gebhart/patrepeval huggingface dataset:
The annotators' perspective on co-authoring with structured annotations (2011)

In asynchronous collaborative writing, annotations play an important role as a communication medium among co-authors. Research has shown that grouping related annotations together can help those who review an annotated document by reducing their workload and raising the accuracy of their reviewing. Less is known about the impact on users who create such structured annotations — the annotators. The research reported in this thesis had three goals: (1) to better understand current annotation creation practices, (2) to explore how structuring would be used by annotators, both the structuring process and the resulting types of structure, and (3) to evaluate the impact on annotators of having to create structured annotations. We conducted three studies to address each of these goals in turn. The first study was an observational study which strengthened our understanding of how annotators use existing tools to communicate document-related information in the form of annotations. That study revealed annotation practices that could benefit from additional structuring support, such as annotators describing how annotations in a document relate to each other. Our second study used a paper prototype system that supported annotation grouping to investigate how annotators would structure annotations, if given the option. Common behaviour that emerged was the grouping of thematically related annotations, as well as the grouping of annotations specifically targeted to a given co-author. The study also uncovered a range of temporal approaches to structuring annotations, such as top-down and bottom-up grouping. Based on the first two studies, we incorporated a light-weight implicit structuring approach based on tagging into our annotation model and then implemented an extended version of a high-fidelity prototype that supports structured annotation, including tagging. We used the prototype in our third study, a controlled experiment, which compared the impact of structured annotations relative to unstructured annotations. Participants in that study perceived structured annotations to be worth the additional workload required. The study further suggested that the bottom-up grouping approach complements the top-down approach in describing relationships amongst annotations in a document.
Polyunsaturated Fatty Acid Production with Mortierella alpine by Solid Substrate Fermentation (2000)

Polyunsaturated fatty acids (PUFA) were produced with Mortierella alpina by solid substrate fermentation. Rice bran was the most effective substrate for PUFA production, followed by peanut meal residue, wheat bran, and sweet potato residue. The optimal conditions for PUFA production were rice bran supplemented with 2.3 to 5% nitrogen at an initial moisture content of 65 to 68% and a pH range of 6 to 7. Each gram of substrate carbon yielded 122.2 mg of total PUFA, including 12.8 mg of eicosapentaenoic acid (EPA), 47.8 mg of linoleic acid (LA), 7.1 mg of a-linolenic acid (ALA), and 54.5 mg of arachidonic acid (ARA) for 8 to 12 days incubation. C/N ratios between 14.5 and 18.5 favored EPA and LA production, while C/N ratios between 19.8 and 21 enhanced ARA and total PUFA production. Total PUFA, EPA and ARA production increased 12, 84.4 and 46.1%, respectively, when the culture temperature was shifted from 20℃ to 12℃ on the fifth day. Supplement of soybean and linseed oils increased LA by 84.9 and 36%, ARA by 71 and 42.1%, and EPA by 130.6 and 92.1%, respectively.
Genetic organization and sequence of the Pseudomonas cepacia genes for the alpha and beta subunits of protocatechuate 3,4-dioxygenase (1989)

The locations of the genes for the alpha and beta subunits of protocatechuate 3,4-dioxygenase (EC 1.13.11.3) on a 9.5-kilobase-pair PstI fragment cloned from the Pseudomonas cepacia DBO1 chromosome were determined. This was accomplished through the construction of several subclones into the broad-host-range cloning vectors pRO2317, pRO2320, and pRO2321. The ability of each subclone to complement mutations in protocatechuate 3,4-dioxygenase (pcaA) was tested in mutant strains derived from P. cepacia, Pseudomonas aeruginosa, and Pseudomonas putida. These complementation studies also showed that the two subunits were expressed from the same promoter. The nucleotide sequence of the region encoding for protocatechuate 3,4-dioxygenase was determined. The deduced amino acid sequence matched that determined by N-terminal analysis of regions of the isolated enzyme. Although over 400 nucleotides were sequenced before the start of the genes, no homology to known promoters was found. However, a terminator stem-loop structure was found immediately after the genes. The deduced amino acid sequence showed extensive homology with the previously determined amino acid sequence of protocatechuate 3,4-dioxygenase from another Pseudomonas species.
International Journal of Scientific Research in Chemical Engineering (2014)

