Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic Study of Polyketide Synthases and Nonribosomal Peptide Synthetases Involved in the Biosynthesis of Mycotoxins

Polyketide synthase (PKSs) and nonribosomal peptide synthetase (NRPSs) are large multimodular enzymes involved in biosynthesis of polyketide and peptide toxins produced by fungi. Furthermore, hybrid enzymes, in which a reducing PKS region is fused to a single NRPS module, are also responsible of the synthesis of peptide-polyketide metabolites in fungi. The genes encoding for PKSs and NRPSs have been exposed to complex evolutionary mechanisms, which have determined the great number and diversity of metabolites. In this study, we considered the most important polyketide and peptide mycotoxins and, for the first time, a phylogenetic analysis of both PKSs and NRPSs involved in their biosynthesis was assessed using two domains for each enzyme: β-ketosynthase (KS) and acyl-transferase (AT) for PKSs; adenylation (A) and condensation (C) for NRPSs. The analysis of both KS and AT domains confirmed the differentiation of the three classes of highly, partially and non-reducing PKSs. Hybrid PKS-NRPSs involved in mycotoxins biosynthesis grouped together in the phylogenetic trees of all the domains analyzed. For most mycotoxins, the corresponding biosynthetic enzymes from distinct fungal species grouped together, except for PKS and NRPS involved in ochratoxin A biosynthesis, for which an unlike process of evolution could be hypothesized in different species.
VP Ellipsis and Contextual Interpretation

A computational account of VP ellipsis is described, in which VP's are represented in the discourse model as contextually dependent semantic objects. It is argued that this approach can handle examples that are not allowed by alternative accounts. An implementation is defined in terms of extensions to the Incremental Interpretation System. The treatment of VP ellipsis is analogous to that of pronominal anaphora. It is suggested that the recency and salience constraints commonly thought to apply to pronominal anaphora might apply in a similar way to VP ellipsis.
Zebrafish: genomics on the fast track.

The zebrafish (Danio rerio) has proven its worth as an excellent model system for the study of vertebrate development. In 1996, in an issue of the journal Development, the results of the characterization of almost 2000 mutations derived from two screens of ENU-mutagenized zebrafish (Driever et al. 1996; Haffter et al. 1996) were reported in 36 articles (Vol. 123, Dec. 1996). The same issue, however, included only one article describing the generation of reagents for genomic analysis that will be required for the positional cloning and characterization of these newly identified developmental anomalies (Knapik et al. 1996). Since then, remarkable progress has been made in zebrafish genomics, based largely on technology that has been developed for mammalian genetic analysis. The rapid implementation of these techniques, which will enable the characterization of the large set of zebrafish mutations, speaks to the utility of research that aims to develop resources for a community of investigators rather than to test a specific hypothesis. The use of saturation mutagenesis in zebrafish as a means to study vertebrate development has evolved from a convergence of diverse experimental approaches. Saturation mutagenesis of Drosophila has been used with extraordinary success to identify abnormalities in early embryonic patterning. The fact that mutations in mammalian homologs of these genes often have profound developmental consequences demonstrates that many of these basic pathways have been maintained in highly divergent organisms. A similar analysis in vertebrates was proposed as a means to uncover additional loci of developmental importance, especially those affecting formation of internal organs, which are not effectively scored in Drosophila embryonic screens (Nusslein-Volhard 1994). Zebrafish are particularly well-suited for this purpose, as they generate large numbers of transparent embryos that develop synchronously to a free-swimming hatchling in a period of 3 days (for review, see Driever et al. 1994). Zebrafish have an additional experimental advantage that has been exploited successfully for the purpose of genetic analysis. Based largely on the studies of George Streisinger, a variety of techniques can be used to manipulate the ploidy and parental origin of genes in zebrafish (Streisinger et al. 1981, 1986). For example, gynogenetic haploid embryos can be generated by fertilization of secondary oocytes with UV-irradiated sperm; these embryos develop to hatching, albeit with specific developmental abnormalities. It is also possible to generate both fully homozygous diploid adults, and ‘‘half-tetrad’’ diploid adults, which are partially homozygous (for review, see Postlethwait and Talbot 1997). The uses of these various genetic ‘‘tricks’’ for genetic mapping are outlined in Box 1.
eb 2 00 0 Boson Stars as Gravitational Lenses

