Miracle-dz/UniFAR-FTUs huggingface dataset:
Physiological status of coho salmon (Oncorhynchus kisutch) captured in commercial nonretention fisheries

The physical, hematological, and metabolic condition of 303 adult coho salmon (Oncorhynchus kisutch )w as examined following capture with three commercial fishing gear types (seine, troll, and gill net) and a variety of meth - ods. All fish arrived onboard in a state of severe metabolic exhaustion, and physiological differences among gear types and fishing methods were few and relatively small. Fish showed less physiological disruption with a brailing versus a ramping method of seine fishing and with a 30-min versus a 60-min net soak time for gillnet fishing. The visual rat- ings of physical condition (nonbleeding, vigorous, and lethargic) correlated significantly with hematocrit, plasma osmolality, plasma lactate, and plasma sodium. Fish placed in recovery boxes for 30-60 min onboard fishing vessels did not show the expected metabolic recovery; only plasma potassium recovered significantly. However, plasma lactate levels declined significantly for 125 fish placed in a net pen for 24 h, suggesting that metabolic recovery was possible after commercial capture. Because of a concern that the current recovery box design does not effect optimum recovery, we recommend that future experiments test a better-designed recovery box that orients fish into flowing water. Resume : Nous avons examine la condition physique, hematologique et metabolique de 303 cohos (Oncorhynchus kisutch) adultes apres leur capture dans trois types d'engins de peche commerciale (senne, lignes et filet maillant). Tous les poissons arrivaient a bord dans un etat de grave epuisement metabolique, et les differences physiologiques etaient peu nombreuses et relativement faibles d'un type d'engin et d'une methode de peche a l'autre. Les poissons presen- taient moins de perturbations physiologiques dans le cas du salabardage qu'avec le hissage sur la rampe dans la peche a la senne, et avec un temps de mouillage de 30 min qu'avec 60 min dans la peche aux filets maillants. Les evalua- tions visuelles de la condition physique (absence de saignement, poisson vigoureux ou lethargique) etaient significative- ment correlees a l'hematocrite, a l'osmolalite plasmique et aux concentrations de lactate et de sodium dans le plasma. Les poissons places dans des viviers de recuperation pendant 30-60 min a bord des bateaux de peche se presentaient pas le retablissement metabolique prevu, car seul le potassium plasmique remontait de facon notable. Toutefois, les concentrations plasmiques de lactate baissaient de facon significative chez 125 poissons places dans un parc de filet pendant 24 h, ce qui permet de penser que la recuperation metabolique est possible apres la capture commerciale. Il semble que la conception actuelle des viviers de recuperation ne soit pas optimale, aussi recommandons-nous que des experiences futures mettent a l'essai un vivier mieux concu qui oriente les poissons dans un courant d'eau. (Traduit par la Redaction) Farrell et al. 1678
Presentation and initial clinical course in patients with chronic inflammatory demyelinating polyradiculoneuropathy

Chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) may occur in association with a monoclonal gammopathy of undetermined significance (MGUS) or a variety of other systemic illnesses. It is not known if the clinical features of CIDP are altered by the presence of an MGUS. We compared demographic features, clinical presentation, improvement and outcome after initial treatment, and electrodiagnostic features of a group of 77 patients with idiopathic CIDP (CIDP-I, no associated systemic illness) with 26 patients with CIDP in whom an MGUS was found during evaluation of the neuropathy (CIDP-MGUS). Patients with CIDP-MGUS had, on average, a more indolent course and less severe weakness than patients with CIDP-I, despite similar motor conduction studies. CIDP-MGUS patients also demonstrated less functional impairment, more frequent sensory loss, and more abnormal sensory conduction studies than patients with CIDP-I. Because of the greater improvement of CIDP-I patients with treatment, both groups had similar outcomes from their initial episodes of weakness. Subgroup analysis of CIDP-MGUS patients did not demonstrate differences between groups with IgM and IgG or IgA gammopathies.
Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2′-O-transphosphorylation

