Miracle-dz/UniFAR-FTUs huggingface dataset:
Relationship between lipid composition, frequency of ethanol‐induced respiratory deficient mutants, and ethanol tolerance in Saccharomyces cerevisiae

The frequency of ethanol‐induced respiratory deficient mutants and lipid composition in two Saccharomyces cerevisiae strains showing different degrees of ethanol tolerance were investigated. The more ethanol‐tolerant strain exhibited a lower frequency of ethanol‐induced respiratory deficient mutants than the less ethanol‐tolerant strain. In addition, the more ethanol‐tolerant strain contained a higher ergosterol/ phospholipid ratio, a higher proportion of phosphatidylcholine, a lower proportion of phosphatidylethanolamine, a higher incorporation of long‐chain fatty acids in total phospholipids, and a slightly higher proportion of unsaturated fatty acids in total phospholipids than the less ethanol‐tolerant strain. These results show a clear relationship between the lipid composition, the frequency of ethanol‐induced respiratory deficient mutants, and the ethanol tolerance of S. cerevisiae. A possible explanation of this relationship is discussed.
Expression profiling of 68 glycosyltransferase genes in 27 different human tissues by the systematic multiplex reverse transcription‐polymerase chain reaction method revealed clustering of sexually related tissues in hierarchical clustering algorithm analysis

We have developed an experimental system to study the expression of 68 human glycosyltransferase genes. Using this system, we examined the expression of those genes in 27 different tissues by the technique which we named systematic multiplex reverse transcription‐polymerase chain reaction (SM RT‐PCR). The panoramic view of a total of 1836 (68×27) expression data demonstrates that some glycosyltransferase genes are differentially expressed whereas some others are ubiquitously expressed. The data gathered provide more information on glycosyltransferase gene expression in tissues than any other paper published, and surpass in quantity all the information combined from previous publications. Although the expression profiling of glycosyltransferase genes alone may not directly explain the repertoires of oligosaccharides synthesized, it is an important step toward a better understanding of the gene expression network involved in oligosaccharide synthesis/degradation. Our modestly high‐throughput gene expression study and the data analysis using a hierarchical clustering algorithm have allowed us to investigate the correlation between tissues and glycosyltransferase gene expression. Similar patterns of glycosyltransferase gene expression were observed in functionally and anatomically related tissues. All, but one, sexually related tissues formed a cluster in a tissue dendrogram, suggesting the involvement of sex hormones in the transcriptional control of many glycosyltransferase genes. Once established, the SM RT‐PCR is cost‐ and time‐efficient and requires small amounts of RNA as template. It is especially useful for the simultaneous analyses of multiple samples. Because of its simple design, the SM RT‐PCR may offer an easy alternative in studying the expression of many other families of genes, as well as groups of related/unrelated genes, in various biological phenomena.
Apolipoprotein E phenotype and cognitive decline in a prospective study of elderly community women.

OBJECTIVE To determine whether apolipoprotein E (Apo E) phenotype is associated with cognitive decline in community-dwelling nondemented elderly women. DESIGN Prospective cohort study. SETTING A university-affiliated clinic near Pittsburgh, Pa. PATIENTS A total of 1750 nondemented community-dwelling women, aged 65 years and older, who were enrolled in the Study of Osteoporotic Fractures. MAIN OUTCOME MEASURES The women completed a baseline interview and performed 3 cognitive tests: the modified Mini-Mental State Examination, Trials B, and Digit Symbol. Serum samples were obtained for Apo E typing. Baseline cognitive scores and repeated scores approximately 6 years after study enrollment were compared in women with and without Apo E epsilon 4. Cognitive decline, defined as the worst 10th percentile change scores, was assessed for each test and by phenotype group. RESULTS After adjustment for age, education, presence of severe tremor, and depression, baseline scores did not differ by Apo E epsilon 4 status except for lower scores on Trails B in the homozygous epsilon 4 group (mean score, 159.7 compared with 127.7 for the heterozygous epsilon 4 group and 125.4 for the no epsilon 4 group; P = .01). However, repeated test performance on follow-up examination was worse on all tests in those women with 1 or more epsilon 4. Reduction on the modified Mini-Mental State Examination was 0% for no epsilon 4 allele, 1.9% for 1 epsilon 4 allele, and 3.7% for 2 epsilon 4 alleles (P < .001); reduction on Digit Symbol was 6.2% for no epsilon 4 allele, 9.0% for 1 epsilon 4 allele, and 17.5% for 2 epsilon 4 alleles (P = .04); and reduction on Trials B was 5.9% for no epsilon 4 allele, 25.0% for 1 epsilon 4 allele, and 10.9% for 2 epsilon 4 alleles (P = .002). Women with at least 1 epsilon 4 had an odds ratio of 1.6 (95% confidence interval, 1.1-2.3) of having cognitive decline during the study period. CONCLUSION Apolipoprotein E epsilon 4 is associated with cognitive decline in community-dwelling nondemented women.
Clarin-1, Encoded by the Usher Syndrome III Causative Gene, Forms a Membranous Microdomain

