Miracle-dz/UniFAR-FTUs huggingface dataset:
The contribution of extensin network formation to rapid , hydrogen peroxide-mediated increases in grapevine callus wall resistance to fungal lytic enzymes

Grapevine (Vitis vinifera cv. Touriga) callus cell walls contain a high level of the monomeric extensin, GvP1. Hydrogen peroxide stimulus of these cultures causes the rapid loss of monomeric GvP1, concomitant with marked increases in insoluble GvP1 amino acids and wall resistance to digestion by fungal lytic enzymes. JIM11 immunolocalization studies indicated that monomeric and network GvP1 were evenly distributed in the callus cell wall. These primary cell walls were used to investigate the specific contribution of extensin and other ionically bound cell-wall proteins to hydrogen peroxide-mediated increases in resistance to fungal lytic enzymes. This was performed by removing ionicallybound proteins and assaying for hydrogen peroxideenhanced resistance after the addition of selected protein fractions. The results indicate that hydrogen peroxide-induced increases in resistance to digestion by fungal lytic enzymes require a co-operative action between network extensin formation and the electrostatic interaction of additional wall proteins with the extracellular matrix.
Query Execution and Maintenance Costs in a Dynamic Distributed Federated Database

—The cost of query evaluation in a Dynamic Distributed Federated Databases (DDFD) depends on the topology connecting the database nodes together. Different topologies provide opportunities to adopt a variety of query optimisation strategies and topology also influences the efficiency of these strategies. We describe a number of strategies to optimise join queries and then derive cost estimation formulae. We use these to visualize and explore the performance of join queries in different distributed topologies. We consider three candidate topologies; a random preferential attachment network and two hypercube based models. The costs of maintaining these topologies are also formulated and compared. Costs formulas are defined at a coarse grained level, using a small number of parameters and derive only the dominant or average behaviours of the queries and topologies considered. This approach is intended to provide insights to likely optimisation candidates, leading to further refinement of the models. We discover that query delegation to well connected hub nodes is beneficial in scale free networks and that knowing the location of the data is beneficial in all topologies. We ascertain that a semi-join strategy can be beneficial in distributed topologies when the join attributes are small, there is repetition of join attributes or the join result in s a small number of results. We show that the cost of scaling a network is better in the preferential attachment network, indicating that a hypercube is more suitable for smaller, stable networks or where the rate of queries is high.
Pirfenidone slows renal function decline in patients with focal segmental glomerulosclerosis.

BACKGROUND AND OBJECTIVES Pirfenidone is an orally available antifibrotic agent that has shown benefit in animal models of pulmonary and renal fibrosis and in clinical trials of pulmonary fibrosis, multiple sclerosis, and hepatic cirrhosis. Our objective was to determine whether pirfenidone slows the loss of renal function in focal segmental glomerulosclerosis. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS An open-label trial was performed to evaluate the safety and efficacy of pirfenidone in patients with idiopathic and postadaptive focal segmental glomerulosclerosis. The monthly change in estimated GFR, expressed as ml/min per 1.73 m2, was compared between the baseline period and the treatment period. During both periods, patients received angiotensin antagonist therapy if tolerated. Twenty-one patients were enrolled, and 18 patients completed a median of 13 mo of pirfenidone treatment. RESULTS The monthly change in GFR improved from a median of -0.61 ml/min per 1.73 m2 (interquartile range -1.31 to -0.41) during the baseline period to -0.45 ml/min per 1.73 m2 (interquartile range -0.78 to -0.16) with pirfenidone therapy. This change represents a median of 25% improvement in the rate of decline (P < 0.01). Pirfenidone had no effect on BP or proteinuria. Adverse events attributed to therapy included dyspepsia, sedation, and photosensitive dermatitis. CONCLUSIONS It is concluded that pirfenidone is an attractive candidate for placebo-controlled trials in patients with progressive chronic kidney disease.
Expression of prostaglandin H2-mediated mechanism of vascular contraction in hypertensive rats. Relation to lipoxygenase and prostacyclin synthase activities.

