gebhart/patrepeval huggingface dataset:
Ontology-based functional classification of genes: Evaluation with reference sets and overlap analysis (2011)

Functional classification involves grouping genes according to their molecular functions or the biological processes they participate in. This unsupervised classification task is essential for interpreting gene datasets produced by post-genomic experiments. As the functional annotation of genes is mostly based on the Gene Ontology (GO), many similarity measures using the GO have been described, but few of them have been used for clustering. In this paper we evaluate functional classification of genes using our previously described IntelliGO semantic similarity measure with the help of reference sets. These sets consist of genes taken from human and yeast KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways and Pfam clans. Hierarchical clustering and heatmap visualization are used to illustrate the advantages of IntelliGO over several other measures. Because genes often belong to more than one reference set, the fuzzy C-means clustering algorithm is then applied to the datasets using IntelliGO. The F-score method is used to estimate the quality of clustering and the optimal number of clusters. The results are compared with those obtained from the state-of-the-art DAVID (Database for Annotation Visualization and Integrated Discovery) functional classification method. Overlap analysis allows to study the matching between clusters and reference sets, and leads us to propose a set-difference method for discovering missing information. The IntelliGO similarity measure, the clustering tool and the reference sets used for evaluation are available at: http://plateforme-mbi.loria.fr/intelligo.
A Novel Method for Optimum Biopsy Specimen Preservation for Histochemical and Immunohistochemical Analysis (1991)

A novel method has been developed for optimally processing biopsy specimens combining freeze-substitution with low-temperature plastic embedding. Immunohistochemistry and conventional histochemical stains were all readily performed on tissue displaying high-quality morphologic preservation. Labile antigens, especially lymphoid cell surface antigens, were well preserved. This new method avoids the need for tissue fixation and combines the superior morphologic preservation of fixed embedded tissue with the reactivity of cryostat sections. This method ensures that diagnostic information from even the smallest biopsy specimen is maximized because a wide range of phenotypic markers can be applied and evaluated in relation to high-quality morphologic preservation of tissue. Biopsy specimens are stored at room temperature without loss of tissue-specific characteristics during storage.
Umsetzungen von Chlorwasserstoff mit 3‐Methyl‐1‐butin: Cyclo‐additions‐ und Umlagerungsreaktionen über Vinyl‐Kationen (1980)

Abstract 3‐Methyl‐1‐butin wurde mit wasserfreiem Chlorwasserstoff in der flüssigen Phase bei Raumtemperatur umgesetzt. Es wurden insgesamt 12 Produkte identifiziert: drei Monoaddukte ( 4, 6, 9 ), drei Diaddukte ( 5, 7, 10 ), ein Substitutionsprodukt ( 8 ) sowie fünf Cycloaddukte mit Cyclobutanringen ( 11–15 ). In Modelluntersuchungen wurden Hinweise auf die Bildungsweise der Reaktionsprodukte erhalten.
ChemInform Abstract: Synthesis and Biological Evaluation of Phenylacetyl Derivatives Having Low Central Nervous System Permeability as Potent and Selective M<sub>2</sub> Muscarinic Receptor Antagonists. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A simple transformation of the environment eliminates standard PE phase errors (2004)

It is shown that, in range-independent sound channels with a single sound speed minimum, the environment can be transformed in such a way that solutions to a standard parabolic wave equation in the transformed environment are asymptotically equivalent to solutions to the Helmholtz equation in the original environment. This equivalence is demonstrated using both ray- and mode-based wavefield expansions. Reasons that equivalence between solutions to the Helmholtz equation and the parabolic wave equation can only be asymptotic will be briefly reviewed. [Work supported by ONR and NSF.]
Parameterization of a Piezoelectric Nanomanipulation Device (2006)