Clarin-1 is the protein product encoded by the gene mutated in Usher syndrome III. Although the molecular function of clarin-1 is unknown, its primary structure predicts four transmembrane domains similar to a large family of membrane proteins that include tetraspanins. Here we investigated the role of clarin-1 by using heterologous expression and in vivo model systems. When expressed in HEK293 cells, clarin-1 localized to the plasma membrane and concentrated in low density compartments distinct from lipid rafts. Clarin-1 reorganized actin filament structures and induced lamellipodia. This actin-reorganizing function was absent in the modified protein encoded by the most prevalent North American Usher syndrome III mutation, the N48K form of clarin-1 deficient in N-linked glycosylation. Proteomics analyses revealed a number of clarin-1-interacting proteins involved in cell-cell adhesion, focal adhesions, cell migration, tight junctions, and regulation of the actin cytoskeleton. Consistent with the hypothesized role of clarin-1 in actin organization, F-actin-enriched stereocilia of auditory hair cells evidenced structural disorganization in Clrn1−/− mice. These observations suggest a possible role for clarin-1 in the regulation and homeostasis of actin filaments, and link clarin-1 to the interactive network of Usher syndrome gene products.
Predicting Bankruptcy with Correlated Credit Components

In this study we suggest an original non-linear corporate credit risk model that accounts for the complete distributional properties of common observed risk modules and their corresponding estimated default threshold values. The proposed model predicts corporate bankruptcies based on the consequential interrelationships within these credit components. We illustrate the theory over a large sample of observations and further authenticate its added value when predicting business failures. Despite the relatively higher complexity involved, compared to linear credit scores or scorecards, the present scheme can serve financial institutions and other lenders to make superior lending decisions and achieve higher overall profitability.
Independent Directors and Risk Taking: Evidence from Listed US Insurance Companies

This study examines the relation of independent directors and their gender diversity, busyness, and experience with risk taking for 112 listed US insurance companies over 2003-2010. Using OLS, system GMM and 3SLS, we find that board independence, females amongst independent directors and busy boards are positively related to risk taking. While board tenure is not related to risk taking, experienced boards are found to be positively related to risk taking. Our study contributes by extending the board structure literature to show that the composition of independent board members matters for monitoring. Female independent directors, rather than simply female directors, improve board monitoring but that more than two does not. A higher percentage of non-busy directors may also mitigate the adverse effect of busy directors. Furthermore, experience gained through serving on the board improves monitoring.
GARCH models in value at risk estimation: empirical evidence from the Montenegrin stock exchange

