Miracle-dz/UniFAR-FTUs huggingface dataset:
Chromatin fiber polymorphism triggered by variations of DNA linker lengths

Significance The structure of the chromatin fiber remains one of the most fundamental open biological questions because structure dictates many template-directed processes. We use coarse-grained modeling to investigate systematically how variations in the linker DNA length that arise naturally for chromatin in different tissues, species, and cell cycle stages affect fiber architecture. We unravel a natural source of fiber polymorphism, in which irregular interdigitated 10-nm and compact 30-nm fibers coexist. These results suggest how structural diversity can be advantageous for gene regulation activity. Interesting DNA design applications also arise. Deciphering the factors that control chromatin fiber structure is key to understanding fundamental chromosomal processes. Although details remain unknown, it is becoming clear that chromatin is polymorphic depending on internal and external factors. In particular, different lengths of the linker DNAs joining successive nucleosomes (measured in nucleosome-repeat lengths or NRLs) that characterize different cell types and cell cycle stages produce different structures. NRL is also nonuniform within single fibers, but how this diversity affects chromatin fiber structure is not clear. Here we perform Monte Carlo simulations of a coarse-grained oligonucleosome model to help interpret fiber structure subject to intrafiber NRL variations, as relevant to proliferating cells of interphase chromatin, fibers subject to remodeling factors, and regulatory DNA sequences. We find that intrafiber NRL variations have a profound impact on chromatin structure, with a wide range of different architectures emerging (highly bent narrow forms, canonical and irregular zigzag fibers, and polymorphic conformations), depending on the NRLs mixed. This stabilization of a wide range of fiber forms might allow NRL variations to regulate both fiber compaction and selective DNA exposure. The polymorphic forms spanning canonical to sharply bent structures, like hairpins and loops, arise from large NRL variations and are surprisingly more compact than uniform NRL structures. They are distinguished by tail-mediated far-nucleosome interactions, in addition to the near-nucleosome interactions of canonical 30-nm fibers. Polymorphism is consistent with chromatin’s diverse biological functions and heterogeneous constituents. Intrafiber NRL variations, in particular, may contribute to fiber bending and looping and thus to distant communication in associated regulatory processes.
Assessing the Influence of Reference Spectra on Synthetic SAM Classification Results

Spectral matching algorithms, such as the Spectral Angle Mapper (SAM), utilize the spectral similarity between individual image pixel spectra and a spectral reference library with known components. Here, we illustrate and quantify the effects that different sources of reference libraries have on SAM classification results. Synthetic images of three mineral endmembers were classified by using reference libraries derived from airborne hyperspectral imagery, ground spectra (Portable Infrared Mineral Analyser), and from a standard library (United States Geologic Survey). Results show that the source of the reference library strongly influences the classification results if all available wavelengths are used. This effect can be partially neutralized by using appropriate preprocessing methods. Two different types of spectral subsetting of the data, two types of continuum removal, and a combination thereof were tested. Best results were achieved by using a feature subset (i.e., limiting the input wavelengths to the diagnostic absorption features). This increased the average classification accuracy from 74% to 95% (ground spectral library) and from 68% to 94% (standard library).
IMPROVED FIELD RELIABILITY OF HIGH PERFORMANCE COATING SYSTEMS. PHASE 2. DEVELOP PROCEDURES AND CRITERIA IN CRITICAL PERFORMANCE AREAS. FINAL REPORT

Topcoated zinc-rich and waterborne bridge paint systems show significant variation in performance over the range of environmental conditions and application factors generally encountered in the field. Observed effects are consistent with the film formation mechanism for each class of paint. Qualification testing should include the realistic extremes of application conditions in order to identify products with low reliability. A simple solvent rub test has demonstrated general applicability for confirming the cure of ethyl silicate based zinc-rich primers. On-site application of this test can prevent premature topcoating and the resultant poorer system performance. Field adaptable techniques for detection of contaminants on cleaned or primed surfaces are available. Improvement is needed in definition of sampling methodology and in quantitation of results. Acceptance limits for contamination are not generally known, particularly for primed surfaces.
SPCS: Secure and Privacy-Preserving Charging-Station Searching using VANET

