Miracle-dz/UniFAR-FTUs huggingface dataset:
Geochemical Perspectives on Coral Mineralization

Corals open an exceptional window into many phenomena of geological, geochemical, climatic, and paleontological interest. From the Paleozoic to the present, corals provide some of the finest high-resolution archives of marine conditions. Corals are likewise exceptional for chronometric purposes, and even the terrestrial C timescale has now been calibrated against coral Th/U. Corals also represent a testing ground for basic ideas about mineralogy and geochemistry. The shapes, sizes, and organization of skeletal crystals have been attributed to factors as diverse as mineral supersaturation levels and organic mediation of crystal growth. The coupling between calcification and photosynthesis in symbiotic corals is likewise attributed to everything from photosynthetic alkalinization of the water, to efforts by the coral to prevent photosynthetic alkalinization. Corals also leave a significant geochemical imprint on the oceans. Their aragonite skeletons accept about 10 times more strontium than does calcite, hence the proportion of marine aragonite precipitation affects the oceanic chemical balance. Biological carbonates represent the biosphere’s largest carbon reservoir, hence calcareous organisms affect the ocean’s pH, CO2 content, and ultimately global temperatures through the greenhouse gas connection. Finally, corals present some geochemical puzzles for ecology and conservation. How do symbiotic corals obtain nutrients in some of the most nutrient deficient parts of the planet? Are global geochemical changes partially responsible for the widespread declines in coral reefs during recent decades? We will address many of these issues, but will concentrate on coral skeletal structure and calcification mechanism. These topics bear most directly on the biomineralization process and generally affect the choice of skeletal materials and analytical techniques used in geochemical investigations.
Effect of a 915-MHz simulated mobile phone signal on cognitive function in man.

PURPOSE To examine whether a simulated mobile telephone transmission at 915 MHz has an effect on cognitive function in man. MATERIALS AND METHODS Thirty-six subjects in two groups were each given two training sessions and then three test sessions in a randomized three-way cross-over design. About 1 W mean power at 915 MHz from a quarter-wave antenna mounted on a physical copy of an analogue phone, as a sine wave, or modulated at 217 Hz with 12.5% duty cycle, or no power, was applied to the left squamous temple region of the subjects while they undertook a series of cognitive function tests lasting approximately 25-30 min. The second group was investigated for sleep, consumption of alcohol and beverages, and any other substances that might affect performance. RESULTS In both groups, the only test affected was the choice reaction time and this showed as an increase in speed (a decrease in reaction time). There were no changes in word, number or picture recall, or in spatial memory. While an effect of visit-order was evident suggesting a learning effect of repeat tests, the design of the study allowed for this. Additionally, there was no systematic error introduced as a result of consumption of substances or sleep time. CONCLUSIONS There was evidence of an increase in responsiveness, strongly in the analogue and less in the digital simulation, in choice reaction time. This could be associated with an effect on the angular gyrus that acts as an interface between the visual and speech centres and which lies directly under and on the same side as the antenna. Such an effect could be consistent with mild localized heating, or possibly a non-thermal response, which is nevertheless power-dependent.
Preparation of a Sulfonated Carbonaceous Material from Lignosulfonate and Its Usefulness as an Esterification Catalyst

Sulfonated carbonaceous material useful as a solid acid catalyst was prepared from lignosulfonate, a waste of the paper-making industry sulfite pulping process, and characterized by 13C-NMR, FT-IR, TGA, SEM and elemental analysis, etc. The sulfonic acid group density and total density of all acid groups in the sulfonated carbonaceous material was determined by titration to be 1.24 mmol/g and 5.90 mmol/g, respectively. Its catalytic activity in the esterification of cyclohexanecarboxylic acid with anhydrous ethanol was shown to be comparable to that of the ionic exchange resin Amberlyst-15, when they were used in the same amount. In the meantime, the sulfonic acid group was found to be leached out by 26%–29% after it was exposed to hot water (95 °C) for 5 h. The catalytic usefulness of the prepared carbonaceous material was investigated by performing esterifications.
Hepatic uptake of hippurate: a multiple-indicator dilution, perfused rat liver study.