Enzymes function by stabilizing reaction transition states; therefore, comparison of the transition states of enzymatic and nonenzymatic model reactions can provide insight into biological catalysis. Catalysis of RNA 2′-O-transphosphorylation by ribonuclease A is proposed to involve electrostatic stabilization and acid/base catalysis, although the structure of the rate-limiting transition state is uncertain. Here, we describe coordinated kinetic isotope effect (KIE) analyses, molecular dynamics simulations, and quantum mechanical calculations to model the transition state and mechanism of RNase A. Comparison of the 18O KIEs on the 2′O nucleophile, 5′O leaving group, and nonbridging phosphoryl oxygens for RNase A to values observed for hydronium- or hydroxide-catalyzed reactions indicate a late anionic transition state. Molecular dynamics simulations using an anionic phosphorane transition state mimic suggest that H-bonding by protonated His12 and Lys41 stabilizes the transition state by neutralizing the negative charge on the nonbridging phosphoryl oxygens. Quantum mechanical calculations consistent with the experimental KIEs indicate that expulsion of the 5′O remains an integral feature of the rate-limiting step both on and off the enzyme. Electrostatic interactions with positively charged amino acid site chains (His12/Lys41), together with proton transfer from His119, render departure of the 5′O less advanced compared with the solution reaction and stabilize charge buildup in the transition state. The ability to obtain a chemically detailed description of 2′-O-transphosphorylation transition states provides an opportunity to advance our understanding of biological catalysis significantly by determining how the catalytic modes and active site environments of phosphoryl transferases influence transition state structure.
Efficient algorithms for Volterra system identification

In this paper, nonlinear filtering and identification based on finite-support Volterra models are considered. The Volterra kernels are estimated via input-output statistics or directly in terms of input-output data. It is shown that the normal equations for a finite-support Volterra system excited by zero mean Gaussian input have a unique solution if, and only if, the power spectral process of the input signal is nonzero at least at m distinct frequencies, where m is the memory of the system. A multichannel embedding approach is introduced. A set of primary signals defined in terms of the input signal serve to map efficiently the nonlinear process to an equivalent multichannel format. Efficient algorithms for the estimation of the Volterra parameters are derived for batch, as well as for adaptive processing. An efficient order-recursive method is presented for the determination of the Volterra model structure. The proposed methods are illustrated by simulations.
Driver drowsiness detection using EEG power spectrum analysis

Driver drowsiness is considered to be a very critical issue causing many fatal accidents, injuries and property damages. Therefore, it has been an area of intensive research in recent years. In this paper, a driving simulator based study was conducted to observe the significant changes that occur in the EEG power spectrum during monotonous driving. Nine healthy university students voluntarily participated in the experiment. The absolute band power of the EEG signal was computed by taking the FFT of the time series signal and then the power spectral density was computed using Welch method. Our findings conclude that alpha and theta band powers increase significantly (p<;0.05) when a subject moves from alert state to drowsy state. These changes are more dominant in the occipital and parietal regions when compared to the other regions. The findings of this study provide a promising drowsiness indicator which can be used to prevent road accidents caused by driver drowsiness.
Effects of Payment Instruments on Unhealthy Purchases

In this online replication study we investigate if the pain of paying in cash - as opposed to paying by cards - can curb impulsive urges to purchase unhealthy or 'vice' products. This effect was found by Thomas et al (2011) when comparing the payment instruments cash and credit card. We investigate whether these results also hold in the Netherlands, where the dominant payment methods are cash and debit card. In total, 2,213 participants bought on average 12.3% more unhealthy supermarket products when paying with cards compared to cash. Participants who paid with cards bought more products in general (5.1%), however, the difference for healthy or 'virtue' products was not significant. The pattern of the mean scores per payment instrument indicate that paying with cards has a specific effect on vice purchases, but this study does not have the statistical power to show that convincingly. A regression analysis shows that the number of purchases of vice products is partly explained by paying with cards. Other explanatory variables are impulsivity, seduceability, gender, age, education and conscious eating behaviour. Pain of paying did not differ by payment instrument, but was larger for participants that paid with their usual means of payment, either debit card or cash. The present study contributes to the literature of so-called "pay cash, eat less trash" - studies, as it shows that the use of cash limits overall spending and purchases of vice products.
Localized DNA circuit design with majority gates

