Miracle-dz/UniFAR-FTUs huggingface dataset:
Master and Commander in Fungal Pathogens: the Two-Component System and the HOG Signaling Pathway

All living organisms, whether they be single- or multicellular, actively interact with their surrounding environments and modulate their physiological status to maintain cellular homeostasis. This adaptation process is highly coordinated via diverse signaling pathways, with the involvement of a series of signaling components, including sensors/receptors, kinases, and transcription factors. For microorganisms, the environment is nonfavorable and can be considered a stress. Sensing and responding to a plethora of environmental stresses are key requirements for pathogenic fungi having a saprophytic life cycle, including Cryptococcus neoformans and Aspergillus fumigatus, to colonize successfully and proliferate within the corresponding host system. In either commensal fungi that are able to cause opportunistic infection when the host immune system is compromised (e.g., Candida albicans) or parasitic fungi whose survival depends on the host without saprophytic cycles (e.g., Pneumocystis jirovecii, the dermatophytes, and the microsporidia), the stress-sensing and adaptation process is still required for survival at different host anatomical sites having distinct environmental conditions, during dissemination of organisms, or to counterbalance changes in overall host physiological conditions. These features confer an underlying distinction between pathogenic and nonpathogenic microbes, along with regulation of diverse virulence factors.
Stroke Risk and Antithrombotic Strategies in Atrial Fibrillation

Background and Purpose— Although the stroke rate associated with atrial fibrillation has declined over the last 10 years, the emerging atrial fibrillation epidemic threatens to increase the incidence of cardioembolic stroke. Summary of Review— Oral anticoagulants are superior antithrombotic agents but are underused due to fear of bleeding and uncertainty about which patients will benefit. Individualized decisions on antithrombotic therapy require balancing the competing risks of thromboembolism and bleeding. The CHADS2 (Congestive heart failure, Hypertension, Age >75 years, and Diabetes mellitus, and 2 points for prior Stroke/transient ischemic attack) score and other schemes provide an estimate of thromboembolic risk; however, the external validity of these estimates in the context of well-controlled risk factors, or a hypercoagulable state, is uncertain. Moreover, it is very difficult to estimate bleeding risk. Recent studies highlight the need for meticulous international normalized ratio control to achieve optimal outcomes hampered by the high bleeding risk during oral anticoagulant inception and other limitations of warfarin. Dabigatran is at least as efficacious as warfarin in preventing stroke and systemic embolism for patients in whom the risk of thromboembolism outweighs bleeding risk. In addition, the results of ongoing trials evaluating alternative anticoagulants such as oral anti-Xa agents are awaited. In this review, we discuss emerging therapies including available and completed trials of direct antithrombins and anti-Xa agents, including ximelagatran, idraparinaux, and dabigatran; and new device therapies including left atrial appendage occlusion devices. Conclusions— In light of these promising new therapies, it is likely that atrial fibrillation thromboembolism guidelines will need to be rewritten and frequently updated.
Oncotargets and Therapy Dovepress Dovepress Significance of Preoperative C-reactive Protein as a Parameter in Patients with Small Cell Carcinoma of the Esophagus

Background: C-reactive protein (CRP) is inversely related to prognosis in many cancers, however, no studies regarding the predictive value of CRP in small cell carcinoma of the esophagus (SCCE) are available. The aim of this study was to determine the prognostic value of preoperative CRP in patients with SCCE. retrospective analysis of 43 consecutive patients with SCCE was conducted. Univariate and multivariate analyses were performed to evaluate the prognostic parameters. Results: In our study, elevated CRP levels (.10 mg/L) were found in 16 patients (37.2%). CRP levels were significantly higher in patients with deeply invasive tumors (P = 0.018) and those associated with nodal metastasis (P = 0.018). Patients with CRP #10 mg/L had a significantly better overall survival than patients with CRP . 10 mg/L (25.9% vs 6.3%, P = 0.004). Multivariate analyses showed that CRP was a significant predictor for overall survival. CRP . 10 mg/L had a hazard ratio of 2.756 (95% confidence interval: 1.115–6.813, P = 0.028) for overall survival. Conclusion: Preoperative CRP is an independent predictive factor for long-term survival in patients with SCCE.
Why is word recognition impaired by disorientation while the identification of single letters is not?

