Miracle-dz/UniFAR-FTUs huggingface dataset:
Serum and liver micronutrient antioxidants and serum oxidative stress in patients with chronic hepatitis C

OBJECTIVES:The exact pathogenesis of liver injury and fibrosis in chronic hepatitis C (CHC) is unclear. Free radicals play a role in CHC liver damage. Antioxidants (AO) (enzymatic and nonenzymatic) scavenge free radicals and prevent tissue injury. The aims of our study were to estimate serum levels of malondialdehyde (MDA), serum and liver levels of nonenzymatic fat-soluble AO, and to correlate the liver AO levels with the degree of inflammation and fibrosis on biopsy.METHODS:AO levels were estimated by high-pressure liquid chromatography in the pretreatment serum and liver biopsy specimen of 20 treatment-naïve patients with CHC who were not on vitamin supplements. Serum levels of MDA were measured as a marker of increased oxidative stress. Twenty-two healthy individuals with no history of vitamin supplementation served as controls. AO analyzed were: retinol, α- and γ-tocopherol, lutein, β-cryptoxanthin, lycopene, and α- and β-carotene.RESULTS:Twenty CHC patients (11 men, nine women, mean age 48.5 ± 7.9 yr) were studied. Patients and controls were comparable in age and sex. Serum MDA levels were significantly higher in CHC patients compared with controls (1.62 ± 0.57 vs 0.23 ± 0.15 μmol/L, p = < 0.0000). Serum levels of all AO except lutein were significantly decreased in CHC patients, and their levels were two to ten times lower than serum levels in controls. Liver levels of α-carotene (p = 0.0004), β-carotene (p = 0.006), and lutein (p = 0.002) correlated with the serum levels, whereas the levels of retinol, α-tocopherol, lycopene, and β-cryptoxanthin showed no correlation. Serum MDA levels were significantly higher in patients with moderate-to-severe inflammation or fibrosis compared with those with mild inflammation or fibrosis. The levels of all liver AO except α-carotene were significantly lower in patients with moderate-to-severe fibrosis. The severity of inflammation (portal or lobular) did not affect liver AO levels.CONCLUSIONS:Our findings suggest that increased oxidative stress is present in patients with CHC. Micronutrient AO are severely depleted in serum and liver tissue of patients with CHC, and liver levels of some AO appear to reflect serum levels. Increasing fibrosis is associated with decreased liver AO levels indicating that severe disease may be a consequence of AO depletion or decreased liver storage resulting from fibrosis.
Erk5 Participates in Neuregulin Signal Transduction and Is Constitutively Active in Breast Cancer Cells Overexpressing ErbB2

ABSTRACT The four receptor tyrosine kinases of the ErbB family play essential roles in several physiological processes and have also been implicated in tumor generation and/or progression. Activation of ErbB1/EGFR is mainly triggered by epidermal growth factor (EGF) and other related ligands, while activation of ErbB2, ErbB3, and ErbB4 receptors occurs by binding to another set of EGF-like ligands termed neuregulins (NRGs). Here we show that the Erk5 mitogen-activated protein kinase (MAPK) pathway participates in NRG signal transduction. In MCF7 cells, NRG activated Erk5 in a time- and dose-dependent fashion. The action of NRG on Erk5 was dependent on the kinase activity of ErbB receptors but was independent of Ras. Expression in MCF7 cells of a dominant negative form of Erk5 resulted in a significant decrease in NRG-induced proliferation of MCF7 cells. Analysis of Erk5 in several human tumor cell lines indicated that a constitutively active form of this kinase was present in the BT474 and SKBR3 cell lines, which also expressed activated forms of ErbB2, ErbB3, and ErbB4. Treatments aimed at decreasing the activity of these receptors caused Erk5 inactivation, indicating that the active form of Erk5 present in BT474 and SKBR3 cells was due to a persistent positive stimulus originating at the ErbB receptors. In BT474 cells expression of the dominant negative form of Erk5 resulted in reduced proliferation, indicating that in these cells Erk5 was also involved in the control of proliferation. Taken together, these results suggest that Erk5 may play a role in the regulation of cell proliferation by NRG receptors and indicate that constitutively active NRG receptors may induce proliferative responses in cancer cells through this MAPK pathway.
Codon Usage Bias and Determining Forces in Taenia solium Genome