There have been many research efforts on the development of molecular DNA circuits, mainly for biomedical applications. Spatially localized DNA circuit, in particular, is considered as a most promising approach because of its fast and robust operations. In the localized DNA circuits, it is important to minimize circuit sizes due to high manufacturing cost of the special molecular board that is used to attach DNA logic gates. A localized DNA majority gate is proposed in this paper to exploit the compact logic representation of majority logic, thereby achieving smaller circuit footprint. A gate version selection algorithm is presented to address how DNA molecules have to be arranged in order to ensure correct functionality.
The Effect of Different Forms of Antioxidant Surface Treatment on the Shear Bond Strength of Composite Restorations to Bonded to Office- Bleached Enamel

Purpose: To investigate the effects of two different forms of sodium ascorbate (solution and gel) as antioxidant surface treatments in reversing the compromised bond strength after vital in-office tooth bleaching with 38% hydrogen peroxide. Materials and Methods: The study included 25 natural teeth (premolars). The crown of each tooth was sectioned in the mesio-distal direction to use both the buccal and lingual enamel surfaces for the bonding procedures. Then, the samples were randomly divided into 5 groups (n=10), according to different treatment options of bleaching and bonding. The specimens were then subjected to a shear bond strength test using a universal testing machine. The modes of bond failure were determined using a stereomicroscope and a digital camera. Results: Bleached enamel immersed in saliva for two weeks before bonding and nonbleached enamel surfaces showed significantly higher bond strengths to composite resin than did enamel surfaces bonded immediately after bleaching without an antioxidant surface treatment (P=.000). There was no significant difference between delaying bonding for two weeks after bleaching and bonding without any bleaching procedure (P=.999). A resin composite bonded to bleached enamel surfaces that were treated with both antioxidants in the different solution forms showed a significantly higher shear bond strength than did a resin composite bonded immediately after bleaching (P=.000). There was no significant difference between the use of sodium ascorbate solution or gel in the shear bond strength (P=.999). It was noted that most the adhesive failures in this study were at the adhesive/resin interface Conclusion: Bonding resin composite immediately after enamel bleaching with 38% hydrogen peroxide reduced the shear bond strength. Both the gel and solution forms of 10% sodium ascorbate can reverse the reduced bond strength after in-office enamel bleaching.
Some Tests of the Marr-Ullman Model of Movement Detection

Several psychophysical experiments are described which test and uphold predictions derived from the Marr–Ullman model of movement detection. First, we demonstrate the existence of adaptation which is specific not merely to the direction of movement of an edge, but also to its contrast polarity. Second, it is shown that adaptation to a spatially homogeneous field whose luminance is modulated according to a temporal sawtooth waveform produces predictable changes in sensitivity to the movement of an edge; these changes, too, are specific to particular conjunctions of direction and edge polarity. Third, similar changes in sensitivity are demonstrated to occur when the luminance of an edge is physically perturbed at the moment of its displacement. Finally, it is shown that, as predicted, the sudden onset of an edge can itself give rise to a momentary impression of movement, the apparent direction of which depends upon the change in luminance that accompanies the onset of the edge.
Nur77 Is Upregulated in B-1a Cells by Chronic Self-Antigen Stimulation and Limits Generation of Natural IgM Plasma Cells

B-1a cells are a unique population of innate-like B cells with a highly restricted and self-reactive BCR repertoire. Preimmune “natural” IgM produced by B-1a–derived plasma cells is essential for homeostatic clearance of cellular debris and forms a primary layer of protection against infection. In this study, we take advantage of a fluorescent reporter of BCR signaling to show that expression of the orphan nuclear hormone receptor Nur77 is upregulated under steady-state conditions in self-reactive B-1a cells in response to chronic Ag stimulation. Nur77-deficient mice exhibit elevated natural serum IgM (but not IgG) and marked expansion of IgM plasma cells of B-1a origin. Moreover, we show that Nur77 restrains the turnover of B-1a cells and the accumulation of immature IgM plasma cells. Thus, we identify a new critical negative-regulatory pathway that serves to maintain B-1a cells in a quiescent state in the face of chronic endogenous Ag stimulation.
Preventive effect of the microalga Chlamydomonas debaryana on the acute phase of experimental colitis in rats