We tested the hypothesis that a prostanoid-mediated mechanism of vascular contraction is expressed in rats with aortic coarctation-induced hypertension. Rings of descending thoracic aorta taken from normotensive and hypertensive rats were contrasted in terms of constrictor responsiveness to arachidonic acid (AA), AA-induced release of eicosanoids, and ability to convert exogenous prostaglandin (PG) H2 to PGI2. AA (10(-8) to 10(-5) mol/L) increased isometric tension in aortic rings (bathed in Krebs' bicarbonate buffer) of hypertensive but not normotensive rats. AA (10(-5) mol/L) also elicited the release of PGI2, PGE2, thromboxane (TX) A2, and monohydroxyeicosatetraenoic acids (HETEs); this release from the aortic rings of hypertensive rats exceeded the corresponding release from the aortic rings of normotensive rats. However, the rate of conversion of exogenous PGH2 to PGI2 by aortic rings of hypertensive rats was < 50% the rate of conversion by aortic rings of normotensive rats. The constrictor effect of AA in aortic rings of hypertensive rats was abolished by an inhibitor of cyclooxygenase (indomethacin, 10 mumol/L) and a blocker of TXA2-PGH2 receptors (SQ29548, 1 mumol/L) but was not affected by an inhibitor of TXA2 synthesis (CGS13080, 10 mumol/L), suggesting mediation by PGH2. The lipoxygenase inhibitor baicalein (75 mumol/L) also attenuated the constrictor effect of AA in aortic rings of hypertensive rats while decreasing the associated release of HETEs and correcting the impairment in the conversion of PGH2 to PGI2. (ABSTRACT TRUNCATED AT 250 WORDS)
Homotopy equivalence of isospectral graphs

In previous work we dened a Quillen model structure, de- termined by cycles, on the category Gph of directed graphs. In this pa- per we give a complete description of the homotopy category of graphs associated to our model structure. We endow the categories of N-sets and Z-sets with related model structures, and show that their homotopy categories are Quillen equivalent to the homotopy category Ho(Gph). This enables us to show that Ho(Gph) is equivalent to the category cZSet of periodic Z-sets, and to show that two nite directed graphs are almost-isospectral if and only if they are homotopy-equivalent in our sense.
Potential alternatives to COX 2 inhibitors

For many years, non-steroidal anti-inflammatory drugs were regarded as a treatment for which there was no gain in arthritis without the pain of gastroduodenal toxicity. This reflected the understanding that non-steroidal anti-inflammatory drugs (NSAIDs) were cyclo-oxygenase inhibitors that reduced prostaglandin synthesis both in inflamed joints with benefit and in the stomach with detriment (figure). Recognition that a highly inducible enzyme, cyclo-oxygenase-2, largely subserved the former and a constitutive enzyme, cyclo-oxygenase-1, the latter provided an obvious selective target. The consequent success of cyclo-oxygenase-2 (COX 2) inhibitors arises, in part, from the conceptual simplicity of this idea. The journey from concept to reality has, however, inevitably been more complex, and one controversial issue is dealt with in an accompanying editorial.1 The failure of the celecoxib long term arthritis safety study (the CLASS study) may have more to do with the design of the trial than with inadequacies of cyclo-oxygenase-2 inhibitors. Other limitations of these agents may eventually deserve more attention. In particular, it was never likely that they would go beyond the indication of pain and arthritis that characterises NSAIDs, given that the goal was to mimic their action more selectively. Pathways of arachidonic acid metabolism. Prostaglandins, synthesised by both constitutive cyclo-oxygenase-1 and highly inducible cyclo-oxygenase-2 can contribute to …
Force-Induced Unfolding of Fibronectin in the Extracellular Matrix of Living Cells

