gebhart/patrepeval huggingface dataset:
Study and development of concepts of auxetic structures in bio-inspired design (2016)

This work discusses the experience of using auxetic (negative Poisson's ratio) materials in different design objects, including chairs, bags, seat belts, etc., developed by the authors with their students. Auxetics have become of interest in engineering, whenever a support instead of a pronounced flexure, of a cellular, therefore lightweight material, is desirable. Structures have been calculated and modelled as chiral with defined geometrical parameters and then applied to concepts with the fabrication of real models using neoprene or generally rubbery material. Indications on the possible sensations of the user are suggested, which provided rationale for likely improved comfort and/or desirability of contact. Limitations of this study in terms of material experience appear the use of a single material as for auxetic properties and the focusing on one single possible auxetic structure, the chiral one. Despite this, this could be considered as a starting point for a possible database of material experience on the use of auxetics. From these considerations, it appears as the use of auxetic structures would lead to a more sustainable scenario for these objects, especially because improved user's experience would extend their duration of life and lead to a lower rate of discarded pieces.
Application of synthetic biology in cyanobacteria and algae (2012)

Cyanobacteria and algae are becoming increasingly attractive cell factories for producing renewable biofuels and chemicals due to their ability to capture solar energy and CO(2) and their relatively simple genetic background for genetic manipulation. Increasing research efforts from the synthetic biology approach have been made in recent years to modify cyanobacteria and algae for various biotechnological applications. In this article, we critically review recent progresses in developing genetic tools for characterizing or manipulating cyanobacteria and algae, the applications of genetically modified strains for synthesizing renewable products such as biofuels and chemicals. In addition, the emergent challenges in the development and application of synthetic biology for cyanobacteria and algae are also discussed.
A Hybrid User Interface for Manipulation of Volumetric Medical Data (2006)

This paper presents a novel system for interactive visualization and manipulation of medical datasets for surgery planning based on a hybrid VR / Tablet PC user interface. The goal of the system is to facilitate efficient visual inspection and correction of surface models generated by automated segmentation algorithms based on x-ray computed tomography scans, needed for planning surgical interventions. Factors like the quality of the visualization, nature of the dataset and interaction efficiency strongly influence system design decisions, in particular the design of the user interface, input devices and interaction techniques, leading to a hybrid setup. Finally, a user study is presented, which characterizes the system in terms of method efficiency and usability.
T-Cell Autoimmunity in Primary Biliary Cirrhosis (1996)

1. Primary biliary cirrhosis is a chronic cholestatic liver disease with an autoimmune aetiology. The classical histopathological lesion, of portal tract biliary epithelial cell damage, is accompanied by a T-cell-rich mononuclear cell infiltrate and upregulation of cell surface markers suggestive of local T-cell activation and cytokine release. This suggests that T-cell mediated mechanisms play an important role in tissue damage in primary biliary cirrhosis. 2. CD4+ T-cells specific for the E2 component of human pyruvate dehydrogenase complex (PDC-E2), a highly conserved enzyme which plays a critical role in intermediate metabolism, are present in the peripheral repertoire of the majority of patients with primary biliary cirrhosis. These cells are almost entirely absent from normal and chronic liver disease control subjects. The observations that peripheral blood PDC-E2-specific cells are most commonly seen in early stage disease, when active bile duct damage is occurring, and that PDC-E2- specific cells can be found in the portal tract infiltrate at times when this damage is occurring, suggest that these autoreactive cells may have a role to play in the aetiology of primary biliary cirrhosis. 3. T-cells specific for the whole PDC and its E1 component are seen in significant numbers of normal control subjects as well as patients with primary biliary cirrhosis. Retention of potentially autoreactive cells in the normal T-cell repertoire has been reported for a number of other autoantigens. 4. T-cell epitopes appear to be widely distributed throughout PDC-E2. This is in contrast to the B-cell epitopes which are highly restricted to the inner lipoyl binding domain of the protein.
Nitrogen-Doped Graphene Quantum Dots with Oxygen-Rich Functional Groups (2011)

