gebhart/patrepeval huggingface dataset:
Word Cloud Model for Text Categorization (2011)

In centroid-based classification, each class is represented by a prototype or centroid document vector that is formed by averaging all member vectors during the training phase. In the prediction phase, the label of a test document vector is assigned to that of its nearest class prototype. Recently there has been revived interest in reformulating the prototype/centroid to improve classification performance. In this paper, we study the theoretical properties of the recently proposed Class Feature Centroid (CFC) classifier by considering the rate of change of each prototype vector with respect to individual dimensions (terms). The implication of our theoretical finding is that CFC is inherently biased towards large (dominant majority) classes, which means it is destined to perform poorly for highly class-imbalanced data. Another practical concern about CFC lies in its overly-aggressive design in weeding out terms that appear in all classes. To overcome these CFC limitations while retaining its intrinsic and worthy design goals, we propose an improved and robust centroid-based classifier that uses precise term-class distribution properties instead of simple presence or absence of terms in classes. Specifically, terms are weighted based on the Kullback-Leibler divergence measure between pairs of class-conditional term probabilities, we call this the CFC-KL centroid classifier. We then generalized CFC-KL to handle multi-class data by summing pair wise class-conditioned word probability ratios. Our proposed approach has been evaluated on 5 datasets, on which it consistently outperforms CFC and the baseline Support Vector Machine classifier. We also devise a word cloud visualization approach to highlight the important class-specific words picked out by our CFC-KL, and visually compare it with other popular term weigthing approaches. Our encouraging results show that the centroid based generalized CFC-KL classifier is both robust and efficient to deal with real-world text classification.
Conversion of Pyruvic Acid Fermentation to Tryptophan Production by the Combination of Pyruvic Acid-producing Microorganisms and<i>Enterobacter aerogenes</i>Having High Tryptophanase Activity (1984)

Conditions for tryptophan synthesis from pyruvic acid, indole and NH4Cl by Enterobacter aerogenes AHU 1540 having a high tryptophanase activity, were investigated using a reaction mixture containing 1.7% of pyruvic acid. Under optimum conditions, 16.4g/liter of tryptophan was accumulated after 24 hr of incubation. Agaricus campestris AHU 9382 produced pyruvic acid in amounts of 22 ~ 26.5 g/liter from 5% of glucose after 3-days shaking culture. When E. aerogenes was added to this fermentation broth together with indole and NH4Cl, pyruvic acid produced was rapidly converted to tryptophan and yields of tryptophan as high as 15 g/liter were obtained after 12 hr of incubation. Furthermore, pyruvic acid fermentation by Saccharomyces exiguus AHU 3110 or Corynebacterium sp. 37-3A could also be used as a pyruvic acid source for subsequent tryptophan production.
De- and remyelination in the CNS white and grey matter induced by cuprizone: the old, the new, and the unexpected. (2011)

The copper chelator cuprizone (bis-cyclohexanone oxaldihydrazone) was established as a neurotoxin in rodents in 1966 by Carlton. During the following years the usefulness of cuprizone feeding in mice to induce oligodendrocyte death with secondary demyelination of the superior cerebellar peduncles was described by Blakemore. In 1998 the cuprizone model experienced a renaissance as the group of Matsushima described the effects of cuprizone on the white matter of the cerebrum and focussed on demyelination in the corpus callosum, where the extent of demyelination could be scored more easily and consistently. Since then the toxic cuprizone model has been widely used to study experimental de- and remyelination in the corpus callosum. Recently, we and others have extended these studies and have shown several new aspects characteristic for this model. Many lessons can be learned from these recent findings that have implications for the basic understanding of remyelination and the design of remyelinating and neuroprotective strategies in demyelinating diseases of the CNS. Although the model is often mentioned in the context of multiple sclerosis, it must always be kept in mind that this model has a fundamentally different induction of demyelination. We highlight the important findings delineated from this model and critically discuss both the advantages and the shortcomings of cuprizone induced demyelination.
The Genome of <i>M. acetivorans</i> Reveals Extensive Metabolic and Physiological Diversity (2002)

Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived from acetate. Here we report the complete genome sequence of an acetate-utilizing methanogen, Methanosarcina acetivorans C2A. Methanosarcineae are the most metabolically diverse methanogens, thrive in a broad range of environments, and are unique among the Archaea in forming complex multicellular structures. This diversity is reflected in the genome of M. acetivorans. At 5,751,492 base pairs it is by far the largest known archaeal genome. The 4524 open reading frames code for a strikingly wide and unanticipated variety of metabolic and cellular capabilities. The presence of novel methyltransferases indicates the likelihood of undiscovered natural energy sources for methanogenesis, whereas the presence of single-subunit carbon monoxide dehydrogenases raises the possibility of nonmethanogenic growth. Although motility has not been observed in any Methanosarcineae, a flagellin gene cluster and two complete chemotaxis gene clusters were identified. The availability of genetic methods, coupled with its physiological and metabolic diversity, makes M. acetivorans a powerful model organism for the study of archaeal biology. [Sequence, data, annotations and analyses are available at http://www-genome.wi.mit.edu/.]
Site-specific mutagenesis of the alpha-helices of calmodulin. Effects of altering a charge cluster in the helix that links the two halves of calmodulin. (1987)

Alteration of residues 82-84 in the alpha-helix that links the two halves of calmodulin results in a differential effect on activator activity. Previous studies (Lukas, T. J., Burgess, W. H., Prendergast, F. G., Lau, W., and Watterson, D. M. (1986) Biochemistry 25, 1458-1464) indicated the importance of positive charge clusters in the calmodulin-binding protein, myosin light chain kinase. This suggested the possible importance of complementary negative charge clusters in calmodulin. By using an efficient cassette mutagenesis approach and a synthetic calmodulin gene (Roberts, D. M., Crea, R., Malecha, M., Alvarado-Urbina, G., Chiarello, R. H., and Watterson, D. M. (1985) Biochemistry 24, 5090-5098), this possibility was directly addressed by engineering a new calmodulin, VU-8 calmodulin, in which the glutamate cluster at residues 82-84 in the synthetic gene product (VU-1 calmodulin) was replaced by three lysines. VU-8 calmodulin activated phosphodiesterase to the same maximal extent as VU-1 calmodulin, although there was an alteration in the concentration of calmodulin required for half-maximal stimulation. In contrast, myosin light chain kinase was activated to only 30% of maximal activity and NAD kinase was not activated. These results provide insight into the functional role of the unusual central helix structure found in the calmodulin family of proteins and indicate that different, although possibly overlapping, chemical complementarities are employed in the interaction between calmodulin and its various physiological targets.
Incorporation of Isosorbide into Poly(butylene terephthalate) via Solid-State Polymerization (2008)

The biomass-based monomer isosorbide was incorporated into poly(butylene terephthalate) (PBT) by solid-state polymerization (SSP) using the macrodiol monomer BTITB-(OH) 2, which consists of isosorbide (I), terephthalic acid (T), and 1,4-butandiol (B) residues. This macromonomer can be synthesized by a simple one-pot, two-step reaction. Polymers with number-average molecular weights up to 100,000 g x mol (-1) were readily synthesized from various ratios of PBT/BTITB-(OH) 2. Their molecular weights, thermal properties, and colors were compared with corresponding copolyesters that were obtained by melt polycondensation. We found that T m, T c, and especially T g were superior for materials that were obtained by SSP. This is ascribed to differences in the microstructures of both types of copolyesters; the SSP products exhibit a more blocky structure than do the more random melt-polymerized counterparts. The SSP method resulted in much higher molecular weights and much less colored polymers, and it seems to be the preferred route for incorporating biobased monomers that exhibit limited thermal stability into engineering plastics.
Pancreatic Resection Versus Peritoneal Lavage in Acute Necrotizing Pancreatitis (1991)