Whether mechanically unfolded fibronectin (Fn) is present within native extracellular matrix fibrils is controversial. Fn extensibility under the influence of cell traction forces has been proposed to originate either from the force-induced lengthening of an initially compact, folded quaternary structure as is found in solution (quaternary structure model, where the dimeric arms of Fn cross each other), or from the force-induced unfolding of type III modules (unfolding model). Clarification of this issue is central to our understanding of the structural arrangement of Fn within fibrils, the mechanism of fibrillogenesis, and whether cryptic sites, which are exposed by partial protein unfolding, can be exposed by cell-derived force. In order to differentiate between these two models, two fluorescence resonance energy transfer schemes to label plasma Fn were applied, with sensitivity to either compact-to-extended conformation (arm separation) without loss of secondary structure or compact-to-unfolded conformation. Fluorescence resonance energy transfer studies revealed that a significant fraction of fibrillar Fn within a three-dimensional human fibroblast matrix is partially unfolded. Complete relaxation of Fn fibrils led to a refolding of Fn. The compactly folded quaternary structure with crossed Fn arms, however, was never detected within extracellular matrix fibrils. We conclude that the resting state of Fn fibrils does not contain Fn molecules with crossed-over arms, and that the several-fold extensibility of Fn fibrils involves the unfolding of type III modules. This could imply that Fn might play a significant role in mechanotransduction processes.
Stochastic Subgradient Algorithms for Strongly Convex Optimization Over Distributed Networks

We study diffusion and consensus based optimization of a sum of unknown convex objective functions over distributed networks. The only access to these functions is through stochastic gradient oracles, each of which is only available at a different node; and a limited number of gradient oracle calls is allowed at each node. In this framework, we introduce a convex optimization algorithm based on stochastic subgradient descent (SSD) updates. We use a carefully designed time-dependent weighted averaging of the SSD iterates, which yields a convergence rate of <inline-formula> <tex-math notation="LaTeX">$O\left(\frac{N\sqrt{N}}{(1-\sigma)T}\right)$</tex-math><alternatives> <inline-graphic xlink:href="sayin-ieq1-2713396.gif"/></alternatives></inline-formula> after <inline-formula> <tex-math notation="LaTeX">$T$</tex-math><alternatives><inline-graphic xlink:href="sayin-ieq2-2713396.gif"/> </alternatives></inline-formula> gradient updates for each node on a network of <inline-formula> <tex-math notation="LaTeX">$N$</tex-math><alternatives><inline-graphic xlink:href="sayin-ieq3-2713396.gif"/> </alternatives></inline-formula> nodes, where <inline-formula><tex-math notation="LaTeX">$0\leq \sigma <1$</tex-math> <alternatives><inline-graphic xlink:href="sayin-ieq4-2713396.gif"/></alternatives></inline-formula> denotes the second largest singular value of the communication matrix. This rate of convergence matches the performance lower bound up to constant terms. Similar to the SSD algorithm, the computational complexity of the proposed algorithm also scales linearly with the dimensionality of the data. Furthermore, the communication load of the proposed method is the same as the communication load of the SSD algorithm. Thus, the proposed algorithm is highly efficient in terms of complexity and communication load. We illustrate the merits of the algorithm with respect to the state-of-art methods over benchmark real life data sets.
Long-Term Effects of Attentional Performance on Functional Brain Network Topology

Individuals differ in their cognitive resilience. Less resilient people demonstrate a greater tendency to vigilance decrements within sustained attention tasks. We hypothesized that a period of sustained attention is followed by prolonged changes in the organization of “resting state” brain networks and that individual differences in cognitive resilience are related to differences in post-task network reorganization. We compared the topological and spatial properties of brain networks as derived from functional MRI data (N = 20) recorded for 6 mins before and 12 mins after the performance of an attentional task. Furthermore we analysed changes in brain topology during task performance and during the switches between rest and task conditions. The cognitive resilience of each individual was quantified as the rate of increase in response latencies over the 32-minute time course of the attentional paradigm. On average, functional networks measured immediately post-task demonstrated significant and prolonged changes in network organization compared to pre-task networks with higher connectivity strength, more clustering, less efficiency, and shorter distance connections. Individual differences in cognitive resilience were significantly correlated with differences in the degree of recovery of some network parameters. Changes in network measures were still present in less resilient individuals in the second half of the post-task period (i.e. 6–12 mins after task completion), while resilient individuals already demonstrated significant reductions of functional connectivity and clustering towards pre-task levels. During task performance brain topology became more integrated with less clustering and higher global efficiency, but linearly decreased with ongoing time-on-task. We conclude that sustained attentional task performance has prolonged, “hang-over” effects on the organization of post-task resting-state brain networks; and that more cognitively resilient individuals demonstrate faster rates of network recovery following a period of attentional effort.
Hip strength and hip and knee kinematics during stair descent in females with and without patellofemoral pain syndrome.

