gebhart/patrepeval huggingface dataset:
INTRODUCTION (2006)

Abstract Proposing that ecological thinking can effect a revolution in philosophy comparable to Kant’s Copernican revolution, the introduction eschews the abstraction and reductivism of orthodox western epistemology, to relocate inquiry “down on the ground”, in everyday lives and situations. In a series of ecological cautionary tales which display the negative effects of epistemologies of mastery, the introduction argues for mining the untapped resources ecological thinking affords, while warning against ecology’s propensity to romanticize “nature” and to align women and other Others with nature thus romanticized. It indicates why this book cannot be identified as an eco-feminist text, despite productive alliances between ecological thinkers and eco-feminists.
Conformational analysis. 130. MM2. A hydrocarbon force field utilizing V1 and V2 torsional terms (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTConformational analysis. 130. MM2. A hydrocarbon force field utilizing V1 and V2 torsional termsNorman L. AllingerCite this: J. Am. Chem. Soc. 1977, 99, 25, 8127–8134Publication Date (Print):December 1, 1977Publication History Published online1 May 2002Published inissue 1 December 1977https://doi.org/10.1021/ja00467a001RIGHTS & PERMISSIONSArticle Views4034Altmetric-Citations3094LEARN 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 InReddit PDF (1 MB) Get e-Alertsclose Get e-Alerts
Smooth Shape‐Aware Functions with Controlled Extrema (2012)

Abstract Functions that optimize Laplacian‐based energies have become popular in geometry processing, e.g. for shape deformation, smoothing, multiscale kernel construction and interpolation. Minimizers of Dirichlet energies, or solutions of Laplace equations, are harmonic functions that enjoy the maximum principle, ensuring no spurious local extrema in the interior of the solved domain occur. However, these functions are only C 0 at the constrained points, which often causes smoothness problems. For this reason, many applications optimize higher‐order Laplacian energies such as biharmonic or triharmonic. Their minimizers exhibit increasing orders of continuity but lose the maximum principle and show oscillations. In this work, we identify characteristic artifacts caused by spurious local extrema, and provide a framework for minimizing quadratic energies on manifolds while constraining the solution to obey the maximum principle in the solved region. Our framework allows the user to specify locations and values of desired local maxima and minima, while preventing any other local extrema. We demonstrate our method on the smoothness energies corresponding to popular polyharmonic functions and show its usefulness for fast handle‐based shape deformation, controllable color diffusion, and topologically‐constrained data smoothing.
The roles of receptor and ligand endocytosis in regulating Notch signaling (2005)

Cell-cell signaling is a central process in the formation of multicellular organisms. Notch (N) is the receptor of a conserved signaling pathway that regulates numerous developmental decisions, and the misregulation of N has been linked to various physiological and developmental disorders. The endocytosis of N and its ligands is a key mechanism by which N-mediated cell-cell signaling is developmentally regulated. We review here the recent findings that have highlighted the importance and complexity of this regulation.
Plants Synthesize Ethanolamine by Direct Decarboxylation of Serine Using a Pyridoxal Phosphate Enzyme (2001)

The established pathways from serine to ethanolamine are indirect and involve decarboxylation of phosphatidylserine. Here we show that plants can decarboxylate serine directly. Using a radioassay based on ethanolamine (Etn) formation, pyridoxal 5'-phosphate-dependent l-serine decarboxylase (SDC) activity was readily detected in soluble extracts from leaves of diverse species, including spinach, Arabidopsis, and rapeseed. A putative Arabidopsis SDC cDNA was identified by searching GenBank for sequences homologous to other amino acid decarboxylases and shown by expression in Escherichia coli to encode a soluble protein with SDC activity. This cDNA was further authenticated by complementing the Etn requirement of a yeast psd1 psd2 mutant. In a parallel approach, a cDNA was isolated from a rapeseed library by its ability to complement the Etn requirement of a yeast cho1 mutant and shown by expression in E. coli to specify SDC. The deduced Arabidopsis and rapeseed SDC polypeptides are 90% identical, lack obvious targeting signals, and belong to amino acid decarboxylase group II. Recombinant Arabidopsis SDC was shown to exist as a tetramer and to contain pyridoxal 5'-phosphate. It does not attack d-serine, l-phosphoserine, other l-amino acids, or phosphatidylserine and is not inhibited by Etn, choline, or their phosphoesters. As a soluble, pyridoxal 5'-phosphate enzyme, SDC contrasts sharply with phosphatidylserine decarboxylases, which are membrane proteins that have a pyruvoyl cofactor.
Generation of trimethylsulfonium cation from dimethyl sulfoxide and dimethyl sulfate: implications for the synthesis of epoxides from aldehydes and ketones (1995)