Twenty-one patients with acute fulminant alcoholic pancreatitis were randomly allocated to either pancreatic resection group (11 patients) or nonoperative peritoneal lavage group (10 patients). Only patients under 50 years were included in the study to minimize the role of other severe disease. These patients represented the most severe cases of acute pancreatitis at our Department, constituting only 2% of all patients with acute pancreatitis during this period. The diagnosis was based on clinical symptoms and on signs indicating severely impaired systemic organ functions. All patients underwent contrast-enhanced computed tomography (CT), which showed contrast enhancement below 30 Hounsfield units. In the operated cases, the diagnosis of necrotizing pancreatitis was verified histologically. All patients with conservative treatment had dark brown fluid at peritoneal puncture. There was a difference (nonsignificant) in mortality (3/11 and 1/10, respectively), complication rate, or in the need of reoperations between the groups. Nonoperative peritoneal lavage was followed with shorter treatment at the intensive care unit (16.2 versus 25.9 days, respectively). The hospital stay also was significantly shorter in the nonoperative group (44.3 versus 56.1 days). The results indicate that intensive conservative treatment is justified as an initial therapy even in the most severe cases of acute pancreatitis.
Catalytic Copolymerization of Ethylene and Norbornene in Emulsion (2006)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTCatalytic Copolymerization of Ethylene and Norbornene in EmulsionKirill M. Skupov, Pooja R. Marella, Jason L. Hobbs, Lester H. McIntosh, Brian L. Goodall, and Jerome P. ClaverieView Author Information Materials Science Program, University of New Hampshire, Durham, New Hampshire 03824, and Emerging Technology Department, Rohm and Haas Company, 727 Norristown Road, PO Box 904, Spring House, Pennsylvania 19477 Cite this: Macromolecules 2006, 39, 13, 4279–4281Publication Date (Web):June 1, 2006Publication History Received15 May 2006Revised21 May 2006Published online1 June 2006Published inissue 1 June 2006https://pubs.acs.org/doi/10.1021/ma061089hhttps://doi.org/10.1021/ma061089hrapid-communicationACS PublicationsCopyright © 2006 American Chemical SocietyRequest reuse permissionsArticle Views828Altmetric-Citations56LEARN 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 SUBJECTS:Catalysts,Emulsions,Hydrocarbons,Polymers,Radical polymerization Get e-Alerts
R Region Sequences in the Long Terminal Repeat of a Murine Retrovirus Specifically Increase Expression of Unspliced RNAs (1999)

A stem-loop structure at the 5' end of the R region of the long terminal repeat (LTR) of the murine leukemia virus SL3 and other type C mammalian retroviruses is important for maximum levels of expression of a reporter gene under the control of the viral LTR. This element, termed the R region stem-loop (RSL), has a small effect on transcriptional initiation and no effect on RNA polymerase processivity. Its major effect is on posttranscriptional processing of LTR-driven transcripts. Here we tested whether the RSL affected the production of RNAs from a full-length SL3 genome. Mutation of the RSL in the 5' LTR of SL3 reduced the cytoplasmic levels of full-length viral transcripts but not those of spliced, env mRNA transcripts. Thus, the RSL specifically affected the cytoplasmic levels of the unspliced viral RNA. To test further whether the effect was specific for unspliced transcripts, a system was devised in which the expression of a reporter gene under the control of the viral LTR was tested in the presence or absence of an intron. Mutation of the RSL resulted in only about a twofold decline in the level of reporter gene expression when the transcripts contained an intron. However, when the intron was removed, mutation of the RSL reduced expression of the reporter gene about 10- to 60-fold in various cell lines. The secondary structure of the RSL was essential for its activity on the intronless transcript. Thus, the RSL appears to be important for the cytoplasmic accumulation of unspliced viral RNA and unspliced RNA from chimeric transcription units under the control of the viral LTR.
Plant Receptor-Like Kinase Gene Family: Diversity, Function, and Signaling (2001)