STUDY DESIGN Cross-sectional. OBJECTIVE To determine if females presenting with patellofemoral pain syndrome (PFPS) from no discernable cause other than overuse demonstrate hip weakness and increased hip internal rotation, hip adduction, and knee valgus during stair descent. BACKGROUND Historically, PFPS has been viewed exclusively as a knee problem. Recent findings have indicated an association between hip weakness and PFPS. Researchers have hypothesized that patients who demonstrate hip weakness would exhibit increased hip internal rotation, hip adduction, and knee valgus during functional activities. To date, researchers have not simultaneously examined hip and knee strength and kinematics in subjects with PFPS to make this determination. METHODS AND MEASURES Eighteen females diagnosed with PFPS and 18 matched controls participated. Strength measures were taken for the hip external rotators and hip abductors. Hip and knee kinematics were collected as subjects completed a standardized stair-stepping task. Independent t tests were used to determine between-group differences in strength and kinematics during stair descent. RESULTS Subjects with PFPS generated 24% less hip external rotator (P = .002) and 26% less hip abductor (P =. 006) torque. No between-group differences (P > .05) were found for average hip and knee transverse and frontal plane angles during stair descent. CONCLUSION Subjects with PFPS had significant hip weakness but did not demonstrate altered hip and knee kinematics as previously theorized. Additional investigations are needed to better understand the association between hip weakness and PFPS etiology.
Two equivalent circuit realizations of the Ueda's oscillator

Synthesis, simulation and measurements of the sinusoidally driven chaotic Ueda's oscillator based on the state equations is presented in this brief paper. In the first part mathematical model of the Ueda's oscillator and his numerical time integration is discussed. In other part two equivalent conceptions in voltage mode respectively hybrid mode of the chaotic oscillator are presented and discussed. Those conceptions were experimentally verified in both time domain and frequency domain. Simulation and measurements results are compared.
Sorting Via Screening Versus Signaling: A Theoretic and Experimental Comparison

Similar to Kubler et al. (2008, GEB 64, p. 219-236), we compare sorting in games with asymmetric incomplete information theoretically and experimentally. Rather than distinguishing two very different sequential games, we use the same game format and capture the structural difference of screening and signaling only via their payoff specification. The experiment thus relies on the same verbal instructions. Although the equilibrium outcomes coincide, greater efficiency losses off the equilibrium play due to sorting under signaling, compared to screening, is predicted and confirmed experimentally.
Risk of enamel fluorosis in nonfluoridated and optimally fluoridated populations: considerations for the dental professional.

BACKGROUND Few studies have evaluated the impact of specific fluoride sources on the prevalence of enamel fluorosis in the population. The author conducted research to determine attributable risk percent estimates for mild-to-moderate enamel fluorosis in two populations of middle-school-aged children. METHODS The author recruited two groups of children 10 to 14 years of age. One group of 429 had grown up in nonfluoridated communities; the other group of 234 had grown up in optimally fluoridated communities. Trained examiners measured enamel fluorosis using the Fluorosis Risk Index and measured early childhood fluoride exposure using a questionnaire completed by the parent. The author then calculated attributable risk percent estimates, or the proportion of cases of mild-to-moderate enamel fluorosis associated with exposure to specific early fluoride sources, based on logistic regression models. RESULTS In the nonfluoridated study sample, sixty-five percent of the enamel fluorosis cases were attributed to fluoride supplementation under the pre-1994 protocol. An additional 34 percent were explained by the children having brushed more than once per day during the first two years of life. In the optimally fluoridated study sample, 68 percent of the enamel fluorosis cases were explained by the children using more than a pea-sized amount of toothpaste during the first year of life, 13 percent by having been inappropriately given a fluoride supplement, and 9 percent by the use of infant formula in the form of a powdered concentrate. CONCLUSIONS Enamel fluorosis in the nonfluoridated study sample was attributed to fluoride supplementation under the pre-1994 protocol and early toothbrushing behaviors. Enamel fluorosis in the optimally fluoridated study sample was attributed to early toothbrushing behaviors, inappropriate fluoride supplementation and the use of infant formula in the form of a powdered concentrate. CLINICAL IMPLICATIONS By advising parents about the best early use of fluoride agents, health professionals play an important role in reducing the prevalence of clinically noticeable enamel fluorosis.
On the Number of Walks in a Triangular Domain