Past research has shown that speed of identifying single letters or digits is largely indifferent to orientation, whereas the recognition of single words or connected text is markedly disrupted by disorientation. In a series of four experiments, we attempted to reconcile these findings. The results suggest that disorientation does not impair the identification of the characters but disrupts the perception of their spatial arrangement. When spatial order information is critical for distinguishing between different stimuli, disorientation is disruptive because some rectification process is required to restore order information. Utilizing the similarity between the letter B and the number 13, we found strong effects of orientation when a stimulus was interpreted as the two-digit number 13 but not when interpreted as the single letter B. This, however, occurred only when the set of numbers to be classified included permutations of the same digits (Experiments 1 and 2). Odd-even decisions on single-digit and two-digit numbers (Experiment 3) yielded strong effects of stimulus orientation for order-dependent numbers (e.g., 32), weaker effects for order-independent numbers (e.g., 24), and none for repeated-digit (e.g., 22) or single-digit numbers. Classification time for two-letter Hebrew words evidenced strong effects of orientation for words that differed only in letter order but much weaker effects for words that had no letters in common, even when these were embedded within some words that did (Experiment 4).
Ecology and Management of Pemphigus betae (Hemiptera: Aphididae) in Sugar Beet

Pemphigus betae Doane (Hemiptera: Aphididae), is a sporadic pest of sugar beet ( Beta vulgaris L. var. vulgaris ) in all major sugar beet production regions of North America. These oval-shaped, pale-yellowish insects, with a body length ranging from 1.9–2.4 mm, secrete a waxy material, giving their subterranean colonies a moldy appearance. Poplars in the genus Populus L. are the preferred primary hosts, while sugar beet and certain weed species, such as common lambsquarters ( Chenopodium album L.) and kochia ( Kochia scoparia (L.)), are among the secondary hosts. Pemphigus betae has a complex and varied life cycle and is usually heteroecious and holocyclic, although anholocyclic apterae are known to overwinter in the soil. Heavy infestations of this aphid can induce significant reductions in yield, sugar content, and recoverable sugar. Under conditions of extreme stress and heavy infestations, the alienicolae can induce stunting, chlorosis, wilting, and even death of sugar beet plants. Accurately establishing population densities for sugarbeet root aphids presents a challenge, because the economic important stage of this insect is subterranean. However, use of a fall root rating index aids in estimating relative population densities. Furthermore, root aphids are especially difficult to control by means of conventional insecticides. For this reason, integrated pest management tactics, including the use of host plant resistance, cultural control techniques, and the use of natural enemies, should take precedence.
Predicting the impact of demand- and supply-side measures on bus ridership in Putrajaya, Malaysia

Putrajaya is a unique Malaysian city from a transport policy perspective, as its explicit goal is to achieve a 70% share of public transport to its core precincts. A study was recently commissioned with the aim of quantifying travelers’ responses to policy measures to ensure effective strategy formulation. This paper describes and discusses the methods, results, and policy implications of the study. Econometric estimation results show that improvement in public transport alone is incapable of inducing sufficient modal shift to achieve the goal of a 70:30 split between public and private transport. Although service quality positively influences ridership, modal split is generally not sensitive to variation in the quality of public transport service. Thus, demand management measures appear to be indispensable as a policy tool to reduce dependence on private transport.
Wavelength Selective WDM Network Design: How Bad is Shortest Path Routing?

Given a collection of lightpath requests, we consider the problem of allocating fibers to the links of a WDM network at minimum cost, such that all lightpath requests can be simultaneously realized. It is known that, under modular fiber capacity assumptions, shortest path routing may not minimize the total fiber cost. In this paper, we extend our previous work for wavelength convertible networks, and theoretically quantify the increase in fiber cost due to shortest path routing in networks without wavelength converters. In particular, we prove that shortest path routing is asymptotically cost-optimal in heavily loaded networks, and asymptotically near-optimal in large, sparse networks that support all-to-all communication.
Improvement of ground to satellite fso link performance using transmit diversity in weak atmospheric turbulence

The performance of ground to satellite Free Space Optical (FSO) communication link is degraded due to the presence of atmospheric turbulence that causes fluctuations in both intensity and phase of the received optical signal. In this paper, bit error rate (BER) performance of FSO link using transmit diversity is investigated for coherent (sub-carrier BPSK and sub-carrier QPSK) and non-coherent (OOK and Q-PPM) modulation schemes in weak atmospheric turbulence channel. It is seen that multiple transmitting antennae help to overcome the turbulence induced fading effect. It is observed that sub-carrier BPSK modulation outperforms the other modulation schemes in terms of minimum SNR requirement for a given BER. Among non-coherent modulation schemes, Q-PPM performs better than OOK. However, as the level of Q in Q-PPM increases, its performance degrades and it becomes worse than OOK for certain values of atmospheric turbulence. Also, the effect of correlation among different transmitting antennae beams is analysed on the link performance.
PSNR Based Analysis of Block Matching Algorithms for Motion Estimation