Graphene quantum dots (GQDs) represent a new class of quantum dots with unique properties. Doping GQDs with heteroatoms provides an attractive means of effectively tuning their intrinsic properties and exploiting new phenomena for advanced device applications. Herein we report a simple electrochemical approach to luminescent and electrocatalytically active nitrogen-doped GQDs (N-GQDs) with oxygen-rich functional groups. Unlike their N-free counterparts, the newly produced N-GQDs with a N/C atomic ratio of ca. 4.3% emit blue luminescence and possess an electrocatalytic activity comparable to that of a commercially available Pt/C catalyst for the oxygen reduction reaction (ORR) in an alkaline medium. In addition to their use as metal-free ORR catalysts in fuel cells, the superior luminescence characteristic of N-GQDs allows them to be used for biomedical imaging and other optoelectronic applications.
Chk2/hCds1 functions as a DNA damage checkpoint in G1by stabilizing p53 (2000)

Chk2/hcds1, the human homolog of the Saccharomyces cerevisiae RAD53/SPK1 and Schizosaccharomyces pombe cds1 DNA damage checkpoint genes, encodes a protein kinase that is post-translationally modified after DNA damage. Like its yeast homologs, the Chk2/hCds1 protein phosphorylates Cdc25C in vitro, suggesting that it arrests cells in G(2) in response to DNA damage. We expressed Chk2/hCds1 in human cells and analyzed their cell cycle profile. Wild-type, but not catalytically inactive, Chk2/hCds1 led to G(1) arrest after DNA damage. The arrest was inhibited by cotransfection of a dominant-negative p53 mutant, indicating that Chk2/hCds1 acted upstream of p53. In vitro, Chk2/hCds1 phosphorylated p53 on Ser-20 and dissociated preformed complexes of p53 with Mdm2, a protein that targets p53 for degradation. In vivo, ectopic expression of wild-type Chk2/hCds1 led to increased p53 stabilization after DNA damage, whereas expression of a dominant-negative Chk2/hCds1 mutant abrogated both phosphorylation of p53 on Ser-20 and p53 stabilization. Thus, in response to DNA damage, Chk2/hCds1 stabilizes the p53 tumor suppressor protein leading to cell cycle arrest in G(1).
Vitamin D insufficiency in a population of healthy western Canadians. (2002)

We documented a high prevalence of vitamin D insufficiency, which warrants consideration of dietary vitamin D supplementation.
Production of Transgenic Male Sterile Tobacco Plants with the cDNA Encoding a Ribosome Inactivating Protein in Dianthus sinensis L. (2001)

The ribosome inactivating protein (RIP) gene from D. sinensis was used as a cytotoxin gene to induce male sterility in tobacco plants. The TA29 promoter, obtained by PCR amplification from tobacco, was fused to the RIP cDNA, and the chimaeric molecule was then introduced into tobacco plants by Agrobacterium-mediated transformation. Out of twenty-one independent transformants, twenty transgenic tobacco plants exhibited male sterility. Southern blot analysis revealed that four of the transgenic plants contained a single copy of the RIP gene, while the rest of the transgenic tobacco plants had two to four copies of the gene. The transgenic male sterile plants set seeds normally when pollinated with pollens from untransformed control plants, indicating that the RIP gene does not affect the pistil development. Furthermore, the seed yield of the transgenic plant was similar to that of the untransformed, self-pollinated control plant. A light microscopic observation of anther cross sections clearly showed that the tapetal tissue of the anther was selectively and completely destroyed causing male sterility. This study suggests that the RIP gene can be used as a cytotoxin gene for induction of male sterility in the plant.
Variation in the Arousal Pattern after Obstructive Events in Obstructive Sleep Apnea (1999)