We consider walks on a triangular domain that is a subset of the triangular lattice. We then specialise this by dividing the lattice into two directed sublattices with different weights. Our central result is an explicit formula for the generating function of walks starting at a fixed point in this domain and ending anywhere within the domain. Intriguingly, the specialisation of this formula to walks starting in a fixed corner of the triangle shows that these are equinumerous to two-coloured Motzkin paths, and two-coloured three-candidate Ballot paths, in a strip of finite height.
Effects of severe diabetes and insulin on the femoral neck of the immature rat

The interactive effects of severe diabetes and insulin therapy on the geometrical, biomechanical, and histomorphological characteristics of the femoral neck were studies in rats that had streptozotocin‐induced, insulin‐dependent (Type‐I) diabetes. Thirty‐six female Sprague‐Dawley rats (8 weeks of age) were assigned randomly to one of three groups: 12 to control (C), 12 to severe diabetes mellitus (SDM), and 12 to severe diabetes with insulin treatment (SDI). At the conclusion of 10 weeks, the femoral necks were loaded to failure via cantilever‐bending tests, and the geometrical, structural, and material properties of the femoral neck were measured and correlated with fracture‐surface cross sections. Decalcified cross sections of the femoral necks were analyzed histomorphometrically to determine the porosity, the bone‐cell counts, and the bone spicule/marrow space ratio. Rats with severe insulin‐dependent diabetes had significantly lower total body mass than did control rats, as well as significantly less femur mass, femur length, total‐bone cross‐sectional area, and cortical‐shell cross‐sectional area. Insulin therapy ameliorated some, but not all, of the detrimental effects of diabetes on femoral neck geometry. Compared with control and SDI rats, SDM rats had lower values for femoral neck structural properties, although differences in structural properties may have been related to retarded growth as well as to diabetes. SDM rats had a significantly lower bone spicule/marrow space ratio and number of osteoclasts than did either the control or SDI rats and had significantly greater porosity in the femoral neck cortex than did control rats. Decrements in femoral neck material properties — which were independent of differences in body size — were significantly and linearly correlated with severity of diabetes (as measured by blood glucose level).
Yeast DNA polymerase ζ maintains consistent activity and mutagenicity across a wide range of physiological dNTP concentrations

Abstract In yeast, dNTP pools expand drastically during DNA damage response. We show that similar dNTP elevation occurs in strains, in which intrinsic replisome defects promote the participation of error-prone DNA polymerase ζ (Polζ) in replication of undamaged DNA. To understand the significance of dNTP pools increase for Polζ function, we studied the activity and fidelity of four-subunit Polζ (Polζ4) and Polζ4-Rev1 (Polζ5) complexes in vitro at ‘normal S-phase’ and ‘damage-response’ dNTP concentrations. The presence of Rev1 inhibited the activity of Polζ and greatly increased the rate of all three ‘X-dCTP’ mispairs, which Polζ4 alone made extremely inefficiently. Both Polζ4 and Polζ5 were most promiscuous at G nucleotides and frequently generated multiple closely spaced sequence changes. Surprisingly, the shift from ‘S-phase’ to ‘damage-response’ dNTP levels only minimally affected the activity, fidelity and error specificity of Polζ complexes. Moreover, Polζ-dependent mutagenesis triggered by replisome defects or UV irradiation in vivo was not decreased when dNTP synthesis was suppressed by hydroxyurea, indicating that Polζ function does not require high dNTP levels. The results support a model wherein dNTP elevation is needed to facilitate non-mutagenic tolerance pathways, while Polζ synthesis represents a unique mechanism of rescuing stalled replication when dNTP supply is low.