The tapeworm Taenia solium is an important human zoonotic parasite that causes great economic loss and also endangers public health. At present, an effective vaccine that will prevent infection and chemotherapy without any side effect remains to be developed. In this study, codon usage patterns in the T. solium genome were examined through 8,484 protein-coding genes. Neutrality analysis showed that T. solium had a narrow GC distribution, and a significant correlation was observed between GC12 and GC3. Examination of an NC (ENC vs GC3s)-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENC (the effective number of codons) values were detected below the expected curve, suggesting that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally. We also identified 26 optimal codons in the T. solium genome, all of which ended with either a G or C residue. These optimal codons in the T. solium genome are likely consistent with tRNAs that are highly expressed in the cell, suggesting that mutational and translational selection forces are probably driving factors of codon usage bias in the T. solium genome.
Ventricular Response to a Pressure Load: LEFT VENTRICULAR FUNCTION CURVES IN INTACT ANIMAL

The response of the left ventricle of the anesthetized dog to graded proximal aortic obstruction was expressed as a ventricular “pressure-function” curve relating peak ventricular pressure to end-diastolic ventricular pressure. Indices were suggested for numerical representation of the pressure-function curve and the normal variations of such indices in the same animal were defined. Pressure-function curves were found to be reproducible in the same animal during changes of cardiac output induced by arteriovenous fistulae or hemorrhage, but not after prolonged ventricular distention by high pressure loads. Changes of the pressure-function curves in both open-chest and closed-chest dogs paralleled changes of ventricular contractility which were expected during anoxia or the action of metaraminol, and which were measured in some experiments by strain-gauge arch or “flow-function” (Starling) curves. A theoretical basis for this relation of the pressure-function curve to ventricular contractility was discussed.
Analysis and Design of Optimization Algorithms via Integral Quadratic Constraints

This manuscript develops a new framework to analyze and design iterative optimization algorithms built on the notion of Integral Quadratic Constraints (IQC) from robust control theory. IQCs provide sufficient conditions for the stability of complicated interconnected systems, and these conditions can be checked by semidefinite programming. We discuss how to adapt IQC theory to study optimization algorithms, proving new inequalities about convex functions and providing a version of IQC theory adapted for use by optimization researchers. Using these inequalities, we derive numerical upper bounds on convergence rates for the gradient method, the heavy-ball method, Nesterov's accelerated method, and related variants by solving small, simple semidefinite programming problems. We also briefly show how these techniques can be used to search for optimization algorithms with desired performance characteristics, establishing a new methodology for algorithm design.
Boundary spanning and public accountant role stress.

Summary This study investigated the relationship between client influence, public accountant (partner and manager) role stress, and various work-related outcomes. Client influence increased partners' role conflict and overload. It also increased managers' role overload, but decreased their role conflict and ambiguity. Both role ambiguity and overload (but not conflict) were associated with job related anxiety, propensity to leave the organization, and job dissatisfaction for both partners and managers.
Relationship of Anterior Alveolar Dimensions with Mandibular Divergence in Class I Malocclusion - A Cephalometric Study.