The relationship between the severity of obstructive sleep apnea (OSA) (measured by sleep study) and daytime sleepiness is poor. Variation in the degree of arousal accompanying obstructive respiratory events might help explain this poor correlation. Polysomnographic records from patients with OSA were reviewed in order to extract representative examples of apneas and hypopneas (in 10 patients), as well as events both supine and decubitus (in 12 patients). The EEG accompanying each obstructive event was processed with a neural network technique to describe sleep depth on a second-by-second basis. The lengths of any visually evident microarousals were also measured manually. There was considerable interindividual variation in the degree of sleep disturbance using the neural network technique (p < 0.005), but not using the lengths of the visually scored microarousals (p = 0.6). The arousals accompanying apneic events caused greater variability in sleep depth quantified using the neural network technique (p = 0.03), and also lasted longer based on the visual scoring (mean, 12.6; SD, 1.7 s) than the hypopneic events (mean, 9.9; SD, 2.4 s; p = 0.02). There were no significant differences between events occurring supine versus decubitus with either technique (p = 0.7). These differences in arousal magnitude may explain some of the poor correlations between conventional measures of sleep apnea severity and daytime sleepiness.
Identification of thein vivoandin vitroorigin of transcription in human rDNA (1982)

A Hela cell /-100 extract primed with a purified human rDNA containing clone, has been shown to be capable of initiating specific alpha-amanitin-resistant RNA transcripts. By using a number of truncated templates, the site of RNA polymerase I initiation in vitro has been identified. The origin of transcription in vitro and in vivo was further defined by S1-mapping studies with total Hela cell RNA or RNA isolated from the in vitro transcription reaction. The initiation site was found to be the same. The nucleotide sequence of an 848 bp region around the initiation site, has also been determined. A perfect 15 bp homology has been found to exist between human and mouse rDNA very close to the origin of transcription, although little homology exists elsewhere. Sequences homologous to the origin of transcription region were not found repeated within a 12 kb non-transcribed spacer segment upstream from it.
Hemoglobins From Bacteria to Man: Evolution of Different Patterns of Gene Expression (1998)

The discovery of hemoglobins in virtually all kingdoms of organisms has shown (1) that the ancestral gene for hemoglobin is ancient, and (2) that hemoglobins can serve additional functions besides transport of oxygen between tissues, ranging from intracellular oxygen transport to catalysis of redox reactions. These different functions of the hemoglobins illustrate the acquisition of new roles by a pre-existing structural gene, which requires changes not only in the coding regions but also in the regulatory elements of the genes. The evolution of different regulated functions within an ancient gene family allows an examination of the types of biosequence data that are informative for various types of issues. Alignment of amino acid sequences is informative for the phylogenetic relationships among the hemoglobins in bacteria, fungi, protists, plants and animals. Although many of these diverse hemoglobins are induced by low oxygen concentrations, to date none of the molecular mechanisms for their hypoxic induction shows common regulatory proteins; hence, a search for matches in non-coding DNA sequences would not be expected to be fruitful. Indeed, alignments of non-coding DNA sequences do not reveal significant matches even between mammalian alpha- and beta-globin gene clusters, which diverged approximately 450 million years ago and are still expressed in a coordinated and balanced manner. They are in very different genomic contexts that show pronounced differences in regulatory mechanisms. The alpha-globin gene is in constitutively active chromatin and is encompassed by a CpG island, which is a dominant determinant of its regulation, whereas the beta-globin gene is in A+T-rich genomic DNA. Non-coding sequence matches are not seen between avian and mammalian beta-globin gene clusters, which diverged approximately 250 million years ago, despite the fact that regulation of both gene clusters requires tissue-specific activation of a chromatin domain regulated by a locus control region. The cis-regulatory sequences needed for domain opening and enhancement do show common binding sites for transcription factors. In contrast, alignments of non-coding sequences from species representing multiple eutherian mammalian orders, some of which diverged as long as 135 million years ago, are reliable predictors of novel cis-regulatory elements, both proximal and distal to the genes. Examples include a potential target for the hematopoietic transcription factor TAL1.
Characterization of a mammalian smooth muscle myosin heavy-chain gene: complete nucleotide and protein coding sequence and analysis of the 5' end of the gene. (1991)

