Miracle-dz/UniFAR-FTUs huggingface dataset:
In Vitro Pharmacodynamic Characteristics of Nystatin Including Time-Kill and Postantifungal Effect

ABSTRACT Four Candida albicans isolates and six non-albicans Candida isolates were evaluated by time-kill methods to characterize the relationship between nystatin concentrations, the rate and extent of fungicidal activity, and the postantifungal effect (PAFE). Against Candida species, nystatin exhibits concentration-dependent fungicidal activity and a pronounced PAFE.
The strongest resistance of Staphylococcus aureus to erythromycin is caused by decreasing uptake of the antibiotic into the cells

The consequence of excessive use of macrolides is a high occurrence of mechanisms responsible for resistance to these drugs. Of 97 erythromycin-resistant bacterial strains gathered in the Wrocław area in Poland, 60% exhibited very high resistance, and those with the inducible MLSB (macrolide-lincosamide-streptogramin B) resistance phenotype predominated. Direct genetic investigation revealed that the erm genes coding for ribosomal methylases are the most frequently occurring erythromycin resistance-determining genes. No genetic resistance determinant was detected in 13% of the erythromycin-resistant strains. The efflux mechanism occurs in strains isolated from the nasopharyngeal cavity twice as often as in those isolated from other material, where the mechanism connected with target site modification predominates. Measurements of radiolabelled antibiotic accumulation inside bacterial cells revealed that in highly resistant strains (MIC > 1024 μg/ml), an important factor responsible for the resistance is the permeability barrier at the cell wall level. This would be a hitherto unknown mechanism of resistance to erythromycin in Staphylococcus aureus.
Predicting Fault Incidence Using Software Change History

This paper is an attempt to understand the processes by which software ages. We define code to be aged or decayed if its structure makes it unnecessarily difficult to understand or change and we measure the extent of decay by counting the number of faults in code in a period of time. Using change management data from a very large, long-lived software system, we explore the extent to which measurements from the change history are successful in predicting the distribution over modules of these incidences of faults. In general, process measures based on the change history are more useful in predicting fault rates than product metrics of the code: For instance, the number of times code has been changed is a better indication of how many faults it will contain than is its length. We also compare the fault rates of code of various ages, finding that if a module is, on the average, a year older than an otherwise similar module, the older module will have roughly a third fewer faults. Our most successful model measures the fault potential of a module as the sum of contributions from all of the times the module has been changed, with large, recent changes receiving the most weight.
Improvements in the reconstruction of time-varying gene regulatory networks: dynamic programming and regularization by information sharing among genes

METHOD Dynamic Bayesian networks (DBNs) have been applied widely to reconstruct the structure of regulatory processes from time series data, and they have established themselves as a standard modelling tool in computational systems biology. The conventional approach is based on the assumption of a homogeneous Markov chain, and many recent research efforts have focused on relaxing this restriction. An approach that enjoys particular popularity is based on a combination of a DBN with a multiple changepoint process, and the application of a Bayesian inference scheme via reversible jump Markov chain Monte Carlo (RJMCMC). In the present article, we expand this approach in two ways. First, we show that a dynamic programming scheme allows the changepoints to be sampled from the correct conditional distribution, which results in improved convergence over RJMCMC. Second, we introduce a novel Bayesian clustering and information sharing scheme among nodes, which provides a mechanism for automatic model complexity tuning. RESULTS We evaluate the dynamic programming scheme on expression time series for Arabidopsis thaliana genes involved in circadian regulation. In a simulation study we demonstrate that the regularization scheme improves the network reconstruction accuracy over that obtained with recently proposed inhomogeneous DBNs. For gene expression profiles from a synthetically designed Saccharomyces cerevisiae strain under switching carbon metabolism we show that the combination of both: dynamic programming and regularization yields an inference procedure that outperforms two alternative established network reconstruction methods from the biology literature. AVAILABILITY AND IMPLEMENTATION A MATLAB implementation of the algorithm and a supplementary paper with algorithmic details and further results for the Arabidopsis data can be downloaded from: http://www.statistik. tu-dortmund.de/bio2010.html.
The Time-Invariant Multidimensional Gaussian Sequential Rate-Distortion Problem Revisited