INTRODUCTION One of the major limiting factors in retraction of proclined teeth is the width of the alveolus both in maxilla and mandible. AIM The objective of this study was to assess the maxillary and mandibular anterior alveolar dimensions and to correlate with mandibular divergence in Class I bi-dento-alveolar protrusion patients. MATERIALS AND METHODS Pretreatment lateral cephalograms (n=88) were analysed using a composite analysis with cephalometric software. Both maxillary and mandibular anterior alveolar widths and heights were measured and correlated with mandibular divergence. One-way analysis (ANOVA) and Pearson correlation test were used to compare and establish the significance between groups. RESULTS Segregation of the data based on variation in the bi-cortical widths and heights showed that lesser alveolar widths and greater alveolar heights were associated with the high angled subjects and greater alveolar widths and lesser heights were associated with low angled subjects. CONCLUSION Patients with hyperdivergent mandible exhibited thin anterior alveolar width and greater alveolar height whereas low angled subjects had wider alveolar width and lesser alveolar height. Orthodontic treatment plan for retraction of anterior teeth must be based on these differences caused by variations in mandibular divergence.
V-ROOM: Virtual meeting system trial

Virtual meeting environments are providing a viable alternative for conventional meetings bringing benefits of reduced costs and better use of time by removing the need for attendees to travel to national, international or global locations in order to attend meetings. This paper builds on the work of previous papers which discussed the functional and technical requirements for a virtual meeting system, reporting on a user trial and evaluating the prototype system. The trial was performed by students as users deploying the prototype for collaboration in group work focussed on the design of a computer system as part of the final year of their undergraduate study. The users were asked to comment on the features of the prototype as well as offering suggestions on useful features that should be included in a virtual meeting system. A summary of their comments and suggestions and the results of the evaluation are included in the paper. Security aspects of virtual meeting systems are also considered in some detail.
Temporal integration in structure from motion.

A temporal integration model is proposed that predicts the results reported in 4 psychophysical experiments. The main findings were (a) the initial part of a structure-from-motion (SFM) sequence influences the orientation evoked by the final part of that sequence (an effect lasting for more than 1 s), and (b) for oscillating SFM sequences, perceived slant is affected by the oscillation frequency and by the sign of the final gradient. For contracting optic flows (i.e., rotations away from the image plane), the sequence with the lowest oscillation frequency appeared more slanted; for expanding optic flows (i.e., rotations toward the image plane), the sequence with the highest oscillation frequency appeared more slanted.
DNA repair gene excision repair cross complementing‐group 1 (ERCC1) in head and neck squamous cell carcinoma: analysis of methylation and polymorphism (G19007A), protein expression and association with epidemiological and clinicopathological factors

Lima L M C, de Souza L R, da Silva T F, Pereira C S, Guimarães A L S, de Paula A M B & Carvalho H A (2012) Histopathology 60, 489–496 DNA repair gene excision repair cross complementing‐group 1 (ERCC1) in head and neck squamous cell carcinoma: analysis of methylation and polymorphism (G19007A), protein expression and association with epidemiological and clinicopathological factors
Contrasting patterns of genetic diversity across the ranges of Pinus monticola and P. strobus: a comparison between eastern and western North American postglacial colonization histories.

UNLABELLED • Premises of the study: Understanding the influence of recent glacial and postglacial periods on species' distributions is key for predicting the effects of future environmental changes. We investigated the influence of two physiographic landscapes on population structure and postglacial colonization of two white pine species of contrasting habitats: P. monticola, which occurs in the highly mountainous region of western North America, and P. strobus, which occurs in a much less mountainous area in eastern North America. • METHODS To characterize the patterns of genetic diversity and population structure across the ranges of both species, 158 and 153 single nucleotide polymorphism (SNP) markers derived from expressed genes were genotyped on range-wide samples of 61 P. monticola and 133 P. strobus populations, respectively. • KEY RESULTS In P. monticola, a steep latitudinal decrease in genetic diversity likely resulted from postglacial colonization involving rare long-distance dispersal (LDD) events. In contrast, no geographic patterns of diversity were detected in P. strobus, suggesting recolonization via a gradually advancing front or frequent LDD events. For each species, structure analyses identified two distinct southern and northern genetic groups that likely originated from two different glacial lineages. At a finer scale, and for the two species, smaller subgroups were detected that could be remnants of cryptic refugia. • CONCLUSION During postglacial colonization, the western and eastern North American landscapes had different impacts on genetic signatures in P. monticola compared with P. strobus. We discuss the importance of our findings for conservation programs and predictions of species' response to climate change.
Access to primary care: advanced... or smart?