Through measurement of hysteresis and drift in a piezoelectrically driven multi-axis multi-positioner nanomanipulator, we have quantified error over ranges of three primary operating parameters: gain, duty cycle, and actuation time. A total of sixty-nine curves were plotted, and error and drift measured in a single operating plane. All data shown were collected on the Zyvex L-100 nanomanipulator operating in an open-loop programmed method, in both coarse (12mm range, 2–5 μm precision) and fine mode (100 μm range, 10–50 nm precision). In general, the normalized error was reduced at larger actuation distances and in coarse mode. These results may be used to define optimum operating conditions for piezoelectrically actuated nanomanipulators and micromanipulators whereby the goal is to find a balance between speed and accuracy. The results also are intended to allow for optimal control in closed-loop operation and for task-oriented and pick-and-place operations.
Asymmetric Dearomatizing Spirolactonization of Naphthols Catalyzed by Spirobiindane-Based Chiral Hypervalent Iodine Species (2013)

This report details the development of a spirobiindane-based chiral hypervalent iodine reagent, especially focusing on its structural elucidation for effective asymmetric induction of the chiral spiro center during the oxidative dearomatizing spirolactonization of naphthols. In this study we synthesized a new series of ortho-functionalized spirobiindane catalysts and demonstrated that the enantioselectivity can be dramatically improved by the presence of the substituents ortho to the iodine atom. The structural elucidation of a spirobiindane-based hypervalent iodine catalyst has led to further improvement in the stereoselective construction of the spiro center during the oxidative dearomatizing spirolactonization of naphthols. Thus, catalytic oxidation with the highest reported level of enantioselectivity in hypervalent iodine chemistry has been achieved with also an excellent level of asymmetric induction (92% ee for substrate 3a). As a result, this study, dealing with a series of modified iodine catalysts, can provide important clues about the transition state and reaction intermediate to help scientists understand the origin of the stereoselectivity. A plausible transition-state model and intermediate in the reaction for the stereoselective formation of spirolactone products are postulated by considering the ortho-substituent effect and the results of X-ray analysis. In this reaction model, the high enantiomeric excess obtained by using the spirobiindane catalysts could be well explained by the occupation of the equatorial site and extension of the surroundings around the hypervalent iodine bonds by the introduced ortho-substituent. Thus, this study would contribute to estimation of the chiral hypervalent iodine compounds in asymmetric reactions.
An Optimisation Approach for Long-Term Industrial Investment Planning (2019)

The industrial sector has a large presence in world energy consumption and CO2 emissions, which has made it one of the focal points for energy and resource efficiency studies. However, large investments are required to retrofit existing industrial plants, which remains the largest barrier to implementing energy saving solutions. Process integration methods can be used to identify the best investments to improve the efficiency of plants, yet their timing remains to be answered using an optimisation approach. Even more critically, such decisions must also account for future investments to avoid stranded or regretted investments. This paper presents a method incorporating investment planning over long time horizons in the framework of process integration. The time horizon is included by formulating the problem using multiple investment periods. Investment planning is conducted using a superstructure approach, which permits both commissioning and decommissioning of units in the beginning of each period. The method is applied to a large case study, with an industrial cluster neighbouring an urban centre to also explore options of heat integration between industries and cities. Compared to the business-as-usual operation, optimal investment planning improves the operating cost of the system by 27% without budget constraints and 16–26% with constraints on budget and investment periods, which is reflected as an increase in net present value and a decrease in CO2 emissions. In all cases, the operating cost benefits pay off the investment in less than two years. The present work is efficient in finding energy saving solutions based on the interest of industries. This method adds additional perspectives in the decision-making process and is adaptable to various time horizons, budgets and economic constraints.
An EMF Study of Certain Orthoferrites: YFeO3, GdFeO3 and SmFeO3 (1975)

Abstract The EMF of a solid electrolyte galvanic cell on the formation of orthoferrites, LnFeO3, was measured for Ln=Y, Gd and Sm at 1200–1400 K. The free energy change of the (1/2)Fe2O3+(1/2)Ln2O3→LnFeO3 reaction was calculated.
Restriction fragment length polymorphism of HLA and non-HLA genes in DR3/4 heterozygous Danish insulin-dependent diabetic patients and healthy individuals: reassessment of the influence of alpha DX and insulin-linked polymorphic loci, and new splits of DQw3 haplotypes. (1989)