We discuss boson stars as possible gravitational lenses and study the lensing effect by these objects made of scalar particles. The mass and the size of a boson star may vary from an individual Newtonian object similar to the Sun to the general relativistic size and mass of a galaxy close to its Schwarzschild radius. We assume boson stars to be transparent which allows the light to pass through them though the light is gravitationally deflected. We assume boson stars of the mass M = 10M⊙ to be on noncosmological distance from the observer. We discuss the lens equation for these stars as well as the details of magnification. We find that there are typically three images of a star but the deflection angles may vary from arcseconds to even degrees. There is one tangential critical curve (Einstein ring) and one radial critical curve for tangential and radial magnification, respectively. Moreover, the deflection angles for the light passing in the gravitational field of boson stars can be very large (even of the order of degrees) which reflects the fact they are very strong relativistic objects. We derive a suitable formula for the lens equation for such large deflection angles. Although the large deflection angle images are highly demagnified, their existence in the area of the tangential critical curve may help in observational detection of suitable lenses possessing characteristic features of boson stars which could also serve as a direct evidence for scalar fields in the universe. Subject headings: gravitational lensing — gravitation — stars: general
On Rates of Convergence for Stochastic Optimization Problems Under Non--Independent and Identically Distributed Sampling

In this paper we discuss the issue of solving stochastic optimization problems by means of sample average approximations. Our focus is on rates of convergence of estimators of optimal solutions and optimal values with respect to the sample size. This is a well-studied problem in case the samples are independent and identically distributed (i.e., when standard Monte Carlo simulation is used); here we study the case where that assumption is dropped. Broadly speaking, our results show that, under appropriate assumptions, the rates of convergence for pointwise estimators under a sampling scheme carry over to the optimization case, in the sense that convergence of approximating optimal solutions and optimal values to their true counterparts has the same rates as in pointwise estimation. We apply our results to two well-established sampling schemes, namely, Latin hypercube sampling and randomized quasi-Monte Carlo (QMC). The novelty of our work arises from the fact that, while there has been some work on the use of variance reduction techniques and QMC methods in stochastic optimization, none of the existing work—to the best of our knowledge—has provided a theoretical study on the effect of these techniques on rates of convergence for the optimization problem. We present numerical results for some two-stage stochastic programs from the literature to illustrate the discussed ideas.
Inventory survival analysis for semiconductor memory manufacturing

The high variety of and intermittent demand for semiconductor memory products frequently limits the use of forecast error normalization in estimating inventory. Inventory turnover is a practical performance indicator that is used to calculate the number of days for which a company retains inventory before selling a product. Although previous studies on inventory level settings have primarily applied information regarding demand variability and forecast error, few studies have investigated the inventory turnover for inventory decisions. Inventory turnover data are time scaled, suited for a small sample, and right censored to fit the input of survival analysis. In this study, a model in which inventory turnover and survival analysis were integrated was developed to estimate the production inventory survival function used to determine inventory level. Data analysis results based on real settings indicated the viability of using inventory survival analysis to determine semiconductor memory inventory level settings.
On the Structure and Function of the Phytoene Desaturase CRTI from Pantoea ananatis, a Membrane-Peripheral and FAD-Dependent Oxidase/Isomerase