Electric vehicle has attracted more and more attention all around the world in recent years because of its many advantages such as low pollution to the environment. However, due to the limitation of current technology, charging remains an important issue. In this paper, we study the problem of finding and making reservation on charging stations via a vehicular ad hoc network (VANET). Our focus is on the privacy concern as drivers would not like to be traced by knowing which charging stations they have visited. Technically, we make use of the property of blind signature to achieve this goal. In brief, an electric vehicle first generates a set of anonymous credentials on its own. A trusted authority then blindly signs on them after verifying the identity of the vehicle. After that, the vehicle can make charging station searching queries and reservations by presenting those signed anonymous credentials. We implemented the scheme and show that the credential signing process (expected to be the most time consuming step) can be completed within reasonable time when the parameters are properly set. In particular, the process can be completed in 5 minutes when 1024 bits of RSA signing key is used. Moreover, we show that our scheme is secure in terms of authentication and privacy-preserving.
A psychometric evaluation of the Cornell Scale for Depression in Dementia in a frail, nursing home population.

OBJECTIVE The authors conducted a psychometric evaluation of the Cornell Scale for Depression in Dementia (CSDD) through factor analysis and assessment of criterion validity in an older, frail nursing home population, with a secondary analysis of pre-intervention data from a longitudinal clinical trial aimed at reducing restraints in nursing homes. METHODS The sample for the present study was 642 nursing home residents (mean [SD] age 84.3 [7.6] years; range: 61-105; 82% women) with completed CSDD scores, who were interviewed immediately before the intervention. Nursing home residents' scores from the 19-item CSDD were subjected to exploratory factor analysis and criterion-validity analysis. RESULTS The factor analysis resulted in four distinct clinically interpretable domains: Depression, Somatic/Vegetative, Disturbed Sleep, and Anxiety. Sixteen items were retained in these domains, and summated score indices and a global score were constructed. The global score and the four indices demonstrated adequate internal consistency and reliability. The indices generated by the factor analysis correlated as expected with criterion variables. CONCLUSION Results suggest that in frail, institutionalized older adults with high rates of dementia, medical illness, and functional disability, depression measurement methods that are less dependent on items highly sensitive to comorbid conditions and not necessarily associated with depression may be more appropriate. Authors recommend further validity testing of the CSDD with similar populations of frail, institutionalized older adults.
Design and Performance of a Multi-Point Scan Confocal Microendoscope

Confocal fluorescence microendoscopy provides high-resolution cellular-level imaging via a minimally invasive procedure, but requires fast scanning to achieve real-time imaging in vivo. Ideal confocal imaging performance is obtained with a point scanning system, but the scan rates required for in vivo biomedical imaging can be difficult to achieve. By scanning a line of illumination in one direction in conjunction with a stationary confocal slit aperture, very high image acquisition speeds can be achieved, but at the cost of a reduction in image quality. Here, the design, implementation, and experimental verification of a custom multi-point aperture modification to a line-scanning multi-spectral confocal microendoscope is presented. This new design improves the axial resolution of a line-scan system while maintaining high imaging rates. In addition, compared to the line-scanning configuration, previously reported simulations predicted that the multi-point aperture geometry greatly reduces the effects of tissue scatter on image quality. Experimental results confirming this prediction are presented.
Aortic pressure-diameter relationship assessed by intravascular ultrasound: experimental validation in dogs.

