Miracle-dz/UniFAR-FTUs huggingface dataset:
Phenotypic Switching in Candida glabrata Involves Phase-Specific Regulation of the Metallothionein Gene MT-IIand the Newly Discovered Hemolysin Gene HLP

ABSTRACT Although Candida glabrata has emerged in recent years as a major fungal pathogen, there have been no reports demonstrating that it undergoes either the bud-hypha transition or high-frequency phenotypic switching, two developmental programs believed to contribute to the pathogenic success of other Candida species. Here it is demonstrated that C. glabrata undergoes reversible, high-frequency phenotypic switching between a white (Wh), light brown (LB), and dark brown (DB) colony phenotype discriminated on an indicator agar containing 1 mM CuSO4. Switching regulates the transcript level of the MT-II metallothionein gene(s) and a newly discovered gene for a hemolysin-like protein,HLP. The relative MT-II transcript levels in Wh, LB, and DB cells grown in the presence of CuSO4 are 1:27:81, and the relative transcript levels of HLP are 1:20:35. The relative MT-II and HLP transcript levels in cells grown in the absence of CuSO4 are 1:20:30 and 1:20:25, respectively. In contrast, switching has little or no effect on the transcript levels of the genes MT-I,AMT-I, TRPI, HIS3,EPAI, and PDHI. Switching of C. glabrata is not associated with microevolutionary changes identified by the DNA fingerprinting probe Cg6 and does not involve tandem amplification of the MT-IIa gene, which has been shown to occur in response to elevated levels of copper. Finally, switching between Wh, LB, and DB occurred in all four clinical isolates examined in this study. As in Candida albicans, switching in C. glabrata may provide colonizing populations with phenotypic plasticity for rapid responses to the changing physiology of the host, antibiotic treatment, and the immune response, through the differential regulation of genes involved in pathogenesis. More importantly, because C. glabrata is haploid, a mutational analysis of switching is now feasible.
The timing and precision of action prediction in the aging brain

Successful social interactions depend on the ability to anticipate other people's actions. Current conceptualizations of brain function propose that causes of sensory input are inferred through their integration with internal predictions generated in the observer's motor system during action observation. Less is known concerning how action prediction changes with age. Previously we showed that internal action representations are less specific in older compared with younger adults at behavioral and neural levels. Here, we characterize how neural activity varies while healthy older adults aged 56–71 years predict the time‐course of an unfolding action as well as the relation to task performance. By using fMRI, brain activity was measured while participants observed partly occluded actions and judged the temporal coherence of the action continuation that was manipulated. We found that neural activity in frontoparietal and occipitotemporal regions increased the more an action continuation was shifted backwards in time. Action continuations that were shifted towards the future preferentially engaged early visual cortices. Increasing age was associated with neural activity that extended from posterior to anterior regions in frontal and superior temporal cortices. Lower sensitivity in action prediction resulted in activity increases in the caudate. These results imply that the neural implementation of predicting actions undergoes similar changes as the neural process of executing actions in older adults. The comparison between internal predictions and sensory input seems to become less precise with age leading to difficulties in anticipating observed actions accurately, possibly due to less specific internal action models. Hum Brain Mapp 37:54–66, 2016. © 2015 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.
Compact Long-Period Fiber Gratings With Resonance at Second-Order Diffraction

Compact 5-mm-long 100-μm-period long-period fiber gratings (LPFGs) are fabricated by femtosecond laser direct writing. Nearly symmetrical photomodified grating segments located at the center of a fiber core lead to well-defined transmission spectra. The LPFGs can couple the guided mode to high-order cladding modes of second-order diffraction, resulting in a high refractive index (RI) sensitivity of 5265 nm/RI units in the RI range of 1.433 ~ 1.443 and a low-temperature sensitivity of -15.52 pm/°C from 20°C to 500°C. The latter property is desired for crosstalk-free high-sensitivity RI sensors.
Display Infrastructure for Virtual Environments ( DIVE )

Display systems suitable for virtual reality applications can prove useful for a variety of domains. The emergence of lowcost head-mounted displays reinvigorated the area of virtual reality significantly. However, there are still applications where fullscale CAVE-type display systems are better suited. Moreover, the cost of most CAVE-type display systems is typically rather high, thereby making it difficult to justify in a research setting. This paper aims at providing a design of less costly display technology combined with inexpensive input devices that implements a virtual environment paradigm suitable for such full-scale visualization and simulation tasks. The focus is on cost-effective display technology that does not break a researchers budget. The software framework utilizing these displays combines different visualization and graphics packages to create an easy-to-use software environment that can run readily on this display. A user study was performed to evaluate the display technology and its usefulness for virtual reality tasks using an accepted measure: presence. It was found that the display technology is capable of delivering a virtual environment in which the user feels
Association between high-normal levels of alanine aminotransferase and risk factors for atherogenesis.