We revisit the sequential rate-distortion (SRD) tradeoff problem for vector-valued Gauss–Markov sources with mean-squared error distortion constraints. Our study is partly motivated by the question recently raised in the paper “Rate-cost tradeoffs in control” (in Proc. 54th Annu. Allerton Conf. Commun., Control, Comput., 2016, pp. 1157–1164) regarding the correctness of its solution algorithm known in the literature. We show via a counterexample that the dynamic reverse water-filling algorithm suggested by (15) of the paper “Stochastic linear control over a communication channel” (IEEE Trans. Autom. Control, vol. 49, pp. 1549–1561, 2004) is not applicable to this problem, and consequently, the closed-form expression of the asymptotic SRD function derived in (17) of the paper “Stochastic linear control over a communication channel” (IEEE Trans. Autom. Control, vol. 49, pp. 1549–1561, 2004) is not correct in general. Nevertheless, we show that the multidimensional Gaussian SRD function is semidefinite representable, and thus, it is readily computable.
Multi-Level Variational Autoencoder: Learning Disentangled Representations from Grouped Observations

We would like to learn a representation of the data that reflects the semantics behind a specific grouping of the data, where within a group the samples share a common factor of variation. For example, consider a set of face images grouped by identity. We wish to anchor the semantics of the grouping into a disentangled representation that we can exploit. However, existing deep probabilistic models often assume that the samples are independent and identically distributed, thereby disregard the grouping information. We present the Multi-Level Variational Autoencoder (ML-VAE), a new deep probabilistic model for learning a disentangled representation of grouped data. The ML-VAE separates the latent representation into semantically relevant parts by working both at the group level and the observation level, while retaining efficient test-time inference. We experimentally show that our model (i) learns a semantically meaningful disentanglement, (ii) enables control over the latent representation, and (iii) generalises to unseen groups.
The role of individuality in collective group movement

How different levels of biological organization interact to shape each other's function is a central question in biology. One particularly important topic in this context is how individuals' variation in behaviour shapes group-level characteristics. We investigated how fish that express different locomotory behaviour in an asocial context move collectively when in groups. First, we established that individual fish have characteristic, repeatable locomotion behaviours (i.e. median speeds, variance in speeds and median turning speeds) when tested on their own. When tested in groups of two, four or eight fish, we found individuals partly maintained their asocial median speed and median turning speed preferences, while their variance in speed preference was lost. The strength of this individuality decreased as group size increased, with individuals conforming to the speed of the group, while also decreasing the variability in their own speed. Further, individuals adopted movement characteristics that were dependent on what group size they were in. This study therefore shows the influence of social context on individual behaviour. If the results found here can be generalized across species and contexts, then although individuality is not entirely lost in groups, social conformity and group-size-dependent effects drive how individuals will adjust their behaviour in groups.
Peptide‐based leptin receptor antagonists for cancer treatment and appetite regulation

