed that the hybridization was due to contaminating pollen and that the single transcript of 1400 nucleotides can be detected exclusively in mature, free (tricellular) pollen. The transcript was not detected in yellow closed flowers, indicating that it is synthesized at a late stage of pollen development. The cDNA is 1293 nucleotides long with a 993-nucleotidelong open reading frame, starting at the first ATG codon of the cDNA sequence (positions 146-148) and tenninating with a TGA stop codon (positions 1139-1141). Although we have no experimental evidence that the cDNA is full length, the initiation codon can be identified without ambiguity because of the presence of an upstream in-frame stop codon TAA (positions 92-94). Translation of the SF16 cDNA sequence revealed an open
Solution Structure of LSIII, a Long Neurotoxin from the Venom of <i>Laticauda semifasciata</i><sup>,</sup> (1996)

We report the sequence-specific proton assignments and solution structure of the long neurotoxin LSIII from the venom of Laticauda semifasciata determined by two- and three-dimensional 1H NMR. Input for structure calculations consisted of 497 NOE-derived distance restraints and 45 dihedral angle restraints obtained from J couplings. A two-particle-per-residue representation of protein structure was used to generate 200 initial structures which were then subjected to all-atom refinement by simulated annealing. Twenty-three final structures consistent with the experimental restraints were obtained; the average atomic RMS difference between the individual structures and the mean structure was 0.82 A for the backbone heavy atoms and 1.3 A for all heavy atoms (residues 1-26, 37-60). The main elements of regular secondary structure are a three-stranded antiparallel beta-sheet and three finger-like loops protruding from a globular core, consistent with previously reported structures of long neurotoxins. The end of the prominent loop II, which is involved in binding to acetylcholine receptor, is disordered relative to the rest of the molecule. A novel finding of this study is that the loop has a well defined local structure; this and other observations suggest this region moves as a rigid body. We propose that this motion is a heretofore unrecognized general feature of long neurotoxins, with specific consequences for binding to the acetylcholine receptor.
Social Capital for Economic Development: Application of Time Series Cluster Analysis on Personal Network Structures (2013)

The availability of cell phone usage data opens up possibilities for using the insights from analysis of these datasets to guide policies and in turn boost economic development. In this paper, we propose the use of time series clustering to social network attributes and metrics as a way to quantify social capital. We demonstrate how our approach can allow policymakers to use the results from clustering to identify particular groups in the population and potentially provide assistance to boost social capital levels, and in turn economic growth.
<b>Studies on Polynucleotides. XXVII.</b><sup>1</sup> <b>The Stepwise Synthesis of Specific Deoxyribopolynucleotides (7).</b><sup>1</sup> <b>The Synthesis of Polynucleotides Containing Deoxycytidine and Deoxyguanosine in Specific Sequences and of Homologous Deoxycytidine Polynucleotides Terminating in Thymidine</b><sup>3</sup> (1963)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies on Polynucleotides. XXVII.1The Stepwise Synthesis of Specific Deoxyribopolynucleotides (7).1The Synthesis of Polynucleotides Containing Deoxycytidine and Deoxyguanosine in Specific Sequences and of Homologous Deoxycytidine Polynucleotides Terminating in Thymidine3H. Schaller and H. G. KhoranaCite this: J. Am. Chem. Soc. 1963, 85, 23, 3841–3851Publication Date (Print):December 1, 1963Publication History Published online1 May 2002Published inissue 1 December 1963https://pubs.acs.org/doi/10.1021/ja00906a024https://doi.org/10.1021/ja00906a024research-articleACS PublicationsRequest reuse permissionsArticle Views99Altmetric-Citations20LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Crystal and molecular structure of an N-arylporphyrin complex: chloro(N-phenyl-5,10,15,20-tetraphenylporphinato)zinc(II) (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCrystal and molecular structure of an N-arylporphyrin complex: chloro(N-phenyl-5,10,15,20-tetraphenylporphinato)zinc(II)Debasish Kuila, David K. Lavalee, Cynthia K. Schauer, and Oren P. AndersonCite this: J. Am. Chem. Soc. 1984, 106, 2, 448–450Publication Date (Print):January 1, 1984Publication History Published online1 May 2002Published inissue 1 January 1984https://pubs.acs.org/doi/10.1021/ja00314a047https://doi.org/10.1021/ja00314a047research-articleACS PublicationsRequest reuse permissionsArticle Views89Altmetric-Citations16LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Power spectral estimates using two-dimensional Morlet-fan wavelets with emphasis on the long wavelengths: jackknife errors, bandwidth resolution and orthogonality properties (2013)