Scope of the journal includes: Chemical Reaction Engineering, Reactor engineering, Materials Synthesis and Processing, Environmental Chemical Engineering, Semiconductors, High-temperature alloys, Kinetic Processes in Materials, Magnetic Properties of Materials, Optimization of mixed materials, Petroleum and  etc.
Genetic organization of the unc-60 region in Caenorhabditis elegans. (1988)

We have investigated the chromosomal region around unc-60 V, a gene affecting muscle structure, in the nematode Caenorhabditis elegans. The region studied covers 3 map units and lies at the left end of linkage group (LG) V. Compared to the region around dpy-11 (at the center of LGV), the unc-60 region has relatively few visible genes per map unit. We found the same to be true for essential genes. By screening simultaneously for recessive lethals closely linked to either dpy-11 or unc-60, we recovered ethyl methanesulfonate-induced mutations in 10 essential genes near dpy-11 but in only two genes near unc-60. Four deficiency breakpoints were mapped to the unc-60 region. Using recombination and deficiency mapping we established the following gene order: let-336, unc-34, let-326, unc-60, emb-29, let-426. Regarding unc-60 itself, we compared the effect of ten alleles (including five isolated during this study) on hermaphrodite mobility and fecundity. We used intragenic mapping to position eight of these alleles. The results show that these alleles are not distributed uniformly within the gene, but map to two groups approximately 0.012 map unit apart.
Silicon nitride thin-film deposition by LPCVD with in situ HF vapor cleaning and its application to stacked DRAM capacitor fabrication (1994)

Silicon nitride film deposited by LPCVD with newly developed in situ HF vapor cleaning has been studied and applied to fabricate dielectric films for stacked DRAM capacitors. Using this method, an oxide-free surface of underlaid poly-Si can be obtained. Silicon nitride film deposited on this surface has been verified by FTIR measurement to have the stoichiometrically proper composition of Si/sub 3/N/sub 4/. However, the film was found to be selectively deposited on poly-Si electrodes. This selective deposition degrades the reliability of the stacked capacitor, because the silicon nitride can not completely cover the periphery of poly-Si electrodes on SiO/sub 2/. We propose a simple process that avoids the problem making it possible to apply silicon nitride film to stacked-capacitor fabrication. Stacked capacitors fabricated by this process exhibit very low leakage current and high electrical reliability even for ultra-thin silicon nitride films less than 5 nm thick.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
3D analysis of MR readback on perpendicular medium (1991)

A 3-D analysis of magnetoresistive (MR) read on perpendicular media using the reciprocity method is presented. It is shown that the conduction of magnetic flux, obtained from an equivalent reciprocity field, away from the active area is an important phenomenon for this structure, and may introduce error if 2-D analysis is used. The authors examine the effect of shield width and show that when the shield width is equal to the width of the active area of the MR head, 3-D analysis closely resembles the 2-D results. This calculation is extended to a differentially connected dual element MR head for perpendicular recording.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Organosilicon Polymers. II. The Open Chain Dimethylsiloxanes with Trimethylsiloxy End Groups<sup>1</sup> (1946)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOrganosilicon Polymers. II. The Open Chain Dimethylsiloxanes with Trimethylsiloxy End Groups1M. J. Hunter, E. L. Warrick, J. F. Hyde, and C. C. CurrieCite this: J. Am. Chem. Soc. 1946, 68, 11, 2284–2290Publication Date (Print):November 1, 1946Publication History Published online1 May 2002Published inissue 1 November 1946https://pubs.acs.org/doi/10.1021/ja01215a048https://doi.org/10.1021/ja01215a048research-articleACS PublicationsRequest reuse permissionsArticle Views343Altmetric-Citations73LEARN 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
Interactive transfer function modification for volume rendering using pre-shaded sample runs (2003)