Intravascular ultrasound (IVUS) has emerged as an important diagnostic method for evaluating vessel diameter and vessel wall motion. To evaluate the validity of IVUS in assessing changes in the pressure-diameter relationship we compared measurements of abdominal aortic diameters derived from IVUS with those simultaneously obtained at the same site using implanted sonomicrometers in five chronically instrumented conscious dogs and in seven acutely instrumented anesthetized dogs. Five hundred eighty beats were analyzed to obtain peak systolic and end-diastolic diameters and to calculate aortic compliance at different blood pressure levels induced either by an aortic pneumatic cuff or by intravenous injections of nitroglycerin or norepinephrine. IVUS agreed closely with sonomicrometer measurements at different blood pressure levels. However, IVUS slightly but significantly underestimated aortic diameters by 0.6 ± 0.7 mm for systolic diameters ( P < 0.001) and by 0.7 ± 0.6 mm for diastolic diameters ( P < 0.001) compared with the sonomicrometer measurements. We conclude that IVUS is a feasible and reliable method to measure dynamic changes in aortic dimensions and has the potential to provide ready access to assess aortic compliance in humans.
[Billroth I anastomosis with biodegradable anastomosis ring in the animal model].

In the present study, the Billroth-I anastomosis with the biofragmentable anastomosis ring was examined in dogs. 24 dogs were randomized into a group of manual suturing (n = 12) and a BAR-group (n = 12). In the group of manual suturing, a distal gastric resection and gastroduodenostomy with sero-submucous suture was performed. In the BAR-group, the distal gastric resection was done with the linear stapler PLC-75, whereby the BAR gastroduodenostomy crossed the stapling line. The dogs were evaluated on p.o. days 4, 14, and 30 and tested for bursting strength and bursting location, appearance of mucosa, hydroxyprolin concentration, and histologic features. There was no functional disorder in the gastrointestinal transit in any animal; in summary with regard to the various parameters, the crossing of BAR and stapling line does not represent any additional risk factor in the Billroth-I anastomosis in dogs.
Using IT for Managing Resources in Business Networks

A case study is used in order to analyse information technology's function in managing the complex network of resources that interact behind a specific product and that contribute to a final product ready for use (see, for instance Wedin, 2001). This "product-centred resource network" is analysed by means of a resource categorisation introduced by Håkansson & Waluszewski (forthcoming). Information, about each used resource and performed activity, enters various firms' information systems and information technology (IS/IT), attempting to “mirror” and “translate” the concrete business network. The collected and processed information is moreover used in order to manage and co-ordinate resources and activities in the business network. How the digital information-based, "meta-network" translates the actual relations between resources and activities affects how they are managed and co-ordinated by means of IS/IT. The analysis focuses on activity co-ordination and on resource utilisation with reference to a specific product, by a Swedish furniture manufacturer. The case study maps how the various activities and resources, behind the focal product, are transformed into information, part of which is also translated and interpreted by the computerised IS/IT systems in use. This type of analysis helps to identify the interplay between information, IT and strategy in a network setting (see Snehota, 1990, and Ford et al., 1998). The link between information and concrete resources appears e.g. in the process of “information development”. The case study analysis introduces the notions of “IT-sation”, “informational needs”, “information horizon” and “network embedded information”. These concepts are used in order to investigate possibilities, requirements and limitations of “IT-based” resource management.
High‐Resolution Strain Mapping Through Time‐of‐Flight Neutron Transmission Diffraction with a Microchannel Plate Neutron Counting Detector

Abstract: Conventional neutron radiography can be strongly enhanced by obtaining Bragg‐edge information spatially correlated with the attenuation coefficient. This can now be achieved through time‐of‐flight techniques at pulsed neutron sources, utilising a neutron counting detector with high‐spatial and high‐temporal resolution. In these measurements, the positions of Bragg edges can in principle be obtained for each 55 × 55 μm2 pixel of the radiographic image. The combination of both Bragg‐edge and attenuation information enables high spatial resolution studies to be carried out on material composition, phase transitions, texture variations, as well as residual strain mapping. In this article, we present the results of high‐resolution strain maps of a ferritic steel cantilever sample measured at different loads by both transmission and conventional diffraction modes, as well as strains in an austenitic steel compact‐tension (CT) crack sample. The proof of principle experiments performed on the ENGIN‐X beamline on a bent cantilever arrangement resulting in a uni‐axial stress field verified that the strain values measured in diffraction and transmission mode are in good agreement. The characteristics of the transmission mode detector as well as the measured strain maps and future possibilities of this technology are discussed.
RoboCup: The Robot World Cup Initiative