Leptin, a multifunctional hormone, controls various processes in both the central nervous system and in peripheral tissues. Because of the presence of multiple leptin/receptor (ObR) interaction sites and diverse leptin activities, the literature lacks truly monofunctional leptin protein derivatives or fragments. To date, selective ObR antagonists have not been reported. We developed short, pharmacologically advantageous peptide analogs of ObR‐binding site III of leptin that acted as selective ObR inhibitors without any partial agonistic activity. These reduced leptin‐dependent growth and signaling in cancer cell lines at picomolar and low nanomolar concentrations. In immunocompromised mice the peptides suppressed the growth of rapidly proliferating orthotopic human breast cancer xenografts by 50% when administered either intraperitoneally (i.p.) or subcutaneously (s.c.) for 38 days at a 0.1 mg/kg/day dose. The peptides were distributed to the brain, and when added to growing C57BL/6 normal mice i.p., s.c. , or orally, the lead antagonist accelerated normal weight increase without producing any toxic effects. Weight gain increases could not be observed after 10–12 days of treatment indicating that the mice became resistant to the central nervous system activity of leptin antagonists. However, in normal growing rats the intranasal administration at 0.1 mg/kg/day for 20 days resulted in a 2% net total body weight gain without signs of resistance induction. In addition to the potential of these peptides in drug development against primary and metastatic tumors and cachexia, our data confirm that resistance to leptin resides at the blood‐brain barrier. © 2010 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 96: 117–125, 2011.
Security Policy Specification and Integration in Business Collaboration

Service oriented computing (SOC) has provided a promising architectural for business collaboration. However challenging security issues concerning business collaboration have arisen because of its dynamic and loosely coupling nature. An important problem is how to specify security policies that belong to different application domains and integrate them to satisfy the requirements of the collaboration. In this paper we will provide analysis on authorization policy requirements for business collaboration, collaboration patterns and various security comparability and integration issues. We believe it is a first step toward a framework for modeling, specifying and handling authorization control for business collaboration.
Sociodemographic and Economic Determinants of Overweight and Obesity for Public-school Children in Geneva State, Switzerland: A Cross-sectional Study

Background: Obesity among children and adolescents is a growing public health problem. The purpose of this study is to assess the prevalence, socioeconomic and demographic determinants of overweight and obesity in schoolchildren from Geneva. Methods: A cross-sectional study was undertaken at the Public School of Geneva canton in Switzerland. A total of 8544 public school children were collected and analyzed: 2577 were in second grade, 2641 in fifth grade and 3326 in eighth grade. To identify overweight and obesity we used the definition issued by the International Obesity Task Force. Child characteristics included gender, age, socioeconomic status (SES) of father and mother, and school grade. The multivariate logistic regression model was used to examine potential predictors of overweight/obesity. Results: The prevalence of overweight or obese children was 14.4% in second grade, 17.3% in fifth grade and 18.6% in eighth grade. Multivariate logistic regression analyses reveal that children that have a low economic status or certain citizenships are more likely to be overweight or obese. Children of Kosovar origin, have a higher risk of OBO in second grade (adjusted odds ratio [OR] = 2.19; 95% confidence interval [CI]: 1.20–4.00), fifth grade (adjusted OR = 2.36 95% CI: 1.27–4.39) and in eighth grade (adjusted OR = 2.15 95% CI: 1.27–4.39). Association between SES and overweight was high with regards to the father's SES in fifth grade (adjusted OR = 4.21 95% CI: 2.83–6.25). Conclusions: Overweight and obesity is associated to socioeconomic and sociodemographic factors. The analyzes reveals that children with a low economic status and/or from certain countries are more likely to be overweight or obese than Swiss children. There is an urgent need for action to prevent further increase in overweight or obesity among children.
Enrichment of an intraspecific genetic map of upland cotton by developing markers using parental RAD sequencing

RAD sequencing was performed using DH962 and Jimian5 as upland cotton mapping parents. Sequencing data for DH962 and Jimian5 were assembled into the genome sequences of ≈55.27 and ≈57.06 Mb, respectively. Analysing genome sequences of the two parents, 1,323 SSR, 3,838 insertion/deletion (InDel), and 9,366 single-nucleotide polymorphism (SNP) primer pairs were developed. All of the SSRs, 121 InDels, 441 SNPs, and other 6,747 primer pairs were screened in the two parents, and a total of 535 new polymorphic loci were identified. A genetic map including 1,013 loci was constructed using these results and 506 loci previously published for this population. Twenty-seven new QTLs for yield and fibre quality were identified, indicating that the efficiency of QTL detection was greatly improved by the increase in map density. Comparative genomics showed there to be considerable homology and collinearity between the AT and A2 genomes and between the DT and D5 genomes, although there were a few exchanges and introgressions among the chromosomes of the A2 genome. Here, the development of markers using parental RAD sequencing was effective, and a high-density intraspecific genetic map was constructed. This map can be used for molecular marker-assisted selection in cotton.
The New Regionalism in the Americas: The Case of MERCOSUR