Access is back. Recent pronouncements by the prime minister and several UK health ministers have once again moved access to UK primary care services' centre stage, replacing choice, voice, and practice-based commissioning of services. The spectre of extended opening hours for GP services accompanies the politicians' commentary on access targets, and on the contribution of walk-in centres, NHS Direct, A&E departments, and primary care out-of-hours services to the increasingly complex patchwork of front-line NHS provision. But this explosion in provision, accompanied by substantial investment in NHS service delivery, has not resulted in the end-user benefits that were anticipated. Significant sections of the population feel disenfranchised from primary care, as reported by the Secretary of State for Health who has warned that the results of the forthcoming GP–Patient Survey of 5 million NHS patients, and costing £11 million, may make ‘uncomfortable reading for some doctors’ on account of reported difficulties ‘for a significant minority of patients’ in accessing GP services.1 In these public statements, the spectre of political expediency and the courting of political popularity loom large. The recently announced review of NHS care led by Professor Ara Darzi has, as a central focus, the delivery of ‘more accessible and more convenient care integrated across primary and secondary providers, reflecting best value for money and offering services in the most appropriate settings for patients’. 2 But such aspirations are not new. Building on proposals outlined in the NHS Plan,3 Department of Health initiatives in 2002 encouraged practices to meet recently defined targets for the accessibility of GP care included the wholesale roll-out of ‘Advanced Access’. 4 This approach to managing appointment systems was developed in the …
The Role of Dopamine in Drosophila Larval Classical Olfactory Conditioning

Learning and memory is not an attribute of higher animals. Even Drosophila larvae are able to form and recall an association of a given odor with an aversive or appetitive gustatory reinforcer. As the Drosophila larva has turned into a particularly simple model for studying odor processing, a detailed neuronal and functional map of the olfactory pathway is available up to the third order neurons in the mushroom bodies. At this point, a convergence of olfactory processing and gustatory reinforcement is suggested to underlie associative memory formation. The dopaminergic system was shown to be involved in mammalian and insect olfactory conditioning. To analyze the anatomy and function of the larval dopaminergic system, we first characterize dopaminergic neurons immunohistochemically up to the single cell level and subsequent test for the effects of distortions in the dopamine system upon aversive (odor-salt) as well as appetitive (odor-sugar) associative learning. Single cell analysis suggests that dopaminergic neurons do not directly connect gustatory input in the larval suboesophageal ganglion to olfactory information in the mushroom bodies. However, a number of dopaminergic neurons innervate different regions of the brain, including protocerebra, mushroom bodies and suboesophageal ganglion. We found that dopamine receptors are highly enriched in the mushroom bodies and that aversive and appetitive olfactory learning is strongly impaired in dopamine receptor mutants. Genetically interfering with dopaminergic signaling supports this finding, although our data do not exclude on naïve odor and sugar preferences of the larvae. Our data suggest that dopaminergic neurons provide input to different brain regions including protocerebra, suboesophageal ganglion and mushroom bodies by more than one route. We therefore propose that different types of dopaminergic neurons might be involved in different types of signaling necessary for aversive and appetitive olfactory memory formation respectively, or for the retrieval of these memory traces. Future studies of the dopaminergic system need to take into account such cellular dissociations in function in order to be meaningful.
Down-regulation of 8-hydroxydeoxyguanosine and peroxiredoxin II in the pathogenesis of endometriosis-associated ovarian cancer.