BACKGROUND & AIMS Liver disease has been associated with cardiovascular disorders, but little is known about the relationship between serum levels of alanine aminotransferase (ALT) and markers of atherogenesis. We investigated the relationship between low-normal and high-normal levels of ALT and an extended panel of cardiovascular risk factors among individuals with no known diseases in a primary care setting. METHODS We performed a retrospective analysis of data collected from 6442 asymptomatic patients at wellness visits to a primary care setting in central Virginia from 2010 through 2011. Serum levels of ALT were compared with levels of lipids and lipoproteins, as well as metabolic, inflammatory, and coagulation-related factors associated with risk for cardiovascular disease. RESULTS Serum levels of ALT were higher than 40 IU/L in 12% of subjects, and in the high-normal range (19-40 IU/L in women and 31-40 IU/L in men) in 25% of subjects. ALT level was associated with the apolipoprotein B level, concentration and particle size of very-low-density lipoproteins, concentration of low-density lipoprotein (LDL) particles (LDL-P), and percentages of small dense LDL (sdLDL) and sdLDL-cholesterol (sdLDL-C) (P < .0001 for all). A high-normal level of ALT was associated with higher levels of LDL-C, LDL-P, sdLDL-C, and sdLDL particles (P < .001 for all). These effects were independent of age, body mass index, and hyperinsulinemia. Increasing levels of ALT and fasting hyperinsulinemia (>12 μU/mL) synergized with increasing levels of triglycerides, very-low-density lipoprotein particles, LDL-P, sdLDL-C, and percentage of sdLDL-C. Levels of APOA1, high-density lipoprotein-cholesterol, and high-density lipoprotein-class 2 were associated inversely with serum level of ALT (P < .0001 for all). CONCLUSIONS In an analysis of asymptomatic individuals, increased serum levels of ALT (even high-normal levels) are associated with markers of cardiovascular disease.
Effects of Toxoplasma gondii infection on plasma testosterone and cortisol level and stress index on patients referred to Sina hospital, Tehran

Introduction and objective: Toxoplasma gondii is an intra cellular protozoan parasite which infects 30 to 60% of the world population. A wide range of toxoplasmosis conditions has been studied, but there are still unknown damages which must be explored. In the present research, the effect of this parasite on testosterone and cortisol changes in the infected men and women was examined. Materials and methods: A total of 180 patients (73 females and 107 males), were examined for lgG antiToxoplasma antibody, cortisol and testosterone in their plasma. In addition, the patients also filled in personality questionnaire DASS21 (depression, anxiety, and stress). Results: Results showed that 24(%13/33) females and 39(%20) males were positive with lgG anti-Toxoplasma antibody, respectively. A statistically significant correlation between Toxoplasma infection and testosterone and cortisol increase in women and men were observed. Stress and anxiety index also increased in men and women whereas depression index increased only in men. Conclusion: The results show a direct relation between raise Toxoplasma infection and cortisol, and testosterone increase in bout men and women and high DASS21 test score in Toxoplasma infected group.
A phytochemical comparison of saw palmetto products using gas chromatography and 1H nuclear magnetic resonance spectroscopy metabolomic profiling

Preparations containing saw palmetto berries are used in the treatment of benign prostatic hyperplasia (BPH). There are many products on the market, and relatively little is known about their chemical variability and specifically the composition and quality of different saw palmetto products notwithstanding that in 2000, an international consultation paper from the major urological associations from the five continents on treatments for BPH demanded further research on this topic. Here, we compare two analytical approaches and characterise 57 different saw palmetto products.
Acute Spinal Cord Injury: A Study Using Physical Examination and Magnetic Resonance Imaging

Magnetic resonance imaging (MRI) was performed on 37 patients with acute spinal injury using T1− and T2-weighted images. Three different types of MRI signal patterns were detected in association with these spinal cord injuries. A classification was developed using these three patterns. Type I, seen in ten (27.0%) of the patients, demonstrated a decreased signal intensity consistent with acute intraspinal hemorrhage. Type II, seen in 16 (43.2%) of the patients, demonstrated a bright signal intensity consistent with acute cord edema. Type III, seen in three (8.1%) of the patients, demonstrated a mixed signal of hypointensity centrally and hyperintensity peripherally consistent with contusion. The remaining eight patients had normal cords by MRI. All 37 patients had an admitting neurologic assessment and classification of their spinal injury according to the Frankel classification and the Trauma Motor Index (TMI). At an average of 12.1 months postinjury, their neurologic function was reassessed. Patients with Type I patterns showed no improvement in their Frankel classification and minimal improvement in their TMI, 32.1 to 42.4. In comparison, all of the Type II and III patterns improved at least one Frankel classification. The Type II TMI increased from 70.8 to 91.9 and Type III from 37.3 to 75.7. This preliminary report indicates a distinct correlation between the pattern of spinal cord injury as identified by MRI and neurologic recovery. It appears that the ability of MRI to aid in examination of the condition of the spinal cord will offer a means of predicting neurologic recovery following acute spinal cord injury.
Therapeutic effect of hysterosalpingography: oil- versus water-soluble contrast media--a randomized prospective study.