The hepatic transport of hippuric acid (HA), a glycine-conjugated metabolite of benzoic acid that exhibits only modest plasma albumin binding (binding association constant of 2.1 x 10(3) M-1), was studied in the single-pass perfused rat liver (12 ml/min), using the multiple indicator dilution (MID) technique. The venous recovery of [3H]HA on portal venous injection of a MID dose containing a mixture of a set of noneliminated reference indicators and [3H]HA revealed a survival fraction of unity, corroborating the lack of disappearance of bulk HA from plasma. When the outflow recovery was fitted to the barrier-limited model of Goresky et al. (C.A. Goresky, G. G. Bach, and B. E. Nadeau. J. Clin. Invest. 52: 991-1009, 1973), the derived influx (P(in)S) and efflux (P(out)S) permeability-surface area products were found to be dependent on the concentration of HA (1-930 microM); P(in)S and P(out)S were approximately 3.5 times the plasma flow rate at low HA concentration, but decreased with increasing HA concentration. All values, however, greatly exceeded the expected contribution from passive diffusion, because the equilibrium distribution ratio of chloroform to buffer for HA was extremely low (0.0001 at pH 7.4). The tissue equilibrium partition coefficient (P(in)/P(out), or ratio of influx to efflux rate constants, k1/k-1) was less than unity and decreased with concentration. The optimized apparent Michaelis-Menten constant and maximal velocity were 182 +/- 60 microM and 12 +/- 4 nmol.s-1.g-1, respectively, for influx and 390 +/- 190 microM and 29 +/- 13 nmol.s-1.g-1, respectively, for efflux. In the presence of L-lactate (20 mM), however, P(in)S for the uptake of HA (174 +/- 3 microM) was reduced. Benzoic acid (10-873 microM) was also effective in reducing hepatic uptake of HA (5.3 +/- 0.9 microM). These interactions suggest that MCT2, the monocarboxylate transporter that mediates the hepatic uptake of lactate and other monocarboxylic acids, may be involved in HA transport.
Topographic Controls on the Extension and Retraction of Flowing Streams

Flowing stream networks extend and retract as their surrounding landscapes wet up and dry out, both seasonally and during rainstorms, with implications for aquatic ecosystems and greenhouse gas exchange. Some networks are much more dynamic than others, however, and the reasons for this difference are unknown. Here we show that the tendency of stream networks to extend and retract can be predicted from down‐valley changes in topographic attributes (slope, curvature, and contributing drainage area), without measuring subsurface hydrologic properties. Topography determines where water accumulates within valley networks, and we propose that it also modulates flow partitioning between the surface and subsurface. Measurements from 17 mountain stream networks support this hypothesis, showing that undissected valley heads have greater subsurface transport capacities than sharply incised valleys downstream. In catchments where broad valley heads rapidly transition to sharply incised valleys, subsurface transport capacity decreases abruptly, stabilizing stream length through wet and dry periods.
Supervision patterns in discrete event systems diagnosis

In this paper, we are interested in the diagnosis of discrete event systems modeled by finite transition systems. We propose a model of supervision patterns general enough to capture past occurrences of particular trajectories of the system. Modeling the diagnosis objective by a supervision pattern allows us to generalize the properties to be diagnosed and to render them independent of the description of the system. We first formally define the diagnosis problem in this context. We then derive techniques for the construction of a diagnoser and for the verification of the diagnosability based on standard operations on transition systems. We show that these techniques are general enough to express and solve in a unified way a broad class of diagnosis problems found in the literature, e.g. diagnosing permanent faults, multiple faults, fault sequences and some problems of intermittent faults
A randomized noninferiority trial of standard versus enhanced risk reduction and adherence counseling for individuals receiving post-exposure prophylaxis following sexual exposures to HIV.