Inflammatory bowel diseases (IBD) are characterised by chronic uncontrolled inflammation of intestinal mucosa. Diet and nutritional factors have emerged as possible interventions for IBD. Microalgae are rich sources of n-3 PUFA and derived oxylipins. Oxylipins are lipid mediators involved in the resolution of many inflammatory disorders. The aim of the present study was to investigate the effects of the oxylipin-containing biomass of the microalga Chlamydomonas debaryana and its major oxylipin constituent, (9Z,11E,13S,15Z)-13-hydroxyoctadeca-9,11,15-trienoic acid ((13S)-HOTE), on acute 2,4,6-trinitrobenzenesulfonic acid (TNBS)-induced colitis in rats. Lyophilised microalgal biomass and (13S)-HOTE were administered by oral route 48, 24 and 1 h before the induction of colitis and 24 h later, and the rats were killed after 48 h. The treatment with the lyophilised microalga and (13S)-HOTE improved body-weight loss and colon shortening, as well as attenuated the extent of colonic damage and increased mucus production. Cellular neutrophil infiltration, with the subsequent increase in myeloperoxidase levels induced by TNBS, were also reduced after the administration of the lyophilised microalga or (13S)-HOTE. The anti-inflammatory effects of these treatments were confirmed by the inhibition of colonic TNF-α production. Moreover, lyophilised microalga or (13S)-HOTE down-regulated cyclo-oxygenase-2 and inducible nitric oxide synthase expression. The present study was the first to show the prophylactic effects of a lyophilised biomass sample of the microalga C. debaryana and the oxylipin (13S)-HOTE on TNBS-induced acute colitis in rats. Our findings suggest that the microalga C. debaryana or derived oxylipins could be used as nutraceuticals in the treatment of the active phase of IBD.
Smart City Narrative in Indonesia: Comparing Policy Documents in Four Cities

This paper aims to investigate the narrative of smart city policy in four Indonesian cities. Yogyakarta City, Surabaya City, Magelang City, and Madiun City were chosen as the locus of this study since these cities were winners of the Indonesian Smart City Index 2015.The author compares their medium-term development planning documents using analysis of policy narrative approach which reconstructs the stories that actors tellabout policy issues written in the official policy document. This study endeavours to analyse how these cities engage with smart city policy and initiative from a comparativebased study.Based on the content analysis as a research method, it can be concluded that these cities conceptualise the smart city program in different ways since there is no specific regulation guiding smart city policy in Indonesia. The result of this study also maps the main themes of smart city as stated in their medium-term development planning document. Theoretically, it contributes the discourse of smart city policy studies in a developing country context. Practically, this study suggests a policy implication that cities need to consider as a specific grand design on how local government implement smart city initiative.
Evidence That Hydrogen Sulfide Is a Genotoxic Agent

Hydrogen sulfide (H2S) produced by commensal sulfate-reducing bacteria, which are often members of normal colonic microbiota, represents an environmental insult to the intestinal epithelium potentially contributing to chronic intestinal disorders that are dependent on gene-environment interactions. For example, epidemiologic studies reveal either persistent sulfate-reducing bacteria colonization or H2S in the gut or feces of patients suffering from ulcerative colitis and colorectal cancer. However, a mechanistic model that explains the connection between H2S and ulcerative colitis or colorectal cancer development has not been completely formulated. In this study, we examined the chronic cytotoxicity of sulfide using a microplate assay and genotoxicity using the single-cell gel electrophoresis (SCGE; comet assay) in Chinese hamster ovary (CHO) and HT29-Cl.16E cells. Sulfide showed chronic cytotoxicity in CHO cells with a %C1/2 of 368.57 μmol/L. Sulfide was not genotoxic in the standard SCGE assay. However, in a modified SCGE assay in which DNA repair was inhibited, a marked genotoxic effect was observed. A sulfide concentration as low as 250 μmol/L (similar to that found in human colon) caused significant genomic DNA damage. The HT29-Cl.16E colonocyte cell line also exhibited increased genomic DNA damage as a function of Na2S concentration when DNA repair was inhibited, although these cells were less sensitive to sulfide than CHO cells. These data indicate that given a predisposing genetic background that compromises DNA repair, H2S may lead to genomic instability or the cumulative mutations found in adenomatous polyps leading to colorectal cancer. (Mol Cancer Res 2006;4(1):9–14)
Timing and intensity of precommercial thinning and their effects on the first commercial thinning in Scots pine stands