Plant receptor-like kinases (RLKs) are transmembrane proteins with putative amino-terminal extracellular domains and carboxyl-terminal intracellular kinase domains, with striking resemblance in domain organization to the animal receptor tyrosine kinases such as epidermal growth factor receptor. The recently sequenced Arabidopsis genome contains more than 600 RLK homologs, representing nearly 2.5% of the annotated protein-coding genes in Arabidopsis. Although only a handful of these genes have known functions and fewer still have identified ligands or downstream targets, the studies of several RLKs such as CLAVATA1, Brassinosteroid Insensitive 1, Flagellin Insensitive 2, and S-locus receptor kinase provide much-needed information on the functions mediated by members of this large gene family. RLKs control a wide range of processes, including development, disease resistance, hormone perception, and self-incompatibility. Combined with the expression studies and biochemical analysis of other RLKs, more details of RLK function and signaling are emerging.
Dexamethasone Treatment of Virilizing Congenital Adrenal Hyperplasia: The Ability to Achieve Normal Growth (2000)

These observations show that children treated with dexamethasone for CAH can achieve normal growth with the convenience of once-a-day dosing in most cases.congenital adrenal hyperplasia, dexamethasone, growth.
The RNA-dependent RNA polymerases of different members of the family Flaviviridae exhibit similar properties in vitro (1999)

The virus-encoded RNA-dependent RNA polymerase (RdRp), which is required for replication of the positive-strand RNA genome, is a key enzyme of members of the virus family Flaviviridae. By using heterologously expressed proteins, we demonstrate that the 77 kDa NS5B protein of two pestiviruses, bovine viral diarrhoea virus and classical swine fever virus, and the 100 kDa NS5 protein of the West Nile flavivirus possess RdRp activity in vitro. As originally shown for the RdRp of hepatitis C virus, RNA synthesis catalysed by the pestivirus and flavivirus enzymes is strictly primer-dependent in vitro. Accordingly, initiation of RNA polymerization on homopolymeric RNAs and heteropolymeric templates, the latter with a blocked 3'-hydroxyl group, was found to be dependent on the presence of complementary oligonucleotide primer molecules. On unblocked heteropolymeric templates, including authentic viral RNAs, the RdRps were shown to initiate RNA synthesis via intramolecular priming at the 3'-hydroxyl group of the template and 'copy-back' transcription, thus yielding RNase-resistant hairpin molecules. Taken together, the RdRps of different members of the Flaviviridae were demonstrated to exhibit a common reactivity profile in vitro, typical of nucleic acid-polymerizing enzymes.
The immeasurable wrongfulness of being : the denial of the claim for wrongful life (2010)

CITATION: Human, S. &amp; Mills, L. 2010. The immeasurable wrongfulness of being : the denial of the claim for wrongful life. Stellenbosch Law Review = Stellenbosch Regstydskrif 21(1):67-89.
NRC-Interacting Factor 1 Is a Novel Cotransducer That Interacts with and Regulates the Activity of the Nuclear Hormone Receptor Coactivator NRC (2002)

We previously reported the cloning and characterization of a novel nuclear hormone receptor transcriptional coactivator, which we refer to as NRC. NRC is a 2,063-amino-acid nuclear protein which contains a potent N-terminal activation domain and several C-terminal modules which interact with CBP and ligand-bound nuclear hormone receptors as well as c-Fos and c-Jun. In this study we sought to clone and identify novel factors that interact with NRC to modulate its transcriptional activity. Here we describe the cloning and characterization of a novel protein we refer to as NIF-1 (NRC-interacting factor 1). NIF-1 was cloned from rat pituitary and human cell lines and was found to interact in vivo and in vitro with NRC. NIF-1 is a 1,342-amino-acid nuclear protein containing a number of conserved domains, including six Cys-2/His-2 zinc fingers, an N-terminal stretch of acidic amino acids, and a C-terminal leucine zipper-like motif. Zinc fingers 1 to 3 are potential DNA-binding BED finger domains recently proposed to play a role in altering local chromatin architecture. We mapped the interaction domains of NRC and NIF-1. Although NIF-1 does not directly interact with nuclear receptors, it markedly enhances ligand-dependent transcriptional activation by nuclear hormone receptors in vivo as well as activation by c-Fos and c-Jun. These results, and the finding that NIF-1 interacts with NRC in vivo, suggest that NIF-1 functions to regulate transcriptional activation through NRC. We suggest that NIF-1, and factors which associate with coactivators but not receptors, be referred to as cotransducers, which act in vivo either as part of a coactivator complex or downstream of a coactivator complex to modulate transcriptional activity. Our findings suggest that NIF-1 may be a functional component of an NRC complex and acts as a regulator or cotransducer of NRC function.
Analysis of Multicast ATM Switching Networks Using CRWR Scheme. (1998)