We have investigated restriction fragment length polymorphism (RFLP) of HLA and non-HLA regions of the genome in the homogeneous Danish population. Insulin-dependent diabetes mellitus (IDDM) patients and healthy individuals were selected for being HLA-DR 3/4 heterozygous to evaluate the influence of genes other than DR on disease susceptibility. Five different probes were used: HLA alpha and beta DQ (chromosome 6), the Ins 310 genomic fragment which detects a polymorphic region 5' to the insulin gene (chromosome 11), and cDNA for the constant regions of the T cell receptor alpha and beta genes (chromosomes 14 and 7). Fifteen cells homozygous for the HLA-D region were used to obtain reference DNA patterns. This allowed us to describe four splits among the HLA-DQw3 haplotypes (DQw3.1 to DQw3.4). The two new haplotypes DQw3.3 and DQw3.4 do not code for the TA10 serological marker which is found on DQw3.1 positive cells. One-hundred per cent of IDDM patients were typed as DQw3.2 versus 68 per cent for controls (p = 0.003). However, our results do not indicate a role for the Ins 310 or for the alpha DX locus region in IDDM susceptibility, in contrast to previous reports by others. The restriction enzymes that we have used did not reveal significant differences between DNA patterns of patients and controls with probes for the constant region of the T cell receptor genes.
Incremental Maintenance of Materialized Path Query OODB Views. (1996)

Materialized database views allow applications to benefit from the powerful flexibility of views while minimizing the performance penalties traditionally associated with views. However, the need to maintain materialized views in the face of updates limits the variety of queries that can be used to define them. In this paper we address the problem of incrementally maintaining OODB views formed using path queries. The indexing needs of the path query view problem are unique in that because the contents of the materialized view are cached and can be queried directly, the primary use for a supplemental index is during the propagation of updates rather than during query processing. Furthermore, traditional index organizations do not distinguish between single-valued and multivalued attributes, and thus do not account for the fact that multi-valued attributes enable a single object at the head of a path to be associated with multiple instantiations of the path, any number of which could sati...
A REEXAMINATION OF THE EFFECTS OF ADSORBATES ON THE RAMAN SPECTRUM OF GIBBSITE (1983)

A substantial change in the Raman intensities of the OH- stretching bands of solid, powdered gibbsite [α-Al(OH)3, surface area 10 m2/g] has been attributed to surface interactions with the adsorbates Ca+2, HxPO4-3x, SiO2 · xH2O, and mixtures thereof. The treatment of gibbsite with CaCl2 has been reported to reduce the OH- intensity of the 3360 cm-1 band to 48 percent of that of pure gibbsite at one extreme, and treatment with H3PO4 to increase the OH- intensity of the 3360 cm-1 band 82 percent more than that of pure gibbsite at the other extreme. Small changes in the relative peak heights of the four bands were observed, depending on the treatment used. Such interactions, however, should have little effect on what is essentially a Raman spectrum of bulk OH-. We have reexamined this system using an internal intensity standard (Na2C2O4 crystals and gibbsite with surface area of 39 m2/g). Adsorbate solutions, treatment regimes, and spectroscopic techniques were similar to those in the Alvarez study. Our results show no effects, within probable error, of the different adsorbates on OH- band parameters.
NetSTAR: Methodology to Identify Enemy Network Structure, Tasks, Activities, and Roles (2005)

The mechanism by which arcuate nucleus kisspeptin (ARN<sup>KISS</sup>) neurons co-expressing glutamate, neurokinin B, and dynorphin intermittently synchronize their activity to generate pulsatile hormone secretion remains unknown. An acute brain slice preparation maintaining synchronized ARN<sup>KISS</sup> neuron burst firing was used alongside in vivo GCaMP GRIN lens microendoscope and fiber photometry imaging coupled with intra-ARN microinfusion. Studies in intact and gonadectomized male mice revealed that ARN<sup>KISS</sup> neuron synchronizations result from near-random emergent network activity within the population and that this was critically dependent on local glutamate-AMPA signaling. Whereas neurokinin B operated to potentiate glutamate-generated synchronizations, dynorphin-kappa opioid tone within the network served as a gate for synchronization initiation. These observations force a departure from the existing "KNDy hypothesis" for ARN<sup>KISS</sup> neuron synchronization. A "glutamate two-transition" mechanism is proposed to underlie synchronizations in this key hypothalamic central pattern generator driving mammalian fertility.
Imaging Implanted Keratoprostheses With Anterior-Segment Optical Coherence Tomography and Ultrasound Biomicroscopy (2008)