BACKGROUND The National HIV/AIDS Strategy proposes to scale-up post-exposure prophylaxis (PEP). Intensive risk reduction and adherence counseling appear to be effective but are resource intensive. Identifying simpler interventions that maximize the HIV prevention potential of PEP is critical. METHODS A randomized noninferiority study comparing 2 (standard) or 5 (enhanced) risk reduction counseling sessions was performed. Adherence counseling was provided in the enhanced arm. We measured changes in unprotected sexual intercourse acts at 12 months, compared with baseline; HIV acquisition; and PEP adherence. Outcomes were stratified by degree of baseline risk. RESULTS We enrolled 457 individuals reporting unprotected intercourse within 72 h with an HIV-infected or at-risk partner. Participants were 96% male and 71% white. There were 1.8 and 2.3 fewer unprotected sex acts in the standard and enhanced groups. The maximum potential risk difference, reflected by the upper bound of the 95% confidence interval, was 3.9 acts. The difference in the riskier subset may have been as many as 19.6 acts. The incidence of HIV seroconversion was 2.9% and 2.6% among persons randomized to standard and enhanced counseling, respectively, with a maximum potential difference of 3.4%. The absolute and maximal HIV seroconversion incidence was 9.9% and 20.4% greater in the riskier group randomized to standard, compared with enhanced, counseling. Adherence outcomes were similar, with noninferiority in the lower risk group and concerning differences among the higher-risk group. CONCLUSIONS Risk assessment is critical at PEP initiation. Standard counseling is only noninferior for individuals with lower baseline risk; thus, enhanced counseling should be targeted to individuals at higher risk.
The effects of tolterodine extended release and alfuzosin for the treatment of double-j stent-related symptoms.

AIM To evaluate the effects of tolterodine extended release (ER) and alfuzosin for the treatment of Double-J stent-related lower urinary tract symptoms. MATERIALS AND METHODS Fifty-two patients (33 men and 19 women; mean age 52.0 years) who underwent insertion of a Double-J stent after urological surgery were prospectively randomized into three groups. Group 1 included 20 patients who received 10 mg of alfuzosin, once daily for 6 weeks; group 2 included 20 patients who received 4 mg of tolterodine ER, once daily for 6 weeks; group 3 included 12 patients who received a placebo for the same protocol. All patients completed a validated Ureteral Stent Symptom Questionnaire at 6 weeks after the stent placement. RESULTS The mean urinary symptom index was 22.1 in group 1, 22.1 in group 2, and 28.1 in the placebo group (p = 0.032). The mean pain scores were 8.2, 11.7, and 16.2, respectively (p = 0.020). There were no significant differences in urinary symptoms and pain between the alfuzosin and tolterodine ER groups. In addition, there was no significant difference in the general health, work performance, and sexual performance scores among the groups. CONCLUSIONS Tolterodine ER and alfuzosin improve stent-related urinary symptoms and body pain.
HypE: An Algorithm for Fast Hypervolume-Based Many-Objective Optimization

In the field of evolutionary multi-criterion optimization, the hypervolume indicator is the only single set quality measure that is known to be strictly monotonic with regard to Pareto dominance: whenever a Pareto set approximation entirely dominates another one, then the indicator value of the dominant set will also be better. This property is of high interest and relevance for problems involving a large number of objective functions. However, the high computational effort required for hypervolume calculation has so far prevented the full exploitation of this indicator's potential; current hypervolume-based search algorithms are limited to problems with only a few objectives. This paper addresses this issue and proposes a fast search algorithm that uses Monte Carlo simulation to approximate the exact hypervolume values. The main idea is not that the actual indicator values are important, but rather that the rankings of solutions induced by the hypervolume indicator. In detail, we present HypE, a hypervolume estimation algorithm for multi-objective optimization, by which the accuracy of the estimates and the available computing resources can be traded off; thereby, not only do many-objective problems become feasible with hypervolume-based search, but also the runtime can be flexibly adapted. Moreover, we show how the same principle can be used to statistically compare the outcomes of different multi-objective optimizers with respect to the hypervolumeso far, statistical testing has been restricted to scenarios with few objectives. The experimental results indicate that HypE is highly effective for many-objective problems in comparison to existing multi-objective evolutionary algorithms. HypE is available for download at http://www.tik. ee.ethz. ch/sop/download/supplementary/hype/.
Characterization of a Cdc42 Protein Inhibitor and Its Use as a Molecular Probe