We present a method for estimating the errors on local and global wavelet power spectra using the jackknife approach to error estimation, and compare results with jackknifed multitaper (MT) spectrum estimates. We test the methods on both synthetic and real data, the latter being free air gravity over the Congo Basin. To satisfy the independence requirement of the jackknife we investigate the orthogonality properties of the 2-D Morlet wavelet. Although Morlet wavelets are non-orthogonal, we show that careful selection of parameters can yield approximate orthogonality in space and azimuth. We also find that, when computed via the Fourier transform, the continuous wavelet transform (CWT) contains errors at very long wavelengths due to the discretization of large-scale wavelets in the Fourier domain. We hence recommend the use of convolution in the space-domain at these scales, even though this is computationally more expensive. Finally, in providing an investigation into the bandwidth resolution of CWT and MT spectra and errors at long wavelengths, we show that the Morlet wavelet is superior in this regard to Slepian tapers. Wavelets with higher bandwidth resolution deliver smaller spectral error estimates, in contrast to the MT method, where tapers with higher bandwidth resolution deliver larger errors. This results in the fan-WT having better spectral estimation properties at long wavelengths than Slepian MTs.
PREVENTION OF INFECTION OF URINARY TRACT IN PRESENCE OF INDWELLING CATHETERS (1959)

Catheters kept in the urinary bladder as long as four days provoke bacteriuria in almost every case. The technique here described prevents this complication by continuous irrigation with 0.25% acetic acid through a catheter with three lumens. One passage permits distention of the retaining balloon; the other two passages are for inflow and outflow. The method was successful in more than 100 patients. The rate of inflow of the acetic acid solution was roughly equal to that of urine production, but it was adjusted so that the effluent was kept at pH 5.0 or less and the bacterial count at less than 1 million per milliliter. Outflow was interrupted periodically by use of an electromechanical valve to permit filling of the bladder and avoid prolonged contraction. In some patients it was possible to leave the catheter in situ as long as 60 days without inducing bacteriuria.
Ultrasonic measurements of the elastic moduli of ultradrawn polyoxymethylene (1987)

Abstract We have employed an ultrasonic method to measure from −40 to 60°C the five independent elastic moduli C 11 , C 13 , C 33 , C 44 , and C 66 of polyoxymethylene with draw ratio λ from 1 to 26 prepared by continuous drawing under microwave heating. The elastic moduli are controlled by three major factors: molecular orientation in the crystalline regions, fraction of noncrystalline taut tie molecules, and void content. The steep rise in the axial extensional modulus C 33 and axial Young's modulus E 0 with increasing draw ratio results from the alignment of chains in the crystalline blocks and an increase in the number of disordered taut tie molecules. Below the γ relaxation (located at 0°C at our measurement frequency of 10 MHz), these two factors also give rise to a slight decrease in the transverse extensional modulus C 11 , Young's modulus E 90 and shear modulus C 66 . At high temperature where the amorphous regions have very low modulus, the stiffening effect of taut tie molecules becomes dominant, leading to an increase in all moduli as λ increases from 1 to 10. At higher λ the void fraction increases appreciably, causing small decreases in E 90 , C 11 , and C 66 at all temperatures.
Efficient Language Model Construction for Spoken Dialog Systems by Inducting Language Resources of Different Languages. (2012)