This paper mainly focuses on the two main classification of motion estimation algorithms used for video compression. Motion Estimation (ME) algorithms vary with respect to the a priori information and constraints they employ, as well as the method of computation they use to obtain the estimate. The classifications for ME algorithms are based on feature/region matching, gradient based methods, spatiotemporal energy methods, deter- ministic model based methods and stochastic model based methods. This paper focuses more on block matching algorithms which comes under fea- ture/region matching and gradient based methods. This paper compares 2 important ME algorithms. They are Full Search (FS) or ES and a newly found adaptive algorithm called AMEA. These algorithms are used for implementing various standards, which ranges from MPEG1 / H.261 to MPEG4 / H.263 and H.264/AVC. A very brief introduction to the entire flow of video compression is also presented in this paper.
Consumer Acceptance of Genetically Modified Food Products in the Developing World

World-wide consumer response toward food products made from genetically modified ingredients has been largely negative. However, the majority of the previous studies on consumer attitudes towards genetically modified food products were conducted in developed countries in Europe as well as Japan. The small number of studies conducted in developing countries obtained different results from the developed world. This paper considers the motivations for consumer attitudes towards genetically modified foods in developing countries. We conclude that the generally positive perception towards genetically modified foods in developing countries could be the result of a cost-benefit analysis consistent with expected utility theory. Developing countries have more urgent needs in terms of food availability and nutritional content. Additionally, perceived levels of risk may be smaller due to trust in government regulation, positive perceptions of scientific discovery, and positive media influences. This is contrary to the small benefits and high perceived risks found in many developed countries, and hence, the rational for low or non-acceptance of genetically modified foods in those countries.
PBL-protocols: Guiding and Controlling Problem Based Learning Processes in Virtual Learning Environments

In this paper we describe our approach for supporting the use of the problem-based learning (PBL) method in virtual learning environments. We identify two key difficulties. Firstly, neither learners nor tutors, who are used to more traditional methods of teaching, know exactly what to expect from PBL or how to behave appropriately within their new roles. Secondly, these problems are compounded by having to interact within a socially unfamiliar computer-based learning environment. We frame these difficulties in terms of schema theory which suggests that people behave and know what to expect from situations according to mentally represented scripts describing the typical course of events. We apply computational descriptions of these scripts, i.e. PBL-protocols, which guide and control social interaction in virtual PBL groups according to (a) the phase of the learning process and (b) the specific roles of tutor, learner and expert; three roles which are typically distinguished in the problem-based learning method. The PBL-protocols restrict the type of contributions allowed for each role type for each phase of the PBL learning process. We describe the implementation of the PBL- protocols in the CROCODILE virtual learning environment, and discuss results and implications of an early pilot study.
Influence of particle-phase state on the hygroscopic behavior of mixed organic-inorganic aerosols

Recent work has demonstrated that organic and mixed organic–inorganic particles can exhibit multiple phase states depending on their chemical composition and on ambient conditions such as relative humidity (RH). To explore the extent to which water uptake varies with particle-phase behavior, hygroscopic growth factors (HGFs) of nine laboratory-generated, organic and organic–inorganic aerosol systems with physical states ranging from well-mixed liquids to phase-separated particles to viscous liquids or semi-solids were measured with the Differential Aerosol Sizing and Hygroscopicity Spectrometer Probe at RH values ranging from 40 to 90%. Water-uptake measurements were accompanied by HGF and RH-dependent thermodynamic equilibrium calculations using the Aerosol Inorganic-Organic Mixtures Functional groups Activity Coefficients (AIOMFAC) model. In addition, AIOMFAC-predicted growth curves are compared to several simplified HGF modeling approaches: (1) representing particles as ideal, well-mixed liquids; (2) forcing a single phase but accounting for non-ideal interactions through activity coefficient calculations; and (3) a Zdanovskii–Stokes–Robinson-like calculation in which complete separation of the inorganic and organic components is assumed at all RH values, with water uptake treated separately in each of the individual phases. We observed variability in the characteristics of measured hygroscopic growth curves across aerosol systems with differing phase behaviors, with growth curves approaching smoother, more continuous water uptake with decreasing prevalence of liquid–liquid phase separation and increasing oxygen : carbon ratios of the organic aerosol components. We also observed indirect evidence for the dehydration-induced formation of highly viscous semi-solid phases and for kinetic limitations to the crystallization of ammonium sulfate at low RH for sucrose-containing particles. AIOMFAC-predicted growth curves are generally in good agreement with the HGF measurements. The performances of the simplified modeling approaches, however, differ for particles with differing phase states. This suggests that no single simplified modeling approach can be used to capture the water-uptake behavior for the diversity of particle-phase behavior expected in the atmosphere. Errors in HGFs calculated with the simplified models are of sufficient magnitude to produce substantial errors in estimates of particle optical and radiative properties, particularly for the assumption that water uptake is driven by absorptive equilibrium partitioning with ideal particle-phase mixing.
Multiple applications of flurbiprofen and chlorhexidine chips in patients with chronic periodontitis: a randomized, double blind, parallel, 2-arms clinical trial