In a prospective randomized study, the number of pregnancies after hysterosalpingography (HSG) was estimated in 398 patients who had been infertile for longer than 1 year. Iohexol was used in 101 patients, ioxaglate in 102 patients, diatrizoate meglumine in 97 patients, and ethiodized poppy-seed oil in 98 patients. Ten months after HSG, the patient, referring physician, and/or hospital department was consulted for information about pregnancies. Questionnaires were obtained from the patients who became pregnant during the waiting period of 3 months. No differences in demographic parameters, infertility status, or diagnosis made with HSG were detected among the four contrast media groups. Significantly more patients became pregnant after HSG in the ethiodized poppy-seed oil group than in the three water-soluble contrast media groups (P less than .01). When only intrauterine pregnancies resulting in full-term births were considered, significant differences in pregnancy rates between the oil-soluble and the water-soluble contrast media groups became more obvious. In the group that received ethiodized poppy-seed oil, almost one-third of the infertile women had normal pregnancies and childbirths after HSG.
Dynamic traitor tracing schemes, revisited

We revisit recent results from the area of collusion-resistant traitor tracing, and show how they can be combined and improved to obtain more efficient dynamic traitor tracing schemes. In particular, we show how the dynamic Tardos scheme of Laarhoven et al. can be combined with the optimized score functions of Oosterwijk et al. to trace coalitions much faster. If the attack strategy is known, in many cases the order of the code length goes down from quadratic to linear in the number of colluders, while if the attack is not known, we show how the interleaving defense may be used to catch all colluders about twice as fast as in the dynamic Tardos scheme. Some of these results also apply to the static traitor tracing setting where the attack strategy is known in advance, and to group testing.
Improving the specificity of the PF4 ELISA in diagnosing heparin‐induced thrombocytopenia

Heparin induced thrombocytopenia (HIT) is a serious complication of heparin therapy. The PF4 ELISA is a serologic assay that provides laboratory support for the clinical diagnosis of HIT, but it is often positive in patients who do not have the syndrome. We examined whether the specificity of the PF4 ELISA can be improved by 1) taking antibody potency into consideration, 2) by measuring only IgG antibodies, and 3) by utilizing a high concentration heparin inhibition step. We reviewed clinical information on 116 patients whose samples were referred for HIT antibody testing and assigned each a clinical score related to the likelihood of the patient having HIT. The scores were then correlated with serologic findings. Patients with strongly positive PF4ELISA results (OD ≥ 1.0) using both versions of the assay (IgG/A/M and IgG only) had clinical scores and SRA activity that were significantly higher than those having reactive or negative results. When the IgG‐only PF4 ELISA was used, only the strongly positive result group had significantly higher clinical scores and SRA release, and fewer samples were classified as weakly positive or reactive, suggesting that detection of IgG only in the PF4 ELISA improves the assay's specificity. The heparin inhibition step identified “reactive” samples that were associated with clinical scores and SRA release indistinguishable from the “negative” result groups, confirming that this step further improves specificity of the test. This study supports utilizing these 3 modifications of the PF4 ELISA to improve specificity in supporting the clinical diagnosis of HIT. Am. J. Hematol. , 2012. © 2012 Wiley Periodicals, Inc.
Variable Step Block Backward Differentiation Formula for Solving First Order Stiff ODEs

This paper focuses on the derivation of implicit 2-point block method based on Backward Differentiation Formulae (BDF) of variable step size for solving first order stiff initial value problems (IVPs) for Ordinary Differential Equations (ODEs). In a 2-point Block Backward Differentiation Formula (BBDF), two solution values are produced simultaneously. Plots of their regions of absolute stability for the method are also presented. The efficiency of the 2-point BBDF is compared with variable step variable order non block BDF (NBDF) method. Numerical results indicate that the resulting 2-point BBDF method outperform the NBDF method in both execution time and accuracy.
Fast and Accurate Registration of Visible and Infrared Videos

In this work, we propose a novel fast and accurate method based on keypoints and temporal information to solve the registration problem on planar scenes with moving objects for infrared-visible stereo pairs. A keypoint descriptor and a temporal buffer (reservoir) filled with matched keypoints are used in order to find the homography transformation for the registration. Inside a given frame, the problem of registration is formulated as correspondences between noisy polygon vertices. Sections of polygons are matched locally to find the corresponding vertices inside a frame. These correspondences are then accumulated temporally using a reservoir of matches for homography calculation. Results show that our method outperforms two recent state-of-the-art global registration methods by a large margin in almost all tested videos.
Hierarchy-based mining of association rules in data warehouses