Since the quality of the language model directly affects the performance of the spoken dialog system (SDS), we should use a statistical language model (LM) trained with a large amount of data that is matched to the task domain. When porting a SDS to another language, however, it is costly to re-collect a large amount of user utterances in the target language. We thus use the language resources in a source language by utilizing statistical machine translation. The main challenge in this work is to induct automatic speech recognition results collected using a speech-input system that differs from the target SDS both in the task and the target language. To select appropriate sentences to be included in the training data for the LM, we induct a spoken language understanding module of the dialog system in the source language. Experimental construction using over three million user utterances showed that it is vital to conduct a selection from the translation results.
ChemInform Abstract: Advances on the Growth and Properties of N‐ and B‐Doped Carbon Nanotubes. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Temperature and injection water source influence microbial community structure in four Alaskan North Slope hydrocarbon reservoirs (2014)

A fundamental knowledge of microbial community structure in petroleum reservoirs can improve predictive modeling of these environments. We used hydrocarbon profiles, stable isotopes, and high-density DNA microarray analysis to characterize microbial communities in produced water from four Alaskan North Slope hydrocarbon reservoirs. Produced fluids from Schrader Bluff (24-27°C), Kuparuk (47-70°C), Sag River (80°C), and Ivishak (80-83°C) reservoirs were collected, with paired soured/non-soured wells sampled from Kuparuk and Ivishak. Chemical and stable isotope data suggested Schrader Bluff had substantial biogenic methane, whereas methane was mostly thermogenic in deeper reservoirs. Acetoclastic methanogens (Methanosaeta) were most prominent in Schrader Bluff samples, and the combined δD and δ(13)C values of methane also indicated acetoclastic methanogenesis could be a primary route for biogenic methane. Conversely, hydrogenotrophic methanogens (e.g., Methanobacteriaceae) and sulfide-producing Archaeoglobus and Thermococcus were more prominent in Kuparuk samples. Sulfide-producing microbes were detected in all reservoirs, uncoupled from souring status (e.g., the non-soured Kuparuk samples had higher relative abundances of many sulfate-reducers compared to the soured sample, suggesting sulfate-reducers may be living fermentatively/syntrophically when sulfate is limited). Sulfate abundance via long-term seawater injection resulted in greater relative abundances of Desulfonauticus, Desulfomicrobium, and Desulfuromonas in the soured Ivishak well compared to the non-soured well. In the non-soured Ivishak sample, several taxa affiliated with Thermoanaerobacter and Halomonas predominated. Archaea were not detected in the deepest reservoirs. Functional group taxa differed in relative abundance among reservoirs, likely reflecting differing thermal and/or geochemical influences.
A new nondestructive assay system combining both neutron and gamma-ray detectors (2002)

A novel nondestructive assay system (four separate identical units) has been constructed which combines a neutron coincidence counter and a high-resolution gamma-ray detector for the simultaneous measurement of plutonium items. The measurement systems have been developed to be used in an unattended mode with the items being presented to the detector automatically as part of the routine handling arrangements in a remotely operated facility. The neutron coincidence counter has been designed to acquire spectra during the neutron coincidence measurement. Particular attention has been paid to the detector layout, shielding collimation, and support and housing. The gamma-ray detector operates continuously in an unattended mode using a closed-cycle helium refrigerator. The neutron counter has been calibrated for the assay of multi-can containers of PuO/sub 2/ powder.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Coherent Transmission of THz Wave through Randomly Packed Subwavelength-sized Aluminium Particles (2006)

In the experiments of THz wave transmission through an ensemble of randomly packed aluminium particles with subwavelength sizes, we observed a strong dependence of the transmission on the lateral boundary conditions. Our results clearly showed that the processes of THz wave re-emitting from the disk-shaped samples were pure surface modes, and it is critically affected by properties of the side interface and the diameter of samples.
Novel <i>TRAF1‐ALK</i> fusion identified by deep RNA sequencing of anaplastic large cell lymphoma (2013)