This paper describes a software-based method for interactive transfer function modification. Our approach exploits the fact that, in general, a user will rarely want to modify the viewpoint and the transfer functions at the same time. In that spirit, we optimize the latter by first fixing the viewpoint and then storing a list of pre-shaded, but uncolored, samples along each ray. Then, each time the RGBA transfer function is modified, the algorithm traverses the sample lists, colors the samples, and composites them along each ray until full opacity is reached. Since neither the expensive sample interpolation nor the shading are no longer necessary, we can obtain near-interactive framerates for a variety of datasets.
Design of an Endoscopic Biopsy Needle (2010)

This paper summarizes the design and testing of a biopsy needle to be used through a flexible endoscope. There is a need for a biopsy needle that can be used through the endoscopic channel to perform zero invasive biopsies on the gastrointestinal system and other organs. In this project, a novel biopsy needle is designed, tested, and compared with an Olympus EZShot single use aspiration needle. The new needle was found to have a higher ratio of mass removed versus removal force.
Sol−Gel Synthesis of High-Quality SrRuO<sub>3</sub> Thin-Film Electrodes Suppressing the Formation of Detrimental RuO<sub>2</sub> and the Dielectric Properties of Integrated Lead Lanthanum Zirconate Titanate Films (2010)

A facile solution chemistry is demonstrated to fabricate high-quality polycrystalline strontium ruthenium oxide (SrRuO3) thin film electrodes on silicon substrates suppressing the formation of undesired ruthenium oxide (RuO2) for the deposition of dielectric and ferroelectric materials like lead lanthanum zirconate titanate (PLZT). The robust, highly crystalline SrRuO3 film fabrication process does not favor the formation of RuO2 because of molecular level modification of the precursors possessing analogous melting points, yielding homogeneous films. This chemistry is further understood and complemented by kinetic and thermodynamic analysis of the DTA data under nonisothermal conditions, with which the activation energies to form RuO2 and SrRuO3 were calculated to be 156 ± 17 and 96 ± 10 kJ/mol, respectively. The room-temperature resistivity of the SrRuO3 film was measured to be ∼850 ± 50 μΩ cm on silicon (100) substrates. The dielectric properties of sol−gel-derived PLZT thin film capacitors on polycrystalline SrRuO3 electrodes were also measured to illustrate the high quality of the formed SrRuO3 bottom electrode. These results have broad implications for the expanded use of these conductive oxide electrodes in many applications that require low thermal budgets. The PLZT (8/52/48) films exhibited well-defined hysteresis loops with remanent polarization of ∼10.5 μC/cm2, dielectric constant of >1450, dielectric loss of <0.06, and leakage current density of ∼3.8 × 10−8 A/cm2. These dielectric properties are similar to those of PLZT on platinized silicon, indicating the high quality of the bottom conductive oxide layer. In addition, the PLZT capacitors were essentially fatigue free for >1 × 109 cycles when deposited over an oxide electrode.
Fluorescent Signaling Based on Sulfoxide Profluorophores: Application to the Visual Detection of the Explosive TATP (2008)

The first visual fluorescence-based assay for the peroxide explosive triacetone triperoxide (TATP) is described. The assay is based on a conceptually new fluorescence signaling mechanism, in which nonemissive pyrenyl sulfoxide profluorophores are oxidized to visibly emissive pyrenyl sulfones. Although not without limitations, these first-generation fluorescent probes can provide a visual response to ca. 100 nmol of TATP. In addition, the success of this assay suggests the potential for broader application of aryl sulfoxides in fluorescent chemosensing.
Chaperonin 60: a paradoxical, evolutionarily conserved protein family with multiple moonlighting functions (2013)