A (large) multicast ATM switch with external structure of output queueing and internal structure of buffered MINs (multistage interconnection networks) is considered in the paper, where the buffered MIN (also called switching network) is composed of switching elements with shared buffer output queueing. The cell replication while routing (CRWR) scheme is used in the switch to implement multicast function. In this paper, we study the performance of the switch with multicast traffic, mainly via computer simulations. The multicast traffic can be random and bursty. We found that compared to unicast traffic, multicast traffic with truncated geometric distribution of cell fanouts has only a slightly worse impact on the performance of switching elements in isolation or in the last stage of the switching network. The multicast traffic has no worse effect on the switch output buffer behavior and cell delay in the switching network. Moreover, using multiple MINs in parallel can substantially improve the switching network performance for highly bursty traffic. Some analytical approximations are given which could be useful in the dimensioning of switching networks.
The use of reverse transcriptase-polymerase chain reaction to investigate environmental samples for the presence of enteroviruses. (1998)

Molecular techniques developed for detection and diagnosis of enteric viruses have been adapted for use with water samples. Although problems of interference and sensitivity remain, reliable and consistent methods should soon be available for the detection in water of enteroviruses, Norwalk-like viruses, and rotavirus.
Glycerol formation after the breaking of dormancy of <i>Phycomyces blakesleeanus</i> spores (1985)

The breaking of dormancy of Phycomyces blakesleeanus spores by a heat shock was followed by a transient production of glycerol, which culminated within 5-10 min and was terminated at 20 min. Extracts of spores contained a magnesium-dependent glycerol-3-phosphatase active on both L-glycerol 3-phosphate and dihydroxyacetone phosphate but having more affinity for the first substrate than for the second. In extracts from dormant spores, the phosphatase was profoundly inhibited by physiological concentrations of inorganic phosphate, which induced cooperativity for the substrate, whereas the enzyme from heat-activated spores was much less inhibited and this difference in kinetic properties persisted after gel filtration of the enzymic preparation. When measured at 1 mM phosphate and 0.1 mM glycerol 3-phosphate, the phosphatase activity was undetectable in dormant spores, increased sharply during the heat treatment and the following 5 min at 25 degrees C, then fell again to a low value by 20 min. A similar transient activation of the enzyme was observed following the breaking of dormancy by incubation of the spores in the presence of 0.1 M ammonium acetate. Incubation of a cell-free extract or of the partially purified glycerol-3-phosphatase in the presence of ATP-Mg and the catalytic subunit of cyclic-AMP-dependent protein kinase released the enzyme from inhibition by phosphate and endowed it with the same kinetic properties as did the heat treatment of the spores. It appears therefore most likely that phosphorylation of glycerol-3-phosphatase by cyclic-AMP-dependent protein kinase causes its activation and that this transient process explains the equally transient formation of glycerol by the spores after the heat shock.
State of the art in surgical robotics: Clinical applications and technology challenges (2001)

Although it has been over 15 years since the first recorded use of a robot for a surgical procedure, the field of medical robotics is still an emerging one that has not yet reached a critical mass. Although robots have the potential to improve the precision and capabilities of physicians, the number of robots in clinical use is still very small. In this review article, we begin with a short historical review of medical robotics, followed by an overview of clinical applications where robots have been applied. The clinical applications are then discussed; they include neurosurgery, orthopedics, urology, maxillofacial surgery, radiosurgery, ophthalmology, and cardiac surgery. We conclude with a listing of technology challenges and research areas, including system architecture, software design, mechanical design, imaging compatible systems, user interface, and safety issues.