The Robot World Cup Initiative (R, oboCup) is attempt to foster AI and intelligent rohoties research by providing a standard problem where wide range of technologies especially concerning multi-agent research (:an be integrated and examined. The first RoboCup competition is to be, heht at. IJCAI-97, Nagoya. In order for a robot team to actually perform a soccer game. various technologies must I)e incorl)orated including: design principles of autononmus agents, multi-agent collaboration, strategy acquisition, real-time rea. ~oning, robotics, and sensor-fllsion. Unlike AAAI robot competition, which is tuned for a single heavy-duty slow-moving robot. RoboCup is a task for a team of multiple f‘ast-moving robots under a dynamic environmen(. Although RoboCnp’s final target is a worhl cup with real robots, RoboCup offers a soft.ware platform for reseaxch on the software aspects of RoboCup. This paper describes teclini(’M challenges involw~d in RoboCup, rules, and simulation environment.
University of Groningen Hyperspectral frequency selection for the classification of vegetation diseases

Reducing the use of pesticides by early visual detection of diseases in precision agriculture is important. Because of the color similarity between potato-plant diseases, narrow band hyper-spectral imaging is required. Payload constraints on unmanned aerial vehicles require reduction of spectral bands. Therefore, we present a methodology for per-patch classification combined with hyper-spectral band selection. In controlled experiments performed on a set of individual leaves, we measure the performance of five classifiers and three dimensionality-reduction methods with three patch sizes. With the best-performing classifier an error rate of 1.5% is achieved for distinguishing two important potato-plant diseases.
The Development of Green Innovation Measurement Based on Inter Rater Agreement Approach: A Preliminary Study

The rising of environmental concerns from customers, buyers, communities, and government regulations have forced company to implement innovative and proactive corporate environmental management such as green supply chain management (GSCM) and green innovation. The aim of the paper is to discuss on the development of green innovation measurement. The data were collected through a questionnaire-based survey from two experts. The data are analyzed using Inter Rater Agreement. The findings show the kappa value is above 80 percent which indicates the perfect agreement between both of the raters on the proposed measurements for green marketing innovation and reverse logistics innovation. By including these two constructs into existing green innovation activity, it is possible to show the complete picture of green innovation to increase the performance of GSCM.
Measurement of bacteriolytic enzymes

R. S. Wolfe, J. Bacteriol. 90:395, 1965; J. W. 0.600 Zyskind, P. A. Pattee, and M. Lache, Science E 0.600 10 20 30 40 147:1458, 1965) have been based on the reducpJg PROTEIN tion in turbidity of suspensions of susceptible 0Og PROTEIN bacterial cells. The assay for the Chalaropsis N2 0 acetylhexosaminidase (Hash, Arch. Biochem. < \ Biophys. 102:379, 1963), which was based on the L 0.400 20 reduction in turbidity of suspensions of StaphyloZ coccus aureus cells, was complicated by buffer I 030 effects, and it was difficult to obtain different °C preparations of cells with the same susceptibility m0.05 M, PH 4.8 to lysis. It was observed that isolated cell walls l from different preparations of ctlls were uni15 30 45 60 formly susceptible to lysis. An assay was deSECONDS veloped that was based on reduction in turbidity FIG. 1. Relationship between Chalaropsis B protein of isolated cell walls rather than intact cells. concentration and changes in absorbance of StaphyloThis assay was independent of buffer concentracoccus aureus cell wall suspensions. tion over the range 0.01 to 0.2 M, and different preparations of cell walls showed the' same 0.300 sensitivity. Other bacteriolytic enzymes have z been tested, and the method appears to be apE2 _/ plicable to all enzymes that solubilize the cell z wall murein. In the present study, these enzymes a include: lysozyme, Chalaropsis B enzyme, lysoM 0. -00 staphin (courtesy of Mead Johnson Research °) Center and M. Glenn Koenig), Pseudomonas < enzyme (courtesy of P. A. Pattee), and Myxo0.600 2 4 6 8 10 12 bacter AL-1 enzyme (courtesy of R. S. Wolfe). ug PROTEIN Lysozyme is a p3-1,4-N-acetylmuramidase and E pg PROTEIN Chalaropsis B is a ,B-1 ,4-N, O-diacetylmuramiO 0.500 0 dase. The Pseudomonas and Myxobacter en2 zymes are peptidases. Lysostaphin contains both W 0.400 4 peptidase and p-1,4-N-acetylglucosaminidase,6 activities. Bacterial cell walls were prepared by stand< 0.300 TRIS BUFFER 12 ard procedures (M. R. J. Salton, The Bacterial O 0.05 M, p H 9.0 Cell Wall, American Elsevier Publishing Co., , I New York, 1964) and were extracted with cold 15 30 45 60 10% trichloroacetic acid to remove techoic acid SECONDS and other polyelectrolytes. Micrococcus lysoFIG. 2. Relationship between Myxobacter AL-I deikticus walls were used for lysozyme and S. protein concentration and changes in absorbance of aureus walls were used for the other enzymes. Staphylococcus aureus cell wall suspensions.
Survival in Speculative Markets