Background: By integrating extracellular signals with actin cytoskeletal changes, Cdc42 plays important roles in cell physiology and has been implicated in human diseases. Results: A small molecule was found to selectively inhibit Cdc42 in biochemical and cellular assays. Conclusion: The identified compound is a highly Cdc42-selective inhibitor. Significance: The described first-in-class Cdc42 GTPase-selective inhibitor will have applications in drug discovery and fundamental research. Cdc42 plays important roles in cytoskeleton organization, cell cycle progression, signal transduction, and vesicle trafficking. Overactive Cdc42 has been implicated in the pathology of cancers, immune diseases, and neuronal disorders. Therefore, Cdc42 inhibitors would be useful in probing molecular pathways and could have therapeutic potential. Previous inhibitors have lacked selectivity and trended toward toxicity. We report here the characterization of a Cdc42-selective guanine nucleotide binding lead inhibitor that was identified by high throughput screening. A second active analog was identified via structure-activity relationship studies. The compounds demonstrated excellent selectivity with no inhibition toward Rho and Rac in the same GTPase family. Biochemical characterization showed that the compounds act as noncompetitive allosteric inhibitors. When tested in cellular assays, the lead compound inhibited Cdc42-related filopodia formation and cell migration. The lead compound was also used to clarify the involvement of Cdc42 in the Sin Nombre virus internalization and the signaling pathway of integrin VLA-4. Together, these data present the characterization of a novel Cdc42-selective allosteric inhibitor and a related analog, the use of which will facilitate drug development targeting Cdc42-related diseases and molecular pathway studies that involve GTPases.
Type 2 diabetes mellitus in relation to place of residence: evaluation of selected aspects of socio-demographic status, course of diabetes and quality of life--a cross-sectional study.

INTRODUCTION AND OBJECTIVE This study aims at answering what are the differences in socio-demographic status of patients with type 2 diabetes living in the city and the countryside and what is the impact of a place of residence on the level of metabolic control, the incidence of complications of diabetes and quality of life (QoL). MATERIALS AND METHODS 274 patients were divided into 2 groups: residents of rural areas-28.2% (n=77) and residents of urban areas-71.9% (n=197). Self-reported questionnaires was used: EQ-5D, DQL-BCI and DSC-R. RESULTS The group of residents of the countryside was characterized by a lower income and education level and a higher number of persons with disability pension. Patients living in the country had a higher body mass index in comparison to town inhabitants (32.6 kg/m(2) vs 30.9 kg/m(2), p=0.008) and shorter diabetes duration (8.4 versus 11.3 years, p=0.008). There were no differences between residents of the countryside and towns in terms of the method of treatment (oral antidiabetic drugs: 70.1% and 65.5%, p=0.3, Insulin: 29.9% and 36.5%, p=0.3, respectively), occurring chronic complications of diabetes (retinopathy: 14.3% and 14.2%, neuropathy: 6.5% and 7.6%, coronary heart disease: 44.45 and 37.1%, respectively) and the availability of diabetologists. Patients living in the countryside did not differ from town inhabitants in metabolic control and QoL assessment (EQ-5D index: 0.80 vs 0.79, p=0.9, EQ-VAS: 56.2 vs 54.3, p=0.2, DQL-BCI: 56.0 vs 53.9, p=0.1, DSC-R: 29.6 vs 29.4, p=0.7). CONCLUSIONS The socio-demographic differences between groups dependent on the place of living did not exert a significant influence on the level of metabolic control of diabetes, the incidence of late complications or QoL assessment in the population studied.
The New Role for an Old Kinase: Protein Kinase CK2 Regulates Metal Ion Transport