CRTI-type phytoene desaturases prevailing in bacteria and fungi can form lycopene directly from phytoene while plants employ two distinct desaturases and two cis-tans isomerases for the same purpose. This property renders CRTI a valuable gene to engineer provitamin A-formation to help combat vitamin A malnutrition, such as with Golden Rice. To understand the biochemical processes involved, recombinant CRTI was produced and obtained in homogeneous form that shows high enzymatic activity with the lipophilic substrate phytoene contained in phosphatidyl-choline (PC) liposome membranes. The first crystal structure of apo-CRTI reveals that CRTI belongs to the flavoprotein superfamily comprising protoporphyrinogen IX oxidoreductase and monoamine oxidase. CRTI is a membrane-peripheral oxidoreductase which utilizes FAD as the sole redox-active cofactor. Oxygen, replaceable by quinones in its absence, is needed as the terminal electron acceptor. FAD, besides its catalytic role also displays a structural function by enabling the formation of enzymatically active CRTI membrane associates. Under anaerobic conditions the enzyme can act as a carotene cis-trans isomerase. In silico-docking experiments yielded information on substrate binding sites, potential catalytic residues and is in favor of single half-site recognition of the symmetrical C40 hydrocarbon substrate.
6-PACK programme to decrease fall injuries in acute hospitals: cluster randomised controlled trial

Objective To evaluate the effect of the 6-PACK programme on falls and fall injuries in acute wards. Design Cluster randomised controlled trial. Setting Six Australian hospitals. Participants All patients admitted to 24 acute wards during the trial period. Interventions Participating wards were randomly assigned to receive either the nurse led 6-PACK programme or usual care over 12 months. The 6-PACK programme included a fall risk tool and individualised use of one or more of six interventions: “falls alert” sign, supervision of patients in the bathroom, ensuring patients’ walking aids are within reach, a toileting regimen, use of a low-low bed, and use of a bed/chair alarm. Main outcome measures The co-primary outcomes were falls and fall injuries per 1000 occupied bed days. Results During the trial, 46 245 admissions to 16 medical and eight surgical wards occurred. As many people were admitted more than once, this represented 31 411 individual patients. Patients’ characteristics and length of stay were similar for intervention and control wards. Use of 6-PACK programme components was higher on intervention wards than on control wards (incidence rate ratio 3.05, 95% confidence interval 2.14 to 4.34; P<0.001). In all, 1831 falls and 613 fall injuries occurred, and the rates of falls (incidence rate ratio 1.04, 0.78 to 1.37; P=0.796) and fall injuries (0.96, 0.72 to 1.27; P=0.766) were similar in intervention and control wards. Conclusions Positive changes in falls prevention practice occurred following the introduction of the 6-PACK programme. However, no difference was seen in falls or fall injuries between groups. High quality evidence showing the effectiveness of falls prevention interventions in acute wards remains absent. Novel solutions to the problem of in-hospital falls are urgently needed. Trial registration Australian New Zealand Clinical Trials Registry ACTRN12611000332921.
Global patterns of freshwater species diversity, threat and endemism

Aim Global-scale studies are required to identify broad-scale patterns in the distributions of species, to evaluate the processes that determine diversity and to determine how similar or different these patterns and processes are among different groups of freshwater species. Broad-scale patterns of spatial variation in species distribution are central to many fundamental questions in macroecology and conservation biology. We aimed to evaluate how congruent three commonly used metrics of diversity were among taxa for six groups of freshwater species. Location Global. Methods We compiled geographical range data on 7083 freshwater species of mammals, amphibians, reptiles, fishes, crabs and crayfish to evaluate how species richness, richness of threatened species and endemism are distributed across freshwater ecosystems. We evaluated how congruent these measures of diversity were among taxa at a global level for a grid cell size of just under 1°. Results We showed that although the risk of extinction faced by freshwater decapods is quite similar to that of freshwater vertebrates, there is a distinct lack of spatial congruence in geographical range between different taxonomic groups at this spatial scale, and a lack of congruence among three commonly used metrics of biodiversity. The risk of extinction for freshwater species was consistently higher than for their terrestrial counterparts. Main conclusions We demonstrate that broad-scale patterns of species richness, threatened-species richness and endemism lack congruence among the six freshwater taxonomic groups examined. Invertebrate species are seldom taken into account in conservation planning. Our study suggests that both the metric of biodiversity and the identity of the taxa on which conservation decisions are based require careful consideration. As geographical range information becomes available for further sets of species, further testing will be warranted into the extent to which geographical variation in the richness of these six freshwater groups reflects broader patterns of biodiversity in fresh water.
Learning Path Queries on Graph Databases