Aim The aim of the present randomized, double blind, parallel, 2-arm clinical study was to examine the safety and efficacy of frequent applications of chlorhexidine chip (CHX) and flurbiprofen chip (FBP) in patients with chronic periodontitis. Methods Sixty patients were randomized into CHX and FBP groups. Following OHI and scaling and root planing (SRP), baseline pocket depth (PD) measurements, gingival recession and bleeding on probing (BOP) were performed and repeated at week 4 and 8. The assigned chip was placed at weeks 0, 1, 2, 3, 5, 7. Results Mean PD reduction in the CHX group was 2.08 mm (7.17 to 5.09, p < 0.0001). Mean PD reduction in the FBP group was 2.27 mm (6.72 to 4.45, p < 0.0001). Ninety-seven percentage and 95% of these sites exhibited PD reduction ≥1 mm, while 38% and 34% of the sites exhibited PD ≥3 mm (FBP and CHX, respectively). Clinical attachment level gain (1.66 and 1.95 mm, respectively) was statistically significant (p < 0.0001). Baseline BOP dropped from 98% and 100% to 24% and 30% for the CHX and FBP groups, respectively (p < 0.0001). Conclusion Frequent applications of CHX and FBP chips resulted in a significant improvement in the periodontal condition in these sites. Furthermore studies will be required to compare this new treatment regimen to SRP or SRP with single chip application.
Oscillation patterns in negative feedback loops

Organisms are equipped with regulatory systems that display a variety of dynamical behavior ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein concentrations or gene expression levels are related to the presence of at least one negative feedback loop in the regulatory network. Here, we study the dynamics of a very general class of negative feedback loops. Our main result is that, when a single negative feedback loop dominates the dynamical behavior, the sequence of maxima and minima of the concentrations exhibit a pattern that uniquely identifies the interactions of the loop. This allows us to devise an algorithm to (i) test whether observed oscillating time series are consistent with a single underlying negative feedback loop, and if so, (ii) reconstruct the precise structure of the loop, i.e., the activating/repressing nature of each interaction. This method applies even when some variables are missing from the data set, or if the time series shows transients, like damped oscillations. We illustrate the relevance and the limits of validity of our method with three examples: p53-Mdm2 oscillations, circadian gene expression in cyanobacteria, and cyclic binding of cofactors at the estrogen-sensitive pS2 promoter.
Who is Willing to Answer Open-ended Questions on the Meaning of Left and Right?

The left-right dimension plays an important role in a wide range of political science studies, and analyses are sometimes based on responses to open-ended survey questions about the meaning of left and right. Due to a considerable non-response to these questions on the 2008 German General Social Survey, the value of the data needs to be evaluated, and response analysis is recommended before Germany’s ideological beliefs are analysed. This paper investigates whether or not respondents’ personality traits, cognitive abilities and socialisation, motivation, and left-right self-placement affect response behaviour to our open-ended questions. We found several explanatory variables: a left-right self-placement, its ideological direction, an Eastern German socialisation background, a high level of education and a strong political interest. These findings indicate that, in addition to methodological issues, substantial variables matter in response behaviour in technical terms, and ideological analysts should consider if their findings can be generalised for the entire German population.
EVOLUTION OF PHACUS (EUGLENOPHYCEAE) AS INFERRED FROM PELLICLE MORPHOLOGY AND SSU rDNA

This research integrates a large morphological data set into a molecular context. Nineteen pellicle characters and 62 states from 13 euglenid taxa were analyzed cladistically. The pellicle morphology of Euglena tripteris (Klebs), Lepocinclis ovata (Conrad), Phacus brachykentron (Pochmann), P. oscillans (Klebs), P. pyrum (Stein), and P. triqueter (Dujardin) is described comprehensively. These data are compared with new information on the pellicle morphology of Euglena acus (Ehrenberg), E. stellata (Mainx), and Peranema trichophorum (Stein) in addition to published data on Entosiphon sulcatum (Dujardin), Euglena gracilis (Klebs), Distigma proteus (Pringsheim), and Petalomonas cantuscygni (Cann and Pennick). Nuclear small subunit (SSU) rDNA sequences provided an independent test for establishing a robust organismal pedigree of the same taxa. A synthetic tree derived from the combined phylogenetic analyses of pellicle morphology and SSU rDNA enabled us to parsimoniously map morphological character states. This approach demonstrated the utility of pellicle morphology for inferring phylogenetic relationships of euglenids and establishing apomorphy‐based clade definitions. Three robust clades with unambiguous pellicle‐based apomorphies can be recognized within taxa traditionally classified as Phacus: (1) L. ovata and P. pyrum, (2) E. tripteris and P. triqueter, and (3) P. brachykentron and P. oscillans. Taxonomic concerns that emerged from these results are discussed.