ABSTRACT Chaperonin 60 is the prototypic molecular chaperone, an essential protein in eukaryotes and prokaryotes, whose sequence conservation provides an excellent basis for phylogenetic analysis. Escherichia coli chaperonin 60 ( GroEL ), the prototype of this family of proteins, has an established oligomeric‐structure‐based folding mechanism and a defined population of folding partners. However, there is a growing number of examples of chaperonin 60 proteins whose crystal structures and oligomeric composition are at variance with GroEL , suggesting that additional complexities in the protein‐folding function of this protein should be expected. In addition, many organisms have multiple chaperonin 60 proteins, some of which have lost their protein‐folding ability. It is emerging that this highly conserved protein has evolved a bewildering variety of additional biological functions – known as moonlighting functions – both within the cell and in the extracellular milieu. Indeed, in some organisms, it is these moonlighting functions that have been left after the loss of the protein‐folding activity. This highlights the major paradox in the biology of chaperonin 60. This article reviews the relationship between the folding and non‐folding (moonlighting) activities of the chaperonin 60 family and discusses current knowledge on their molecular evolution focusing on protein domains involved in the non‐folding chaperonin functions in an attempt to understand the emerging biology of this evolutionarily ancient protein family.
Cloudgene: A graphical execution platform for MapReduce programs on private and public clouds (2012)

Our results show that MapReduce programs can be integrated into Cloudgene with little effort and without adding any computational overhead to existing programs. This platform gives developers the opportunity to focus on the actual implementation task and provides scientists a platform with the aim to hide the complexity of MapReduce. In addition to MapReduce programs, Cloudgene can also be used to launch predefined systems (e.g. Cloud BioLinux, RStudio) in public clouds. Currently, five different bioinformatic programs using MapReduce and two systems are integrated and have been successfully deployed. Cloudgene is freely available at http://cloudgene.uibk.ac.at.
Type II broken-gap quantum wires and quantum dot arrays: A novel concept for self-doping semiconductor nanostructures (1990)

A novel concept for creating self-doping quantum wires and quantum dot arrays based upon the InAs-GaSb material system is proposed. The unusual type II, broken-gap band line-up in this system allows charge transfer across the InAs-GaSb interfaces. We employ a recently developed coupled band formalism to examine analytically the band structure of InAs-GaSb quantum dots and wires. The analysis shows that appropriately engineered nanostructures which contain high free-carrier densities are possible without intentional impurity doping. Quantum dots in this system behave as artificial quasiatoms, with ionization energy and valence determined by fabricationally determined parameters. Synthetic p-(n-)type semiconductors may therefore be formed from arrays of InAs(GaSb) quantum dots embedded in GaSb(InAs). InAs-GaSb quantum wires are also investigated and found to exhibit self-doping behavior. Possible fabrication schemes utilizing recently developed technologies are discussed.
Mechanisms for ganciclovir resistance in gastrointestinal tumor cells transduced with a retroviral vector containing the herpes simplex virus thymidine kinase gene. (1998)

Transfer of the herpes simplex thymidine kinase (HSV-TK) gene into tumor cells confers sensitivity to the cells to the viral drug ganciclovir (GCV). Although the efficacy of the HSV-TK/GCV approach is well studied, the mechanisms for the resistance of HSV-TK-transduced tumor cells to GCV are poorly understood. Here, we examined the mechanisms for GCV resistance in HSV-TK-transduced gastrointestinal (GI) cell lines. Our results show that GCV sensitivities vary in vitro and in vivo among the different HSV-TK-transduced GI tumor cell lines. GCV-resistant colonies were isolated from several different HSV-TK-transduced GI tumor cell lines after 14 days of GCV treatment. Characterization of GCV-resistant colonies demonstrated that the HSV-TK gene was either partially or completely deleted from the resistant HSV-TK-transduced cells. In the HT-29 RM and MIAPACA-2 RM cells, a 220-bp deletion of the gene was found, whereas in the HT-29 R1-R5-resistant cells, the whole TK gene was found to be absent. Immunocytochemical studies using a polyclonal antibody to the TK protein demonstrated that the HSV-TK protein was absent in the GCV-resistant, HSV-TK-transduced cells. Transfection of the resistant cells with an adenoviral vector containing a HSV-TK gene restored sensitivity to GCV. The presence of GCV-resistant cells was only demonstrable in GI tumor cell lines that also demonstrated a poor bystander effect. Our results suggest that GCV resistance found in tumor cells transduced with a retroviral HSV-TK gene is due to the lack of a functional TK protein in the tumor cells rather than any intrinsic resistance of the cells to GCV. In tumor cells with a good bystander effect, the small percentage of TK-transduced cells that do not express the TK protein are probably killed by the bystander effect because GCV-resistant tumor cells were not found in these cell lines. GCV-resistant tumor cells were found only in tumor cell lines with a poor bystander effect, by which, presumably, the transduced tumor cells lacking a functional TK gene were not killed by the bystander killing effect.
Clinical implications of expression of vascular endothelial growth factor in metastatic lesions of ovariancancers (2001)