The purpose of this study was to characterize the complete cDNA sequence encoding the rabbit smooth muscle myosin heavy chain (MHC) and determine the exon/intron organization at the 5' end of the corresponding gene. The full-length cDNA sequence of 6644 base pairs encoding a protein of 1972 amino acids was generated from two cDNA clones: PBRUC1 (approximately 6.3 kilobases), isolated from a rabbit uterus cDNA library, and PBRU-PCR33 (420 base pairs), produced by primer extension and PCR amplification. Compared with the chicken smooth muscle MHC sequence [Yanagisawa, M., Hamada, Y., Katsuragawa, Y., Imamura, M., Mikawa, T. & Masaki, T. (1987) J. Mol. Biol. 198, 143-157] the rabbit MHC shares about 90% amino acid identity in the S1 globular head region but shows a striking sequence divergence at the junction between the 25-kDa and 50-kDa proteolytic fragments of the functionally important S1 head domain. Genomic cloning shows that the rabbit smooth muscle MHC gene is large and has an unusual exon/intron organization at the 5' end. The first eight contiguous exons are located within a region of at least 70 kilobases of genomic DNA. Some introns span several kilobases of DNA and others at the 5' end show a high degree of intron conservation in the Mg(2+)-ATPase domain when compared with more distantly related sarcomeric MHC genes. Primer extension and S1 nuclease mapping analysis demonstrate that transcription initiates from a single site in the rabbit smooth muscle MHC gene.
Automating the injection of believable decoys to detect snooping (2010)

We propose a novel trap-based architecture for enterprise networks that detects "silent" attackers who are eavesdropping network traffic. The primary contributions of our work are the ease of injecting, automatically, large amounts of believable bait, and the integration of various detection mechanisms in the back-end. We demonstrate our methodology in a prototype platform that uses our decoy injection API to dynamically create and dispense network traps on a subset of our campus wireless network. Finally, we present results of a user study that demonstrates the believability of our automatically generated decoy traffic.
Three neural network based, sensor systems for environmental monitoring (1994)

Compact, portable systems capable of quickly identifying contaminants in the field are of great importance when monitoring the environment. One of the missions of the Pacific Northwest Laboratory is to examine and develop new technologies for environmental restoration and waste management at the Hanford Site (a former Plutonium production facility). In this paper, three prototype sensing systems are discussed. These prototypes are composed of sensing elements, data acquisition system, computer, and neural network implemented in software and are capable of automatically identifying contaminants. The first system employs an array of tin-oxide gas sensors and is used to identify chemical vapors. The second system employs an array of optical sensors and is used to identify the composition of chemical dyes in liquids. The third system contains a portable gamma-ray spectrometer and is used to identify radioactive isotopes. In these systems, the neural network is used to identify the composition of the sensed contaminant. With a neural network, the intense computation takes place during the training process. Once the network is trained, operation consists of propagating the data through the network. Since the computation involved during operation consists of vector-matrix multiplication and application of look-up tables (activation function), unknown samples can be rapidly identified in the field.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Ceruloplasmin, Copper Ions, and Angiogenesis<xref ref-type="fn" rid="fn2">2</xref> (1982)

The ability to induce new formation of capillaries in the cornea was tested for ceruloplasmin, the copper carrier of serum, for fragments of the ceruloplasmin molecule with and without copper, for heparin, and for glycyl-L-histidyl-L-lysine, bound or not bound to copper ions. Male or female 2- to 3-kg New Zealand White rabbits were used. These experiments were prompted by the previous observation of copper accumulation in the cornea during angiogenesis and by the inability of copper-deficient rabbits to mount an angiogenic response. The results showed that the three different molecules were all able to induce angiogenesis provided that they were bound to copper. Fragments of the ceruloplasmin molecule also induced angiogenesis but only when copper was bound to the peptides. The data are interpreted to indicate that copper ions are involved in the sequence of events leading to angiogenesis and that the carrier molecules may be of quite a different nature.
Magic Wand: A Hand-Drawn Gesture Input Device in 3-D Space with Inertial Sensors (2004)

This paper presents a gesture input device, magic wand, with which a user can input gestures in 3-D space, inertial sensors embedded in it generate acceleration and angular velocity signals according to a user's hand movement. A trajectory estimation algorithm is employed to convert them into a trajectory on 2-D plane. The recognition algorithm based on Bayesian networks finds the gesture model with the maximum likelihood from it. The recognition performance of the proposed system is quite promising; the writer-independent recognition rate was 99.2% on average for the database of 15 writers and 13 gesture classes.
NAD+ regeneration by NADH oxidase from Lactobacillus Brevis in the biocatalytic hexanol oxidation (2007)