We investigate the problem of learning graph queries by exploiting user examples. The input consists of a graph database in which the user has labeled a few nodes as positive or negative examples, depending on whether or not she would like the nodes as part of the query result. Our goal is to handle such examples to find a query whose output is what the user expects. This kind of scenario is pivotal in several application settings where unfamiliar users need to be assisted to specify their queries. In this paper, we focus on path queries defined by regular expressions, we identify fundamental difficulties of our problem setting, we formalize what it means to be learnable, and we prove that the class of queries under study enjoys this property. We additionally investigate an interactive scenario where we start with an empty set of examples and we identify the informative nodes i.e., those that contribute to the learning process. Then, we ask the user to label these nodes and iterate the learning process until she is satisfied with the learned query. Finally, we present an experimental study on both real and synthetic datasets devoted to gauging the effectiveness of our learning algorithm and the improvement of the interactive approach.
Verfahren zur Charakterisierung und Modellierung von Lithium-Ionen Zellen

In dieser Arbeit werden neue Verfahren zur Charakterisierung des elektrochemischen und thermischen Verhaltens von Lithium-Ionen Zellen vorgestellt. Basierend auf diesen wird ein Modellansatz vorgestellt, der das Zellverhalten in vier Domanen (statisch und dynamisch fur elektrochemisches und thermisches Verhalten) getrennt abzubilden vermag. Hierdurch wird die Ubertragbarkeit auf verschiedenste Materialchemien, skalierbare Genauigkeit und eine automatisierbare Parametrierung moglich.
The role of invasive trophoblast in implantation and placentation of primates

We here review the evolution of invasive placentation in primates towards the deep penetration of the endometrium and its arteries in hominoids. The strepsirrhine primates (lemurs and lorises) have non-invasive, epitheliochorial placentation, although this is thought to be derived from a more invasive type. In haplorhine primates, there is differentiation of trophoblast at the blastocyst stage into syncytial and cellular trophoblast. Implantation involves syncytiotrophoblast that first removes the uterine epithelium then consolidates at the basal lamina before continuing into the stroma. In later stages of pregnancy, especially in Old World monkeys and apes, cytotrophoblast plays a greater role in the invasive process. Columns of trophoblast cells advance to the base of the implantation site where they spread out to form a cytotrophoblastic shell. In addition, cytotrophoblasts advance into the lumen of the spiral arteries. They are responsible for remodelling these vessels to form wide, low-resistance conduits. In human and great apes, there is additional invasion of the endometrium and its vessels by trophoblasts originating from the base of the anchoring villi. Deep trophoblast invasion that extends remodelling of the spiral arteries to segments in the inner myometrium evolved in the common ancestor of gorilla, chimp and human.
Endoscopic therapy for organized pancreatic necrosis.