Development of seeded Scots pine stands from precommercial thinning to first commercial thinning. Folia Forestalia 752. 29 p. (In Finnish with English summary). SAS Institute Inc. SAS/STAT user’s guide, version 8. Cary, NC: SAS Institute Inc 1999. 3809 p. Searle, S.R. , Casella, G. & McGulloch, C.E. 1992. Variance components. Wiley, New York. 501 p. Snijders, T. & Bosker, R. 1999. Multilevel analysis. An introduction to basic and advanced multilevel mod- eling. SAGE Publications Inc., London. 266 p. Tong, Q.J. & Zhang, S.Y. 2005. Impact of initial spac- ing and precommercial thinning on jack pine tree growth and stem quality. The Forestry Chronicle 81(3): 418–428. Tonteri, T. , Hotanen, J.-P. & Kuusipalo, J. 1990. The Finnish forest site type approach: ordination and classification studies of mesic forest sites in south- ern Finland. Vegetatio 87: 85–98. Valinger, E. , Elfving, B. & Morling, T. 2000. Twelve- year growth response of Scots pine to thinning and nitrogen fertilization. Forest Ecology and Manage- ment 134: 45–53. Varmola, M. 1982. Taimikkoja riukuvaiheen man- nikon kehitys harvennuksen jalkeen. Summary: Development of Scots pine stands at the sapling and pole stages after thinning. Folia Forestalia 524. 31 p. (In Finnish with English summary). — 1996. Nuorten viljelymannnikoiden tuotos ja laatu. Abstaract: Yield and quality of young Scots pine cultivation. Metsantutkimuslaitoksen tiedonantoja 585. 70 p. + 6 appendices. (In Finnish with English summary). — & Salminen, H. 2004. Timing and intensity of precommercial thinning in Pinus sylvestris stands. Scandinavian Journal of Forest Research 19: 142– 151. — , Kolstrom, T. & Mehtatalo, E. 1998. The effect of release cutting on the growth and external quality of the dominant trees in a Pinus sylvestris stand established by spot sowing. Scandinavian Journal of Forest Research 13: 151–159. Vestjordet, E. 1977. Avstandsregulering av unge furu- och gran-bestand: I: Materiale, stabilitet, dimen- sjonsfordeling, m.v. Precommercial thinning of young stands of Scots pine and Norway spruce: I: Data, stability, dimension distribution, etc. Med- delser fra norsk Institutt for skogforskning 33: 309–436. (In Norwegian with English summary). Vuokila, Y. 1972. Taimiston kasittely puuntuotannol- liselta kannalta. Summary: Treatment of seedling stands from the viewpoint of production. Folia Forestalia 141. 37 p. (In Finnish with English summary). — 1976. Ensiharvennuskertyma. Summary: Yield from the first thinning. Folia Forestalia 264. 12 p. (In Finnish with English summary). — 1977. Harsintaharvennus puuntuotantoon vaikut- tavana tekijana. Abstract: Selective thinning from above as a factor of growth and yield. Folia Foresta- lia 298. 17 p. (In Finnish with English summary). — 1981. Nuoren mannikon kasvureaktio ensiharven- nuksen jalkeen. Summary: The growth reaction of young pine stands to the first commercial thinning. Folia Forestalia 468. 13 p. (In Finnish with English summary).