This paper takes seriously the recent claim made by Ethier [1998] that the "New Regionalism" reflects the success of the multilateral trading system, not its failure. In fact, the New Regionalism represents a qualitative departure of the old regionalism in several respects, in particular, its development has taken place in a very different international economic environment. Moreover, the traditional Vinerian paradigm is no longer the primary analytical framework for its evaluation. We use this novel approach to analyze the case of one of the most important experiences in regional integration, the formation of the "Mercado Común del Sur" (MERCOSUR). The paper carefully documents the main stylized facts of the development of MERCOSUR arguing that this makes this type of agreement a prime example of the New Regionalism. Then, using a simple Krugman trade model with tariff distortions we show the positive welfare effects on member and non-member countries of these types of agreements. Our conclusions are consistent with Ethier's paper, that is, regionalism can play a key role in expanding and preserving the liberal trade order.
Comparing robotic, laparoscopic and open cystectomy: a systematic review and meta-analysis.

OBJECTIVE To conduct a systematic review and meta-analysis comparing outcomes between Open Radical Cystectomy (ORC), Laparoscopic Radical Cystectomy (LRC) and Robot-assisted Radical Cystectomy (RARC). RARC is to be compared to LRC and ORC and LRC compared to ORC. MATERIAL AND METHODS A systematic review of the literature was conducted, collating studies comparing RARC, LRC and ORC. Surgical and oncological outcome data were extracted and a meta-analysis was performed. RESULTS Twenty-four studies were selected with total of 2,104 cases analyzed. RARC had a longer operative time (OPT) compared to LRC with no statistical difference between length of stay (LOS) and estimated blood loss (EBL). RARC had a significantly shorter LOS, reduced EBL, lower complication rate and longer OPT compared to ORC. There were no significant differences regarding lymph node yield (LNY) and positive surgical margins (PSM.) LRC had a reduced EBL, shorter LOS and increased OPT compared to ORC. There was no significant difference regarding LNY. CONCLUSION RARC is comparable to LRC with better surgical results than ORC. LRC has better surgical outcomes than ORC. With the unique technological features of the robotic surgical system and increasing trend of intra-corporeal reconstruction it is likely that RARC will become the surgical option of choice.
Characterization of a Schwann cell neurite‐promoting activity that directs motoneuron axon outgrowth

Schwann cells support and facilitate axonal growth during development and successful regeneration in the peripheral nerve. In the regenerating rat sciaticnerve, Schwann cells provide a trophic milieu for primary sensory, sympathetic, and motoneurons. We have characterized a neurotrophic activity produced by adult rat sciatic nerve Schwann cells and a spontaneously immortal Schwann cell clone (iSC). This activity elicits neurite outgrowth from chick embryo explants of both CNS and PNS. The iSC activity has been concentrated by cation‐exchange chromatography and compared to known neurotrophins in bioassay. Pooled bound fractions elicit neurite outgrowth from sympathetic, ciliary and motoneurons. In collagen matrix cocultures of iSC and E4 ventral horn(before motor axon extension to muscle targets), the iSC activity can direct the initial axonal extension from motoneurons. The data presented suggest that Schwann cell‐produced activity may mediate motoneuron axonal extension before contact with their peripheral source of neurotrophin. © 1994 Wiley‐Liss, Inc.
Use of Bacterially Expressed dsRNA to Downregulate Entamoeba histolytica Gene Expression