The problem of mining association rules from large databases is knowing an increasing interest from the Data Mining community. Separately, data warehouses axe rapidly becoming a standard platform to collect and analyze huge amounts of data. Their main characteristic is that warehouses maintain the structural complexity of data through a suitable data schema which can represent explicit/implicit concept hierarchies over the dimensions of data. The data mining tools for extracting association rules rarely exploit such hierarchies since they usually consider a flat representation of data. In this paper, we introduce an analysis method to assist the process of extracting association rules by exploiting the implicit and explicit concepts hierarchies that feature data warehouses. This method is devised to automate as mush as possible the process of knowledge discovery on top of data warehouses in the specific case of association rules. Specifically, our method tries to suggest only association rule patterns that can extract potentially interesting knowledge from the data. The method we propose appears to be very general and does not depend on specific mining algorithm or tool•
Trace-orthogonal space-time coding for multiuser systems

In this paper we prove that trace-orthogonal space-time coding provides a necessary and sufficient condition for information lossless coding in a multiple access system, where each user encodes its own symbols independently of the other users. Then, we show that the sub-optimal MMSE decoder can be implemented very simply as a set of scalar decoders and we prove that, under the assumption of using the (sub-optimal) MMSE decoder, the trace-orthogonal design with scaled unitary coding matrices yields minimum BER for each user.
Aggregate Risk and the Choice between Cash and Lines of Credit

We model corporate liquidity policy and show that aggregate risk exposure is a key determinant of how firms choose between cash and bank credit lines. Banks create liquidity for firms by pooling their idiosyncratic risks. As a result, firms with high aggregate risk find it costly to get credit lines and opt for cash in spite of higher opportunity costs and liquidity premium. Likewise, in times when aggregate risk is high, firms rely more on cash than on credit lines. We verify these predictions empirically. Cross-sectional analyses show that firms with high exposure to systematic risk have a higher ratio of cash to credit lines and face higher spreads on their lines. Time-series analyses show that firms' cash reserves rise in times of high aggregate volatility and in such times credit lines initiations fall, their spreads widen, and maturities shorten. Also consistent with the mechanism in the model, we find that exposure to undrawn credit lines increases bank-specific risks in times of high aggregate volatility.
HERSCHEL SPECTROSCOPIC OBSERVATIONS OF LITTLE THINGS DWARF GALAXIES

We present far-infrared (FIR) spectral line observations of five galaxies from the Little Things sample: DDO 69, DDO 70, DDO 75, DDO 155, and WLM. While most studies of dwarfs focus on bright systems or starbursts due to observational constraints, our data extend the observed parameter space into the regime of low surface brightness dwarf galaxies with low metallicities and moderate star formation rates. Our targets were observed with Herschel at the [C ii] 158 μm, [O i] 63 μm, [O iii] 88 μm, and [N ii] 122 μm emission lines using the PACS Spectrometer. These high-resolution maps allow us for the first time to study the FIR properties of these systems on the scales of larger star-forming complexes. The spatial resolution in our maps, in combination with star formation tracers, allows us to identify separate photodissociation regions (PDRs) in some of the regions we observed. Our systems have widespread [C ii] emission that is bright relative to continuum, averaging near 0.5% of the total infrared (TIR) budget—higher than in solar-metallicity galaxies of other types. [N ii] is weak, suggesting that the [C ii] emission in our galaxies comes mostly from PDRs instead of the diffuse ionized interstellar medium (ISM). These systems exhibit efficient cooling at low dust temperatures, as shown by ([O i]+[C ii])/TIR in relation to 60 μm/100 μm, and low [O i]/[C ii] ratios which indicate that [C ii] is the dominant coolant of the ISM. We observe [O iii]/[C ii] ratios in our galaxies that are lower than those published for other dwarfs, but similar to levels noted in spirals.
Lattice Boltzmann simulation of electromechanical resonators in gaseous media

In this work, we employ a kinetic-theory-based approach to predict the hydrodynamic forces on electromechanical resonators operating in gaseous media. Using the Boltzmann–BGK equation, we investigate the influence of the resonator geometry on the fluid resistance in the entire range of non-dimensional frequency variation 0 ≤ τω ≤ ∞; here the fluid relaxation time τ = μ/p is determined by the gas viscosity μ and pressure p at thermodynamic equilibrium, and ω is the (angular) oscillation frequency. Our results here capture two important aspects of recent experimental measurements that covered a broad range of experimental parameters. First, the experimentally observed transition from viscous to viscoelastic flow in simple gases at τω ≈ 1 emerges naturally in the numerical data. Second, the calculated effects of resonator geometry are in agreement with experimental observations.