Cross-sectional AS-OCT adequately imaged the components of the assembled KPro in vivo, as well as its interaction with surrounding anterior-segment structures. It allowed visualization of the anterior chamber, iris, and angle, essential in the postoperative care of these patients. Coronal AS-OCT showed graphic en face images of the KPro device and suspected retrokeratoprosthetic membranes. UBM, on the other hand, adequately imaged glaucoma tube shunts and PCIOL haptics beneath the iris plane.
Anatomic Distribution of Bullet Head Injuries in Combat Fatalities (2010)

These findings imply that gun-shot entry wounds to the head are unevenly distributed. A partially bullet-proof protective helmet may prevent a substantial fraction of injuries (and fatalities) without a significant weight addition to the helmet.
THE PHASE DIAGRAM FOR THE BINARY SYSTEM CADMIUM-TELLURIUM. Report No. 2900-139-R (1960)

The phase diagram for the Cd -Te system was determined using differential thermal analysis. Thermodynamic analysis showed that the system CdTe-Te appeared to form an ideal solution. The latent heat of fusion of CdTe is estimated to be 16,706 cal/gram molecule. It was found that the system Cd-CdTe is an elementary solution and has a relatively large excess partial molar entropy of solution and a large partial molar enthalpy of solution. These partial molar qualities were independent functions of composition, but not of temperature. The eutectic compositions were determined as 10/sup -6/ atom-fraction tellurium and about 0.99 atom-fraction tellurium. (auth)
Fiber Diffraction Studies of Bacterial Polysaccharides (1980)

The possibilities of the double helical structures of xanthan were re-examined thoroughly. Among the several possibilities, only parallel and antiparallel 51 double helices could be built and packed into a unit cell. The conformation of single chains in the parallel and antiparallel chains are very similar to each other. These double helical structures are compatible with several properties of xanthan in solution. The molecular structure of polysaccharides from Klebsiella serotype K8 has been examined by X-ray diffraction and computer-aided molecular modeling. The most favorable molecular model was not the one which had the maximum number of intra-molecular hydrogen bonds. This result suggests that in the analysis one should not a priori choose the molecular model which has the largest number of intra-molecular hydrogen bonds.
Geriatrisch-soziale Dienste in der Bundesrepublik Deutschland (1976)

Die Struktur geriatrischer Kliniken ist in Deutschland bis heute noch nicht einheitlich definiert. Es besteht eine gewisse Einigkeit darüber, daß geriatrische Krankenanstalten interne Kliniken dar stellen, die sich speziell mit Alterskrankheiten beschäftigen. Wichtig ist hierbei, daß viele Kliniken starre Altersgrenzen für die Charakterisierung ihres Krankenguts ablehnen. Typische Alterskrankheiten umfassen chronische arterielle Verschlüsse, chronische Gelenkerkrankungen, chronische Herzinsuffizienz, bestimmte Formen von Inkontinenz, chronisch cerebrale Prozesse etc. Derartige Krankheitsformen können (wenn auch selten) auch in jüngeren Jahren auftreten und werden dann zweckmäßigerweise dem darin erfahrenen Geriater zugewiesen.
Alignment Method of ECH Transmission Lines Based on the Moment and Phase Retrieval Method Using IR Images (2005)

New alignment methods of millimeter-wave transmission lines for Electron Cyclotron resonance Heating are proposed and evaluated on a high power level.These methods are based on the measured data of infrared images on the target, which is irradiated by the high power millimeter-waves at several positions.The first and second moments and retrieved phase obtained from these data are used to determine the propagation direction of the millimeter-wave beam along the waveguide axis.It is demonstrated that these methods have sufficient resolution to discriminate 0.1 deg., which is required to restrict the transmission loss below 1% over the 100 GHz range.
Weakly Supervised Learning of Interactions between Humans and Objects (2011)