Background Modern RNA interference (RNAi) methodologies using small interfering RNA (siRNA) oligonucleotide duplexes or episomally synthesized hairpin RNA are valuable tools for the analysis of gene function in the protozoan parasite Entamoeba histolytica. However, these approaches still require time-consuming procedures including transfection and drug selection, or costly synthetic molecules. Principal Findings Here we report an efficient and handy alternative for E. histolytica gene down-regulation mediated by bacterial double-stranded RNA (dsRNA) targeting parasite genes. The Escherichia coli strain HT115 which is unable to degrade dsRNA, was genetically engineered to produce high quantities of long dsRNA segments targeting the genes that encode E. histolytica β-tubulin and virulence factor KERP1. Trophozoites cultured in vitro were directly fed with dsRNA-expressing bacteria or soaked with purified dsRNA. Both dsRNA delivery methods resulted in significant reduction of protein expression. In vitro host cell-parasite assays showed that efficient downregulation of kerp1 gene expression mediated by bacterial dsRNA resulted in significant reduction of parasite adhesion and lytic capabilities, thus supporting a major role for KERP1 in the pathogenic process. Furthermore, treatment of trophozoites cultured in microtiter plates, with a repertoire of eighty-five distinct bacterial dsRNA segments targeting E. histolytica genes with unknown function, led to the identification of three genes potentially involved in the growth of the parasite. Conclusions Our results showed that the use of bacterial dsRNA is a powerful method for the study of gene function in E. histolytica. This dsRNA delivery method is also technically suitable for the study of a large number of genes, thus opening interesting perspectives for the identification of novel drug and vaccine targets.
Production of slow-released nitrogen fertilizer from urine

Human excreta, especially urine is rich in nitrogen that can be utilized for agricultural purposes, while the slow-release fertilizer allows effective utilization of nutrients in agricultural production. The direct formation of slow-release fertilizer – methylene urea – from urine was being proposed in this study. The experiments were tried to prove formation of methylene urea from human urine, and to investigate the effect of pH and salt concentration on the reaction rate. The synthetic urine and real urine were used for the urea source of the reaction. As a result, the precipitates were prepared from synthetic urine, while the small molecule fractions generated then they grew into precipitate. The nuclear magnetic resonance, infrared spectroscopy, element analyses showed the precipitates in synthetic urine were the same compound found in the urea solution, which was methylene urea. The reaction rate was high at low pH value. The reaction rate in the buffer solution was lower than the synthetic urine at the same pH, because some salts may work as a catalyst. The urea concentration reduction rate in real urine showed the same trend with synthetic urine at the same pH, while the precipitation was quite similar to methylene urea.
Circadian Rhythms of Granzyme B, Perforin, IFN-γ, and NK Cell Cytolytic Activity in the Spleen: Effects of Chronic Ethanol1

Recent studies show that alterations in the body’s biological rhythms can lead to serious pathologies, including cancer. Acute and chronic ethanol consumption impairs the immune system by causing specific defects in the cellular components of the innate immune response and by creating increased risk and susceptibility to infections and cancer. NK cells are critical for immune surveillance against infected and malignant cells. To assess whether NK cell function follows a circadian trend and to determine ethanol effects on this rhythm, we measured, over a 24-h period, mRNA and protein levels of granzyme B, perforin, and the cytokine IFN-γ, as well as NK cell activity, in the splenocytes of ad libitum-fed, pair-fed, and ethanol-fed Sprague Dawley male rats. Circadian rhythms were found in mRNA and protein levels of granzyme B, perforin, and IFN-γ. A circadian pattern was also detected in NK cell cytolytic activity. Our data further demonstrated how chronic ethanol suppressed NK cell activity by directly disrupting the circadian rhythms of granzyme B, perforin, and IFN-γ. These findings identify the circadian functions of splenic NK cells and show the vulnerability of these rhythms to chronic ethanol.