Vascular endothelial growth factor (VEGF) has been identified as an important factor for tumour angiogenesis, which is essential for the growth, invasion and metastasis of solid tumours. Significantly increased VEGF level from the primary tumour to the metastatic lesion of ovarian cancers was found in 8 of 30 cases. The 24-month survival rate of the patients with significantly increased VEGF level was extremely poor (0/8 = 0%) in comparison with that of patients with no change in the level (15/22 = 68%) from the primary tumour to the metastatic lesion. This indicates that VEGF may contribute to the advancement of metastatic lesions, and that VEGF level in metastatic lesions may be a prognostic indicator. © 2001 Cancer Research Campaign
Integrin activation or alpha9 expression allows retinal pigmented epithelial cell adhesion on Bruch’s membrane in wet age-related macular degeneration (2010)

Retinal pigment epithelial cell malfunction is a causative feature of age-related macular degeneration, and transplantation of new retinal pigment epithelial cells is an attractive strategy to prevent further progression and visual loss. However, transplants have shown limited efficacy, mainly because transplanted cells fail to adhere and migrate onto pathological Bruch's membrane. Adhesion to Bruch's membrane is integrin-mediated. Ageing of Bruch's membrane leads to a decline in integrin ligands and, added to this, wet age-related macular degeneration leads to upregulation of anti-adhesive molecules such as tenascin-C. We have therefore investigated whether manipulation of integrin function in retinal pigment epithelial cells can restore their adhesion and migration on wet age-related macular degeneration-damaged Bruch's membrane. Using spontaneously immortalized human retinal pigment epithelial cells (adult retinal pigment epithelium-19), we show that adhesion and migration on the Bruch's membrane components is integrin-dependent and enhanced by integrin-activating agents manganese and TS2/16. These allowed cells to adhere and migrate on low concentrations of ligand, as would be found in aged Bruch's membrane. We next developed a method for stripping cells from Bruch's membrane so that adhesion and migration assays can be performed on its surface. Integrin activation had a moderate effect on enhancing retinal pigmented epithelial cell adhesion and migration on normal human and rat Bruch's membrane. However, on Bruch's membrane prepared from human wet age-related macular degeneration-affected eyes, adhesion was lower and integrin activation had a much greater effect. A candidate molecule for preventing retinal pigmented epithelial interaction with age-related macular degeneration-affected Bruch's membrane is tenascin-C which we confirm is present at high levels in wet age-related macular degeneration membrane. We show that tenascin-C is anti-adhesive for retinal pigmented epithelial cells, but after integrin activation, they can adhere and migrate on it using alphaVbeta3 integrin. Alternatively, we find that transduction of retinal pigmented epithelial cells with alpha9 integrin, a tenascin-C-binding integrin, led to a large increase in alpha9beta1-mediated adhesion and migration on tenascin-C. Both expression of alpha9 integrin and integrin activation greatly enhanced the ability of retinal pigment epithelial cells to adhere to tenascin-rich wet age-related macular degeneration-affected Bruch's membranes. Our results suggest that manipulation of retinal pigment epithelial cell integrins through integrin activating strategies, or expression of new integrins such as alpha9, could be effective in improving the efficacy of retinal pigment epithelial cell transplantation in wet age-related macular degeneration-affected eyes.
Locational Marginal Price Sensitivities (2005)

Within an optimal power flow market clearing framework, this paper provides expressions to compute the sensitivities of locational marginal prices with respect to power demands. Sensitivities with respect to other parameters can also be obtained. An example and a case study are used to illustrate the expressions derived.