The pleiotropic serine/threonine protein kinase CK2 was the first kinase discovered. It is renowned for its role in cell proliferation and anti-apoptosis. The complexity of this kinase is well reflected by the findings of past decades in terms of its heterotetrameric structure, subcellular location, constitutive activity and the extensive catalogue of substrates. With the advent of non-biased high-throughput functional genomics such as genome-wide deletion mutant screening, novel aspects of CK2 functionality have been revealed. Our recent discoveries using the model organism Saccharomyces cerevisiae and mammalian cells demonstrate that CK2 regulates metal toxicity. Extensive literature search reveals that there are few but elegant works on the role of CK2 in regulating the sodium and zinc channels. As both CK2 and metal ions are key players in cell biology and oncogenesis, understanding the details of CK2’s regulation of metal ion homeostasis has a direct bearing on cancer research. In this review, we aim to garner the recent data and gain insights into the role of CK2 in metal ion transport.
Multi-Criteria-based Active Learning for Named Entity Recognition

In this paper, we propose a multi-criteria-based active learning approach and effectively apply it to named entity recognition. Active learning targets to minimize the human annotation efforts by selecting examples for labeling. To maximize the contribution of the selected examples, we consider the multiple criteria: informativeness, representativeness and diversity and propose measures to quantify them. More comprehensively, we incorporate all the criteria using two selection strategies, both of which result in less labeling cost than single-criterion-based method. The results of the named entity recognition in both MUC-6 and GENIA show that the labeling cost can be reduced by at least 80% without degrading the performance.
Vaccine Immunity to Pathogenic Fungi Overcomes the Requirement for CD4 Help in Exogenous Antigen Presentation to CD8+ T Cells

Systemic fungal infections with primary and opportunistic pathogens have become increasingly common and represent a growing health menace in patients with AIDS and other immune deficiencies. T lymphocyte immunity, in particular the CD4+ Th 1 cells, is considered the main defense against these pathogens, and their absence is associated with increased susceptibility. It would seem illogical then to propose vaccinating these vulnerable patients against fungal infections. We report here that CD4+ T cells are dispensable for vaccine-induced resistance against experimental fungal pulmonary infections with two agents, Blastomyces dermatitidis an extracellular pathogen, and Histoplasma capsulatum a facultative intracellular pathogen. In the absence of T helper cells, exogenous fungal antigens activated memory CD8+ cells in a major histocompatibility complex class I–restricted manner and CD8+ T cell–derived cytokines tumor necrosis factor α, interferon γ, and granulocyte/macrophage colony-stimulating factor–mediated durable vaccine immunity. CD8+ T cells could also rely on alternate mechanisms for robust vaccine immunity, in the absence of some of these factors. Our results demonstrate an unexpected plasticity of immunity in compromised hosts at both the cellular and molecular level and point to the feasibility of developing vaccines against invasive fungal infections in patients with severe immune deficiencies, including those with few or no CD4+ T cells.
Selective potentiation of alpha 1 glycine receptors by ginkgolic acid

Glycine receptors (GlyRs) belong to the superfamily of pentameric cys-loop receptor-operated channels and are involved in numerous physiological functions, including movement, vision, and pain. In search for compounds performing subunit-specific modulation of GlyRs we studied action of ginkgolic acid, an abundant Ginkgo biloba product. Using patch-clamp recordings, we analyzed the effects of ginkgolic acid in concentrations from 30 nM to 25 μM on α1–α3 and α1/β, α2/β configurations of GlyR and on GABAARs expressed in cultured CHO-K1 cells and mouse neuroblastoma (N2a) cells. Ginkgolic acid caused an increase in the amplitude of currents mediated by homomeric α1 and heteromeric α1/β GlyRs and provoked a left-shift of the concentration-dependent curves for glycine. Even at high concentrations (10–25 μM) ginkgolic acid was not able to augment ionic currents mediated by α2, α2/β, and α3 GlyRs, or by GABAAR consisting of α1/β2/γ2 subunits. Mutation of three residues (T59A/A261G/A303S) in the α2 GlyR subunit to the corresponding ones from the α1 converted the action of ginkgolic acid to potentiation with a distinct decrease in EC50 for glycine, suggesting an important role for these residues in modulation by ginkgolic acid. Our results suggest that ginkgolic acid is a novel selective enhancer of α1 GlyRs.