Abstract This article considers the adequacy of generalised autoregressive conditional heteroskedasticity (GARCH) model use in measuring risk in the Montenegrin emerging market before and during the global financial crisis. In particular, the purpose of the article is to investigate whether GARCH models are accurate in the evaluation of value at risk (VaR) in emerging stock markets such as the Montenegrin market. The daily return of the Montenegrin stock market index MONEX is analysed for the period January 2004–February 2014. The motivation for this research is the desire to approach quantifying and managing risk in Montenegro more thoroughly, using methodology that has not been used for emerging markets so far. Our backtesting results showed that none of the eight models passed the Kupiec test with 95% of confidence level, while only the ARMA (autoregressive moving-average model) (1,2)–N GARCH model did not pass the Kupiec test with a confidence level of 99%. The results of the Christoffersen test revealed three models (ARMA(1,2)–TS GARCH(1,1) with a Student-t distribution of residuals, the ARMA(1,2)–T GARCH(1,1) model with a Student-t distribution of residuals, and ARMA(1,2)–EGARCH(1,1) with a reparameterised unbounded Johnson distribution [JSU] distribution of residuals) which passed the joint Christoffersen test with a 95% confidence level. It seems that these three models are appropriate for capturing volatility clustering, since all of them failed for a number of exceptions. Finally, none of the analysed models passed the Pearson’s Q test, whether with 90%, 95% or 99%.
New Techniques for Building Timing-Predictable Embedded Systems

Guan, N. 2013. New Techniques for Building Timing-Predictable Embedded Systems. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1094. 45 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-554-8797-3. Embedded systems are becoming ubiquitous in our daily life. Due to close interaction with physical world, embedded systems are typically subject to timing constraints. At design time, it must be ensured that the run-time behaviors of such systems satisfy the pre-specified timing constraints under any circumstance. In this thesis, we develop techniques to address the timing analysis problems brought by the increasing complexity of underlying hardware and software on different levels of abstraction in embedded systems design. On the program level, we develop quantitative analysis techniques to predict the cache hit/ miss behaviors for tight WCET estimation, and study two commonly used replacement policies, MRU and FIFO, which cannot be analyzed adequately using the state-of-the-art qualitative cache analysis method. Our quantitative approach greatly improves the precision of WCET estimation and discloses interesting predictability properties of these replacement policies, which are concealed in the qualitative analysis framework. On the component level, we address the challenges raised by multi-core computing. Several fundamental problems in multiprocessor scheduling are investigated. In global scheduling, we propose an analysis method to rule out a great part of impossible system behaviors for better analysis precision, and establish conditions to guarantee the bounded responsiveness of computing tasks. In partitioned scheduling, we close a long standing open problem to generalize the famous Liu and Layland's utilization bound in uniprocessor real-time scheduling to multiprocessor systems. We also propose to use cache partitioning for multi-core systems to avoid contentions on shared caches, and solve the underlying schedulability analysis problem. On the system level, we present techniques to improve the Real-Time Calculus (RTC) analysis framework in both efficiency and precision. First, we have developed Finitary Real-Time Calculus to solve the scalability problem of the original RTC due to period explosion. The key idea is to only maintain and operate on a limited prefix of each curve that is relevant to the final results during the whole analysis procedure. We further improve the analysis precision of EDF components in RTC, by precisely bounding the response time of each computation request.
A method of 3D model generation of indoor environment with Manhattan world assumption using 3D camera

In this paper, we propose a face set model generation method from 3D point clouds obtained from 3D camera for high-speed and light-weight storing and showing environment information in tele-operation task for robots. In the proposed method, following procedures run in parallel; 3 dominant orthogonal axis estimation and point cloud grouping by normal vectors based on the Manhattan - world assumption, fast registration using dominant axis grouped point cloud, plane position estimation for each dominant axis group, and face set generation by shape estimation for each plane. Experimental results shows that accuracy of plane position estimation is equivalent to measurement accuracy, registration takes about 0.1[s] for each frame, and storage size is reduced to about 10 - 20% from original 3D point cloud size. We also show some generated environment models as experimental results.
Enhanced Variational Mode Features for Hyperspectral Image Classification