Chromosomal translocations leading to expression of abnormal fusion proteins play a major role in the pathogenesis of various hematologic malignancies. The recent development of high-throughput, "deep" sequencing has allowed discovery of novel translocations leading to a rapid increase in understanding these diseases. Translocations involving the anaplastic lymphoma kinase (ALK) gene leading to ALK fusion proteins originally were discovered in anaplastic large cell lymphomas (ALCLs). Among ALCLs, NPM1-ALK fusions are most common and lead to nuclear localization of the fusion protein. Here, we present a 50-year-old male with ALCL demonstrating cytoplasmic ALK immunoreactivity only, suggesting the presence of a non-NPM1 fusion partner. We performed deep RNA sequencing of tumor tissue from this patient and identified a novel transcript fusing Exon 6 of TRAF1 to Exon 20 of ALK. The TRAF1-ALK fusion transcript was confirmed at the mRNA level by Sanger sequencing and the fusion protein was visualized by Western blot. The discovery of this TRAF1-ALK fusion expands the diversity of known ALK fusion partners and highlights the power of deep sequencing for fusion transcript discovery. © 2013 Wiley Periodicals, Inc.
Specific Ion Effects: Why DLVO Theory Fails for Biology and Colloid Systems (2001)

The classical Derjaguin-Landau-Verwey-Overbeek theory that underpins colloid and surface science is shown to be flawed, especially at biological salt concentrations. This is in part because the dispersion forces acting on the ions are ignored. When these are included properly very different results are obtained. These results have substantial implications for biological and for ordinary colloid systems at moderate salt concentrations.
CHOPER Filters Enable Rare Mutation Detection in Complex Mutagenesis Populations by Next-Generation Sequencing (2015)

Next-generation sequencing (NGS) has revolutionized genetics and enabled the accurate identification of many genetic variants across many genomes. However, detection of biologically important low-frequency variants within genetically heterogeneous populations remains challenging, because they are difficult to distinguish from intrinsic NGS sequencing error rates. Approaches to overcome these limitations are essential to detect rare mutations in large cohorts, virus or microbial populations, mitochondria heteroplasmy, and other heterogeneous mixtures such as tumors. Modifications in library preparation can overcome some of these limitations, but are experimentally challenging and restricted to skilled biologists. This paper describes a novel quality filtering and base pruning pipeline, called Complex Heterogeneous Overlapped Paired-End Reads (CHOPER), designed to detect sequence variants in a complex population with high sequence similarity derived from All-Codon-Scanning (ACS) mutagenesis. A novel fast alignment algorithm, designed for the specified application, has O(n) time complexity. CHOPER was applied to a p53 cancer mutant reactivation study derived from ACS mutagenesis. Relative to error filtering based on Phred quality scores, CHOPER improved accuracy by about 13% while discarding only half as many bases. These results are a step toward extending the power of NGS to the analysis of genetically heterogeneous populations.
On The Accuracy of TCP Throughput Prediction for Opportunistic Wireless Networks (2009)

The increasing density of WiFi access points (APs) in metropolitan areas is enabling an opportunistic model of wireless networking, whereby a "guest" user within range of one or more wireless APs can gain temporary Internet access through these APs. In this paper, we address the problem of TCP throughput prediction for opportunistic networks. Applications of opportunistic networking can benefit from such predictions by adapting to prevailing network conditions. Our approach is different from prior efforts to model wireless network throughput in that only the two communicating endpoints participate in the prediction, and no information about network topology or traffic loads generated by interfering sources is required. Our goal is to understand how accurate throughput predictions can be under the above assumptions. The physical environment considered in our study includes varying degrees of interference, indoor and outdoor networks, and nodes that are stationary or moving at walking or driving speeds. We use throughput predictors based on time series analysis and machine learning techniques, as they are well-suited to predicting phenomena with unknown variables. The prediction accuracy that our methods yield is cause for cautious optimism. We find that 80% to 100% of predictions are within a factor of two of actual throughput. This bound on accuracy means that predictions are useful for certain applications, because this bound (a) can be achieved by measurements lasting for as little as 0.3 seconds, and (b) holds even when nodes are driving at speeds of 15-25 mph.
The role of mitochondrial kinases in phospho- and lipid transfer (2013)

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