We introduce a weakly supervised approach for learning human actions modeled as interactions between humans and objects. Our approach is human-centric: We first localize a human in the image and then determine the object relevant for the action and its spatial relation with the human. The model is learned automatically from a set of still images annotated only with the action label. Our approach relies on a human detector to initialize the model learning. For robustness to various degrees of visibility, we build a detector that learns to combine a set of existing part detectors. Starting from humans detected in a set of images depicting the action, our approach determines the action object and its spatial relation to the human. Its final output is a probabilistic model of the human-object interaction, i.e., the spatial relation between the human and the object. We present an extensive experimental evaluation on the sports action data set from [1], the PASCAL Action 2010 data set [2], and a new human-object interaction data set.
Structural and thermodynamical characterisation of interactionbetween a pseudomonas lectin and monosaccharides (2003)

Pseudomonas aeruginosa galactose- and fucose-binding (PA-IL and
PA-IIL) lectins contribute to the virulence of this pathogenic
bacterium, which is a major cause of morbidity and mortality in
cystic fibrosis patients. The crystal structure of PA-IIL
complexed with fucose has been solved at 1.3 A and further
refined at 1 Ĺ resolution. Additional experiments have been
performed in order to understand the molecular basis of both
specificity and affinity of PA-IIL for monosaccharides.
Crystals have been obtained for the complex between PA-ILL and
b-Me-D-arabinopyranoside and the structure has been solved at
1.8 A resolution. PA-IIL exhibits unusually high specificity to
fucose, which can be related to the presence of two calcium
ions in the site. Isothermal titration microcalorimetry (ITC)
experiments were performed in order to characterize the
thermodynamic parameters of the interaction since this method
has been proven to be well adapted to the study of
protein/carbohydrate interactions. Several monosaccharides
differing only by the group at C5 (L-fucose, L-galactose and
D-arabinose) were tested, as well as their methyl-glycosides.
Calculations of charges distribution were performed using
quantum chemistry in order to rationalize the role of calcium
ions in the affinity.
Enzymatic Production of<scp>l</scp>-Tryptophan from<scp>l</scp>- and<scp>dl</scp>-5-Indolyl-methylhydantoin by Newly Isolated Bacterium (1977)

Journal Article Enzymatic Production of l-Tryptophan from l- and dl-5-Indolyl-methylhydantoin by Newly Isolated Bacterium Get access Konosuke Sano, Konosuke Sano Central Research Laboratories of Ajinomoto Co., Inc., Kawasaki, Japan Search for other works by this author on: Oxford Academic Google Scholar Kenzo Yokozeki, Kenzo Yokozeki Central Research Laboratories of Ajinomoto Co., Inc., Kawasaki, Japan Search for other works by this author on: Oxford Academic Google Scholar Chikahiko Eguchi, Chikahiko Eguchi Central Research Laboratories of Ajinomoto Co., Inc., Kawasaki, Japan Search for other works by this author on: Oxford Academic Google Scholar Teruhiko Kagawa, Teruhiko Kagawa Central Research Laboratories of Ajinomoto Co., Inc., Kawasaki, Japan Search for other works by this author on: Oxford Academic Google Scholar Ichiro Noda, Ichiro Noda Central Research Laboratories of Ajinomoto Co., Inc., Kawasaki, Japan Search for other works by this author on: Oxford Academic Google Scholar Koji Mitsugi Koji Mitsugi Central Research Laboratories of Ajinomoto Co., Inc., Kawasaki, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 41, Issue 5, 1 May 1977, Pages 819–825, https://doi.org/10.1080/00021369.1977.10862589 Published: 01 May 1977 Article history Received: 09 December 1976 Published: 01 May 1977
Total Hip Replacement: Incidence of Osteolysis and Clinical Presentation (2005)

Osteolysis is a result of a particle-induced biologic process at the metal-bone or cement-bone interface, resulting in bone loss. Manifestations of this type of bone loss in patients range from new radiolucency around previously well-ﬁxed implants, which usually progress and may result in loosening, to rapidly expanding focal lesions that may result in mechanical instability or pathologic fracture. Among orthopaedic surgeons, for ease of description, the former process is generally termed aseptic loosening and the latter is widely known as ‘‘osteolysis.’’ Due to the popular usage of these two terms, a common misconception is that each phenomenon represents a distinct clinical entity with dissimilar implications. However, it is important to appreciate that the radiological appearance of osteolysis or aseptic loosening depends on the access of the particulate debris to the metal-bone or cement-bone interface and that the underlying biologic process is the same in both instances.