Upotreba NAD+ ili NADP+ zavisnih dehidrogenaza u organskim sintezama ogranicena je cinjenicom da je koenzim prilicno skup reagens, koji se mora dodati u stehiometrijskoj koncentraciji. Regeneracijom koenzima, osim sto se postiže znatna usteda na koenzimu može se utjecati i na pomicanje reakcijske ravnoteže u željenom smjeru [1]. NADH oksidaza (NOX) iz Lactobacillus brevis je enzim koji katalizira oksidaciju koenzima NAD(H) pri cemu nastaje voda, te je stoga pogodan za njegovu regeneraciju [2]. U ovom radu provedena je regeneracija koenzima NAD+, NADH oksidazom u reakciji biokataliticke oksidacije heksanola. Navedena reakcija je katalizirana enzimom alkohol dehidrogenazom (ADH). Kao izvori enzima upotrijebljeni su komercijalni izolirani enzim i cijele stanice pekarskog kvasca. Obzirom da je aktivnost enzima u stanici niska, stanice su tretirane sa detergentom CTAB, kako bi perforirana stanicna stjenka omogucila bržu difuziju supstrata i produkta. Svi koristeni biokatalizatori su kineticki karakterizirani, te su na temelju procijenjenih parametara postavljeni matematicki modeli biokataliticke oksidacije heksanola uz regeneraciju koenzima. Modeli su validirani u kotlastom reaktoru. Biokatalitickom oksidacija heksanola uz izolirani enzim ADH dobivena je 58 %-tna konverzija zbog deaktivacije NOX-a, koja je opisana kinetikom prvog reda, pri cemu je sav oksidirani heksanol presao u heksanal. 100 %-tna konverzija heksanola je ostvarena prilikom provođenja navedene reakcije uz permeabilizirane stanice kvasca. U ovom sustavu nije doslo do deaktivacije regeneracijskog enzima, a kao produkt reakcije identificrana je heksan kiselina.
An overview of three commercial object-oriented database management systems (1992)

We present an analysis of three current object-oriented DBMS products: ONTOS, ObjectStore, and O2, as described by their available documentation. The most attractive feature of ONTOS and Object-Store is their use of C++ as a user interface - a widespread object-oriented language. They also provide persistent data implementation, transaction and recovery mechanisms, and modern application development tool sets following the recommendations of [Atkinson et al. 89]. O2 was chosen for a well-developed data type system and end-user interface, and for its reputation from the literature.
Behavior of Various Organosilicon Molecules in PECVD Processes for Hydrocarbon-Doped Silicon Oxide Films (2007)

Plasma diagnosis was performed by means of optical emission spectroscopy in the plasma-enhanced chemical vapor deposition process for preparation of hydrocarbon-doped silicon oxide films. The chemical bonding states were characterized by a fourier-transform infrared spectrometer. Based on the results of the diagnosis in organosilane plasma and the chemical bonding states, a reaction model for the formation process of hydrocarbon-doped silicon oxide films was discussed. From the results of optical emission spectroscopy, we found that the oxygen atoms of methoxy groups in TMMOS molecules can be dissociated easily in the plasma and behave as a kind of oxidizing agent. Siloxane bondings in HMDSO, on the other hand, hardly expel oxygen atoms.
Chemical composition of essential oil of Calendula officinalis L. (pot marigold) (1991)

Abstract The essential oil of Calendula officinalis L. was obtained in low yield (0.3 %) by steam distillation with cohobation from flowers and whole plants. Sixty‐six components were identified by GC‐MS, mainly sesquiterpene alcohols: α‐cadinol was the main constituent (about 25%). The essential oil from the whole plant differed from that of the flowers by the presence of monoterpene hydrocarbons in addition to the alcohols.
Swiss-PDB Viewer (Deep View) (2001)

Seven popular programs for gene prediction in eukaryotic organisms are described and evaluated on the basis of availability for in-house and on-line use and prediction accuracy. This report outlines generally applicable approaches to computational gene prediction and known limitations in this field.