Variational Mode Decomposition (VMD) is a recent method and is gaining popularity in the area of signal and image processing. The use of this decomposition technique in hyper spectral image classification is discussed in detail in this paper. The role of VMD as a feature extraction technique is exploited here. The proposed method includes an initial stage of dimensionality reduction so as to reduce the computational complexity. A final stage of recursive filtering is also added to further enhance the results. Results obtained by the proposed method on two hyper spectral image datasets –Indian Pines and Salinas-A, suggests that VMD is a promising method in the area of image analysis and classification. Quality indices used for experimental analysis include overall accuracy (OA), average accuracy (AA) and kappa coefficient. Notable classification accuracy has been obtained for both the datasets and a final stage of recursive filtering has further improved the results (more than 98% accuracy in the case of Indian Pines).
Antibody‐directed myostatin inhibition in 21‐mo‐old mice reveals novel roles for myostatin signaling in skeletal muscle structure and function

Sarcopenia is the progressive loss of skeletal muscle mass and function with advancing age, leading to reduced mobility and quality of life. We tested the hypothesis that antibody‐directed myostatin inhibition would attenuate the decline in mass and function of muscles of aged mice and that apoptosis would be reduced. Eighteen‐month‐old C57BL/6 mice were treated for 14 wk with a once‐weekly injection of saline (control, n=9) or a mouse chimera of anti‐human myostatin antibody (PF‐354, 10 mg/kg; n=12). PF‐354 prevented the age‐related reduction in body mass and increased soleus, gastrocnemius, and quadriceps muscle mass (P<0.05). PF‐354 increased fiber cross‐sectional area by 12% and enhanced maximum in situ force of tibialis anterior (TA) muscles by 35% (P<0.05). PF‐354 increased the proportion of type IIa fibers by 114% (P<0.01) and enhanced activity of oxidative enzymes (SDH) by 39% (P<0.01). PF‐354 reduced markers of apoptosis in TA muscle cross‐sections by 56% (P<0.03) and reduced caspase3 mRNA by 65% (P<0.04). Antibody‐directed myostatin inhibition attenuated the decline in mass and function of muscles of aging mice, in part, by reducing apoptosis. These observations identify novel roles for myostatin in regulation of muscle mass and highlight the therapeutic potential of antibody‐directed myostatin inhibition for sarcopenia. —Murphy, K. T. , Koopman, R. , Naim, T. , Léger, B. , Trieu, J., Ibebunjo, C. Lynch, G. S. Antibody‐directed myostatin inhibition in 21‐mo‐old mice reveals novel roles for myostatin signaling in skeletal muscle structure and function. FASEB J. 24, 4433–4442 (2010). www.fasebj. org
Are There Spillover Effects of a Family Supportive Work Environment on Employees without Childcare Responsibilities

This paper focuses on the effects of a family supportive work environment on employees’ attitudes and behaviors. We therefore differentiate between employees with childcare responsibilities and those without. As the implementation of family supportive services is financially costly, it is important to know if and how a family-friendly work policy affects the attitudes and behaviors of the entire workforce. Using a survey of results taken from 1260 randomly selected employees in Switzerland, we analyzed whether the perception of a comprehensive family orientation – involving family supportive services as well as family-friendly dialogue and culture – has an effect on employees with responsibility for childcare, for care of the elderly and also, on those without any care responsibilities. Firstly, the results show that family supportive services only have a specifically positive effect on the life satisfaction of employees with childcare responsibilities. More surprisingly, one can see that spillover effects exist for organizational-related outcomes: A family supportive dialogue and culture both reduce the intention to quit and enhance the organizational commitment of the entire workforce – whether or not there is a direct benefit to the employees.
Heterologous Expression of Mutated Eburicol 14α-Demethylase (CYP51) Proteins of Mycosphaerella graminicola To Assess Effects on Azole Fungicide Sensitivity and Intrinsic Protein Function