AIM To evaluate the roles of oxidative stress marker 8-hydroxydeoxyguanosine (8-OHdG) and peroxiredoxin (PRX) antioxidants in the development of endometriosis and endometriosis-associated ovarian cancer (EAC). MATERIALS AND METHODS Tissue expressions of 8-OHdG, PRX II and PRX IV were determined immunohistochemically in tissue from 22 women with benign endometriosis (BE) and 33 women with EAC, among whom endometriosis and cancer tissues were analyzed separately. RESULTS When all three groups were compared simultaneously, EAC tumor cells had significantly weaker nuclear 8-OHdG and PRX II expression (p<0.05 and p<0.01, respectively) and significantly weaker cytoplasmic 8-OHdG expression (p<0.01) than EAC endometriosis and BE epithelial cells. This same trend was also observed when groups were compared pair-wise. CONCLUSION Nuclear PRX II and 8-OHdG were down-regulated in EAC tumorous tissue compared with BE and EAC endometriotic tissue, suggesting a role of oxidative stress in the pathogenesis of EAC.
Optimal Bidding in Sequential Online Auctions

Auctions are widely used online to conduct commercial transactions. An important feature of online auctions is that even bidders who intend to buy a single object frequently have the opportunity to bid in sequential auctions selling identical objects. This paper studies key features of the optimal bidding strategy, assuming rational, risk-neutral agents with independent private valuations and sealed-bid second-price sequential auctions. In contrast to previous work on this topic, we develop our theory using the concept of the “option value” of an upcoming auction – a measure of the expected payoff from being able to participate in a future auction. This option value depends, among other things, upon the mean and variance of the future number of bidders. We derive an optimal bidding strategy in sequential auctions that incorporates option value assessment. Furthermore, we establish that our optimal bidding strategy is tractable since it is independent of the bidding strategies of other bidders in the current auction and is only dependent on the option value assessment. We test and find support for our theory using data collected on 327 eBay auctions on digital cameras in first two months of 2001. Please address all correspondence to Hao Xu.
On the Power of Tree-Depth for Fully Polynomial FPT Algorithms

There are many classical problems in P whose time complexities have not been improved over the past decades. Recent studies of "Hardness in P" have revealed that, for several of such problems, the current fastest algorithm is the best possible under some complexity assumptions. To bypass this difficulty, Fomin et al. (SODA 2017) introduced the concept of fully polynomial FPT algorithms. For a problem with the current best time complexity $O(n^c)$, the goal is to design an algorithm running in $k^{O(1)}n^{c'}$ time for a parameter $k$ and a constant $c'<c$. In this paper, we investigate the complexity of graph problems in P parameterized by tree-depth, a graph parameter related to tree-width. We show that a simple divide-and-conquer method can solve many graph problems, including Weighted Matching, Negative Cycle Detection, Minimum Weight Cycle, Replacement Paths, and 2-hop Cover, in $O(\mathrm{td}\cdot m)$ time or $O(\mathrm{td}\cdot (m+n\log n))$ time, where $\mathrm{td}$ is the tree-depth of the input graph. Because any graph of tree-width $\mathrm{tw}$ has tree-depth at most $(\mathrm{tw}+1)\log_2 n$, our algorithms also run in $O(\mathrm{tw}\cdot m\log n)$ time or $O(\mathrm{tw}\cdot (m+n\log n)\log n)$ time. These results match or improve the previous best algorithms parameterized by tree-width. Especially, we solve an open problem of fully polynomial FPT algorithm for Weighted Matching parameterized by tree-width posed by Fomin et al.
Essential relationships incorporating the influence of age, size and condition on variables required for estimation of reproductive potential in Atlantic cod Gadus morhua

Evidence accumulated over the last decade indicates that reproductive potential of marine fish stocks is not correctly represented by spawning stock biomass. Fundamental variables that affect reproductive potential of fish stocks (i.e. proportion mature at age, fecundity, and offspring size and viability) have found to vary with age, size, and condition of spawning fish, and/or spawn- ing experience. Modeling initiatives that attempt to describe reproductive potential by incorporating all available information on reproductive variables require extensive, high quality data of a temporal and spatial origin. In this study, we explored the influence of female age, size, and condition on sev- eral reproductive variables for the cod Gadus morhua, including maturity, fecundity, egg density and size, and larval size and growth. In addition, we described the potential for annual variation in these relationships to increase our knowledge of temporal stability for fundamental variables that influence reproductive potential.