The reaction between dimethyl sulfoxide (DMSO) and dimethyl sulfate has been monitored qualitatively by 1H NMR spectroscopy. At reaction temperatures of 20, 50 and 90 °C, the major product is methoxydimethylsulfonium methyl sulfate 5 whereas at 100 °C the major product is trimethylsulfonium methyl sulfate 6 together with minor amounts of methoxydimethylsulfonium methyl sulfate; formaldehyde was qualitatively identified as a product by derivatisation (2,4-dinitrophenylhydrazone). Treatment of the product ensuing from the latter reaction with potassium hydroxide, followed by addition of (separately) benzaldehyde and 1-(2,4-dichlorophenyl)pentan-1-one gave the expected epoxides 4a and 4b, respectively.
Differential Transport and Local Translation of Cytoskeletal, Injury-Response, and Neurodegeneration Protein mRNAs in Axons (2005)

Recent studies have begun to focus on the signals that regulate axonal protein synthesis and the functional significance of localized protein synthesis. However, identification of proteins that are synthesized in mammalian axons has been mainly based on predictions. Here, we used axons purified from cultures of injury-conditioned adult dorsal root ganglion (DRG) neurons and proteomics methodology to identify axonally synthesized proteins. Reverse transcription (RT)-PCR from axonal preparations was used to confirm that the mRNA for each identified protein extended into the DRG axons. Proteins and the encoding mRNAs for the cytoskeletal proteins beta-actin, peripherin, vimentin, gamma-tropomyosin 3, and cofilin 1 were present in the axonal preparations. In addition to the cytoskeletal elements, several heat shock proteins (HSP27, HSP60, HSP70, grp75, alphaB crystallin), resident endoplasmic reticulum (ER) proteins (calreticulin, grp78/BiP, ERp29), proteins associated with neurodegenerative diseases (ubiquitin C-terminal hydrolase L1, rat ortholog of human DJ-1/Park7, gamma-synuclein, superoxide dismutase 1), anti-oxidant proteins (peroxiredoxins 1 and 6), and metabolic proteins (e.g., phosphoglycerate kinase 1 (PGK 1), alpha enolase, aldolase C/Zebrin II) were included among the axonally synthesized proteins. Detection of the mRNAs encoding each of the axonally synthesized proteins identified by mass spectrometry in the axonal compartment indicates that the DRG axons have the potential to synthesize a complex population of proteins. Local treatment of the DRG axons with NGF or BDNF increased levels of cytoskeletal mRNAs into the axonal compartment by twofold to fivefold but had no effect on levels of the other axonal mRNAs studied. Neurotrophins selectively increased transport of beta-actin, peripherin, and vimentin mRNAs from the cell body into the axons rather than changing transcription or mRNA survival in the axonal compartment.
HomeRun Vector Assembly System: A Flexible and Standardized Cloning System for Assembly of Multi-Modular DNA Constructs (2014)

Advances in molecular and synthetic biology call for efficient assembly of multi-modular DNA constructs. We hereby present a novel modular cloning method that obviates the need for restriction endonucleases and significantly improves the efficiency in the design and construction of complex DNA molecules by standardizing all DNA elements and cloning reactions. Our system, named HomeRun Vector Assembly System (HVAS), employs a three-tiered vector series that utilizes both multisite gateway cloning and homing endonucleases, with the former building individual functional modules and the latter linking modules into the final construct. As a proof-of-principle, we first built a two-module construct that supported doxycycline-induced expression of green fluorescent protein (GFP). Further, with a three-module construct we showed quantitatively that there was minimal promoter leakage between neighbouring modules. Finally, we developed a method, in vitro Cre recombinase-mediated cassette exchange (RMCE) cloning, to regenerate a gateway destination vector from a previous multisite gateway cloning reaction, allowing access to existing DNA element libraries in conventional gateway entry clones, and simple creation of constructs ready for in vivo RMCE. We believe these methods constitute a useful addition to the standard molecular cloning techniques that could potentially support industrial scale synthesis of DNA constructs.
The in vitro determination of the D antigens of poliomyelitis viruses. I. The gel diffusion tes. (1966)

1. A technique for the measurement of poliomyelitis virus D antigens by means of gel diffusion tests against antisera obtained from hyperimmunized calves is described in detail. 2. The precision of the method was estimated by performing several replicate tests with three or four dilutions of concentrated antigen of each of the three types. The D antigen content, if measured by means of twelve precipitation hexagons in agar can be calculated with a precision of about 10 per cent (95 per cent confidence limits). 3. The calf sera gave no precipitation with C antigens in the concentrations suitable for measuring D antigens. 4. The local reference antigens, the D antigen concentrations of which were adjusted to equal that of the reference antigens used in the Glaxo Laboratories, contained C as well as D antigens. This was observed in gel diffusion tests with specific anti-C sera from guinea-pigs. 5. The guinea-pig anti-C sera showed a precipitation with the immune calf sera as well as with normal calf serum. This indicated the presence of anti-calf antibodies in the guinea-pig sera, presumably elicited by traces of calf proteins in the vaccines. These antibodies might give rise to non-specific precipitation if antisera used in the test for D antigen were obtained from animal species other than those used to provide components in the tissue culture medium from which the antigens were derived.
The DNA polymerase gene from the hyperthermophilic marine archaebacterium,pyrococcus furiosus, shows sequence homology with α-like DNA polymerases (1991)