ABSTRACT The recent decrease in the sensitivity of the Western European population of the wheat pathogen Mycosphaerella graminicola to azole fungicides has been associated with the emergence and subsequent spread of mutations in the CYP51 gene, encoding the azole target sterol 14α-demethylase. In this study, we have expressed wild-type and mutated M. graminicola CYP51 (MgCYP51) variants in a Saccharomyces cerevisiae mutant carrying a doxycycline-regulatable tetO7-CYC promoter controlling native CYP51 expression. We have shown that the wild-type MgCYP51 protein complements the function of the orthologous protein in S. cerevisiae. Mutant MgCYP51 proteins containing amino acid alterations L50S, Y459D, and Y461H and the two-amino-acid deletion ΔY459/G460, commonly identified in modern M. graminicola populations, have no effect on the capacity of the M. graminicola protein to function in S. cerevisiae. We have also shown that the azole fungicide sensitivities of transformants expressing MgCYP51 variants with these alterations are substantially reduced. Furthermore, we have demonstrated that the I381V substitution, correlated with the recent decline in the effectiveness of azoles, destroys the capacity of MgCYP51 to complement the S. cerevisiae mutant when introduced alone. However, when I381V is combined with changes between residues Y459 and Y461, the function of the M. graminicola protein is partially restored. These findings demonstrate, for the first time for a plant pathogenic fungus, the impacts that naturally occurring CYP51 alterations have on both azole sensitivity and intrinsic protein function. In addition, we also provide functional evidence underlying the order in which CYP51 alterations in the Western European M. graminicola population emerged.
A pore‐forming toxin enables Serratia a nonlytic egress from host cells

Several pathogens co‐opt host intracellular compartments to survive and replicate, and they thereafter disperse progeny to prosper in a new niche. Little is known about strategies displayed by Serratia marcescens to defeat immune responses and disseminate afterwards. Upon invasion of nonphagocytic cells, Serratia multiplies within autophagosome‐like vacuoles. These Serratia‐containing vacuoles (SeCV) circumvent progression into acidic/degradative compartments, avoiding elimination. In this work, we show that ShlA pore‐forming toxin (PFT) commands Serratia escape from invaded cells. While ShlA‐dependent, Ca2+ local increase was shown in SeCVs tight proximity, intracellular Ca2+ sequestration prevented Serratia exit. Accordingly, a Ca2+ surge rescued a ShlA‐deficient strain exit capacity, demonstrating that Ca2+ mobilization is essential for egress. As opposed to wild‐type‐SeCV, the mutant strain‐vacuole was wrapped by actin filaments, showing that ShlA expression rearranges host actin. Moreover, alteration of actin polymerization hindered wild‐type Serratia escape, while increased intracellular Ca2+ reorganized the mutant strain‐SeCV actin distribution, restoring wild‐type‐SeCV phenotype. Our results demonstrate that, by ShlA expression, Serratia triggers a Ca2+ signal that reshapes cytoskeleton dynamics and ends up pushing the SeCV load out of the cell, in an exocytic‐like process. These results disclose that PFTs can be engaged in allowing bacteria to exit without compromising host cell integrity.
Application of molecular epidemiology to understanding campylobacteriosis in the Canterbury region of New Zealand

SUMMARY Pulsed-field gel electrophoresis genotypes of Campylobacter isolates from 603 human patients were compared with 485 isolates from retail offal (primarily chicken and lamb) to identify temporal clusters and possible sources of campylobacteriosis. Detailed epidemiological information was collected from 364 of the patients, and when combined with genotyping data allowed a putative transmission pathway of campylobacteriosis to be assigned for 88% of patients. The sources of infection were 47% food, 28% direct animal contact, 7% overseas travel, 4% person-to-person transmission and 3% water-related. A significant summer increase in campylobacteriosis cases was primarily attributed to an increase in food-related cases. Genotyping of isolates was essential for identifying the likely cause of infection for individuals. However, a more rapid and cheaper typing tool for Campylobacter is needed, which if applied to human and animal isolates on a routine basis could advance greatly our understanding of the ongoing problem of Campylobacter infection in New Zealand.
DESIGNING A PROPER HEDGE: THEORY VERSUS PRACTICE

Determining the hedge ratio based on the slope coefficient of a regression on price changes suffers from several critical shortcomings. First, it is difficult to assemble a properly constructed data set. Second, results vary depending on the length of the change interval. Third, the resulting ex post effective prices realized under this approach are wholly uncertain, ex ante. We show that when the hedge ratio is determined with reference to a regression on the respective price levels, rather than price changes, the resulting hedge ratio solution is superior in that none of these shortcomings apply.