In a stochastic exchange economy where, due to beliefs’ heterogeneity, agents engage in speculative trade, I investigate the Market Selection Hypothesis that speculation rewards the agent with the most accurate beliefs. Assuming that markets are complete, I derive sufficient conditions for agents’ survival in terms of saving and portfolio decisions and use them to show that the Market Selection Hypothesis fails generically. In particular, when agents have Epstein-Zin preferences, beliefs heterogeneity may persist in the long-run or speculation may cause the agent with the most accurate beliefs to vanish. Failures occur because agents’ portfolio average returns are shown to depend not only on beliefs’ accuracy but also on risk preferences, through the comparison with the growth-optimal portfolio. Failures do not occur in bounded CRRA economies because, due to the interdependence of relative risk aversion and intertemporal elasticity of substitution, portfolio returns not related to beliefs’ accuracy are compensated by the component of saving that responds to uncertainty.
Kok effect and the quantum yield of photosynthesis : light partially inhibits dark respiration.

The linear response of photosynthesis to light at low photon flux densities is known to change abruptly in the vicinity of the light compensation point so that the quantum yield seems to decrease as radiation increases. We studied this ;Kok effect' in attached sunflower (Helianthus annuus L. cv IS894) leaves using gas exchange techniques. The effect was present even though respiration was constant in the dark. It was observed at a similar photon flux density (7 to 11 micromole photons per square meter per second absorbed photosynthetically active radiation) despite a wide range of light compensation points as well as rates of photosynthesis. The effect was not apparent when photorespiration was inhibited at low pO(2) (1 kilopascal), but this result was complicated because dark respiration was quite O(2)-sensitive and was partially suppressed under these conditions. The Kok effect was observed at saturating pCO(2) and, therefore, could not be explained by a change in photorespiration. Instead, the magnitude of the effect varied as dark respiration varied in a single leaf, and was minimized when dark respiration was minimized, indicating that a partial suppression of dark respiration by light is responsible. Quantum yields measured at photon flux densities between 0 and 7 to 11 micromole photons per square meter per second, therefore, represent the combined yields of photosynthesis and of the suppression of a component of dark respiration by light. This leads to an overestimate of the quantum yield of photosynthesis. In view of these results, quantum yields of photosynthesis must be measured (a) when respiration is constant in the dark, and (b) when dark respiration has been inhibited either at low pO(2) to eliminate most of the light-induced suppression of dark respiration or at photon flux densities above that required to saturate the light-induced suppression of dark respiration. Significant errors in quantum yields of photosynthesis can result in leaves exhibiting this respiratory behavior if these principles are not followed.