Journal Article The DNA polymerase gene from the hyperthermophilic marine archaebacterium, pyrococcus furiosus, shows sequence homology with α-like DNA polymerases Get access Eric J. Mathur, Eric J. Mathur Search for other works by this author on: Oxford Academic PubMed Google Scholar Michael W.W. Adams, Michael W.W. Adams 1Department of Biochemistry, Center for Metalloenzyme Studies, University of GeorgiaAthens, GA 30602, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Walter N. Callen, Walter N. Callen Search for other works by this author on: Oxford Academic PubMed Google Scholar Janice M. Cline Janice M. Cline Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 19, Issue 24, 25 December 1991, Page 6952, https://doi.org/10.1093/nar/19.24.6952 Published: 25 December 1991 Article history Received: 07 November 1991 Published: 25 December 1991
Fourier Transform Infrared Spectroscopy Studies of the Secondary Structure in mt-PA6 and mt-PA6 Treated with L-Arginine, L-Asparagine, and (+)-Citrulline in Aqueous Solution (1994)

FT-IR studies of the secondary structure of mt-PA6 and mt-PA6 treated with L-arginine, (+)-citrulline, and L-asparagine were carried out in aqueous buffer solution. Spectral subtraction was used to remove the interfering water bands in the amide absorption region, and the amide I absorptions were monitored to investigate changes in the secondary structure of the mt-PA6 induced by the binding of these amino acids. The spectral data showed a narrowing of the amide I absorption of mt-PA6 on treatment with L-arginine, (+)-cirrulline, and L-asparagine. Deconvolution of the amide I absorption revealed vibrational bands characteristic of β-sheet (1632 cm −1 ), disordered or bound water (1644 cm −1 ), and turns (1660 cm −1 ) secondary structures for the mt-PA6. Curve-fitting methods were also used to examine the changes in spectra and secondary structure of the mt-PA6 resulting from amino acid treatment. Analysis of the spectral data shows that loss in intensity of the bands near 1644 and 1660 cm −1 is responsible for the amino acid-induced narrowing of the mt-PA6 amide I absorption. In addition, the spectral data could suggest different binding interactions for L-arginine to mt-PA6 compared to the L-asparagine and (+)-citrulline.
CO<sub>2</sub> Processing and O<sub>2</sub> Reclamation System Selection Process for Future European Space Programmes (1989)

&lt;div class="htmlview paragraph"&gt;This paper describes the process used to select the physico-chemical system configuration to meet the requirements of manned European space development plans from the year 2005 onwards. From the investigated sixty four candidates, eight candidate system configurations were preselected from which one baseline configuration was finally selected. This will enable the European space industry to identify and establish the required capabilities and technologies in Europe.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The selection process took available technology, cost impact, oxygen, water, carbon and hydrogen loop closure considerations and a synergetic approach with the propulsion system into account. Both quantitative and qualitative assessments were used.&lt;/div&gt;
Effectiveness of workplace interventions in the prevention of upper extremity musculoskeletal disorders and symptoms: an update of the evidence (2015)

The burden of disabling musculoskeletal pain and injuries (musculoskeletal disorders, MSDs) arising from work-related causes in many workplaces remains substantial. There is little consensus on the most appropriate interventions for MSDs. Our objective was to update a systematic review of workplace-based interventions for preventing and managing upper extremity MSD (UEMSD). We followed a systematic review process developed by the Institute for Work & Health and an adapted best evidence synthesis. 6 electronic databases were searched (January 2008 until April 2013 inclusive) yielding 9909 non-duplicate references. 26 high-quality and medium-quality studies relevant to our research question were combined with 35 from the original review to synthesise the evidence on 30 different intervention categories. There was strong evidence for one intervention category, resistance training, leading to the recommendation: Implementing a workplace-based resistance training exercise programme can help prevent and manage UEMSD and symptoms. The synthesis also revealed moderate evidence for stretching programmes, mouse use feedback and forearm supports in preventing UEMSD or symptoms. There was also moderate evidence for no benefit for EMG biofeedback, job stress management training, and office workstation adjustment for UEMSD and symptoms. Messages are proposed for both these and other intervention categories.
Sensitive couture for interactive garment modeling and editing (2011)

We present a novel interactive tool for garment design that enables, for the first time, interactive bidirectional editing between 2D patterns and 3D high-fidelity simulated draped forms. This provides a continuous, interactive, and natural design modality in which 2D and 3D representations are simultaneously visible and seamlessly maintain correspondence. Artists can now interactively edit 2D pattern designs and immediately obtain stable accurate feedback online, thus enabling rapid prototyping and an intuitive understanding of complex drape form.
The Search for α-Secretase and its Potential as a Therapeutic Approach to Alzheimer's Disease (2002)

In the nonamyloidogenic processing pathway the Alzheimer s amyloid precursor protein (APP) is proteolytically cleaved by alpha-secretase. As this cleavage occurs at the Lys16-Leu17 bond within the amyloid beta domain, it prevents deposition of intact amyloidogenic peptide. In addition, the large ectodomain (sAPP(alpha)) released by the action of alpha-secretase has several neuroprotective properties. Studies with a range of hydroxamic acid-based compounds, such as batimastat, indicate that alpha-secretase is a zinc metalloproteinase, and members of the adamalysin family of proteins, TACE, ADAM10 and ADAM9, all fulfil some of the criteria required of alpha-secretase. APP is constitutively cleaved by alpha-secretase in most cell lines. However, on stimulation with muscarinic agonists or activators of protein kinase C, such as phorbol esters, the alpha-secretase cleavage of APP is up-regulated. The constitutive alpha-secretase activity is primarily at the cell surface, while the regulated activity is predominantly located within the Golgi. The beneficial action of cholinesterase inhibitors may in part be due to activation of muscarinic receptors, resulting in an up-regulation of alpha-secretase. Other agents can also increase the nonamyloidogenic cleavage of APP including estrogen, testosterone, various neurotransmitters and growth factors. As the alpha-secretase cleavage of APP both precludes the deposition of the amyloid beta peptide and releases the neuroprotective sAPP(alpha), pharmacological up-regulation of alpha-secretase may provide alternative therapeutic approaches for Alzheimer s disease.
The HS:1 serostrain ofCampylobacter jejunihas a complex teichoic acid‐like capsular polysaccharide with nonstoichiometric fructofuranose branches andO‐methyl phosphoramidate groups (2005)

Recently, the CPS biosynthetic loci for several strains of Campylobacter jejuni were sequenced and revealed evidence for multiple mechanisms of structural variation. In this study, the CPS structure for the HS:1 serostrain of C. jejuni was determined using mass spectrometry and NMR at 600 MHz equipped with an ultra-sensitive cryogenically cooled probe. Analysis of CPS purified using a mild enzymatic method revealed a teichoic acid-like [-4)-alpha-d-Galp-(1-2)-(R)-Gro-(1-P](n), repeating unit, where Gro is glycerol. Two branches at C-2 and C-3 of galactose were identified as beta-d-fructofuranoses substituted at C-3 with CH(3)OP(O)(NH(2))(OR) groups. Structural heterogeneity was due to nonstoichiometric glycosylation at C-3 of galactose and variable phosphoramidate groups. Identical structural features were found for cell-bound CPS on intact cells using proton homonuclear and (31)P heteronuclear two-dimensional HR-MAS NMR at 500 MHz. In contrast, spectroscopic data acquired for hot water/phenol purified CPS was complicated by the hydrolysis and subsequent loss of labile groups during extraction. Collectively, the results of this study established the importance of using sensitive isolation techniques and HR-MAS NMR to examine CPS structures in vivo when labile groups are present. This study uncovered how incorporation of variable O-methyl phosphoramidate groups on nonstoichiometric fructose branches is used in C. jejuni HS:1 as a strategy to produce a highly complex polysaccharide from its small CPS biosynthetic locus and a limited number of sugars.
Role of Apoptosis and Bcl-2/Bax in the Development of Tubulointerstitial Fibrosis during Experimental Obstructive Nephropathy (2001)

These findings suggest an important role for apoptosis and its regulatory proteins in the processes of tubular atrophy and fibrogenesis following UUO.
Automatic knowledge extraction from survey data: learning M -of- N constructs using a hybrid approach (2004)

Data collected from a survey typically consist of attributes that are mostly if not completely binary-valued or binary-encoded. We present a method for handling such data where the underlying data analysis can be cast as a classification problem. We propose a hybrid method that combines neural network and decision tree methods. The network is trained to remove irrelevant data attributes and the decision tree is applied to extract comprehensible classification rules from the trained network. The conditions of the rules are in the form of a conjunction of M-of-N constructs. An M-of-N construct is a rule condition that is satisfied if (at least, exactly, at most) M of the N binary attributes in the construct are present. The effectiveness of the method is illustrated on data collected for a study of global car market segmentation. The results show that besides achieving high predictive accuracy, the method also allows meaningful interpretation of the relationships among the data variables.