BACKGROUND & AIMS The treatment of patients with extensive pancreatic necrosis remains controversial; a subpopulation of patients with extensive acute pancreatic necrosis develop complex, organized collections. This study examined the feasibility of endoscopic drainage in patients with extensive organized pancreatic necrosis. METHODS Eleven patients with organized pancreatic necrosis (8 sterile and 3 infected) after severe acute necrotizing pancreatitis underwent attempted endoscopic drainage. Dynamic contrast-enhanced computerized tomography showed > or = 50% pancreatic necrosis in 10 of 11 patients in whom endoscopic drainage was performed. In 8 patients, an intrapancreatic nasobiliary lavage catheter was placed into the collection concurrently with 10F stents. RESULTS Complete resolution was achieved nonoperatively in 9 patients. At a mean follow-up of 12 months, 1 patient developed a pseudocyst, which was successfully drained endoscopically. Complications occurred in 5, including bleeding that precluded entry into one collection. CONCLUSIONS Endoscopic therapy may be a viable management option for a subset of patients who remain symptomatic after an episode of acute pancreatic necrosis after the necrosis has become organized and partially liquefied. Intrapancreatic lavage catheter placement is essential to the success of this procedure. Further evaluation of this technique is needed before this method can be adopted into clinical practice.
The effect of the use of different selective media on the ability to recover salmonellae from seagull faeces

SUMMARY Solid media were compared for their ability to recover salmonellae from seagull faecal material after pro-enrichment in buffered peptone water and enrichment in Rappaport's broth. Of the 847 specimens examined 96 were found to be positive for salmonellae. Use of Brilliant Green agar containing sulphamandelate supplement resulted in the detection of salmonellae from each of the 96 samples found to be positive and was the most efficient medium tested. Brilliant Green agar lacking the supplement was the least effective medium, salmonellae being isolated from only 80 samples using this medium. All of the media tested were shown to support the growth of a wide range of salmonella serotypes, although Salmonella typhi and S. dublin did not form colonies on those media which contained Brilliant Green. Hynes' modification of deoxycholate citrate agar was shown to be considerably less inhibitory to salmonellae after ageing for four days. Ageing of other media had no significant affect on their ability to support the growth of salmonellae.
Quantitative analysis for computation delay induced by network coding

Quantitative complexity of network coding as well as its computation delay on a node is presented in this paper. First, quantitative complexity of four fundamental calculation operations were analyzed. Based on that, quantitative complexity of encoding, decoding as well as independence detection for network coding were given theoretically. At last, the experimental results showed our quantitative results of computation delay have the same order to the delay of practical network coding on a node.
[Ureaplasma urealyticum infection affects sperm plasma membrane integrity in infertile men].

OBJECTIVE To determine the impact of Ureaplasma urealyticum (Uu) infection on the integrity of sperm plasma membrane in infertile males. METHODS Sixty-three semen samples were divided into a Uu infection group (n = 32) and a normal control group (n = 31). Conventional semen analyses were performed by computer-assisted semen analysis (CASA) and Uu detected by the culture method. The semen samples were washed with PBS and dyed by SYBR-14/PI double fluorescent staining, followed by detection of the integrity of sperm plasma membrane by flow cytometry. The percentage of the sperm with intact plasma membrane was indicated as the percentage of sperm emitting green fluorescence (SYBR-14+/PI-%). RESULTS The Uu infection group showed a significantly decreased integrity of sperm plasma membrane ([45.14 +/- 10.69]%) and reduced percentage of grade a + b sperm ([23.29 +/- 8.81]%) as compared with the normal control group ([72.68 +/- 9.91]% and [46.32 +/- 9.54]%) (P < 0.01). But there were no significant differences in the semen volume, pH value, and sperm concentration between the two groups (P > 0.05). CONCLUSION Uu infection decreases the integrity of sperm plasma membrane, which might be an important factor of male infertility.
Purvalanol A, a CDK inhibitor, effectively suppresses Src‐mediated transformation by inhibiting both CDKs and c‐Src

The nonreceptor tyrosine kinase c‐Src is frequently over‐expressed or hyperactivated in various human cancers and contributes to cancer progression in cooperation with up‐regulated growth factor receptors. However, Src‐selective anticancer drugs are still in clinical trials. To identify more effective inhibitors of c‐Src‐mediated cancer progression, we developed a new screening platform using Csk‐deficient cells that can be transformed by c‐Src. We found that purvalanol A, developed as a CDK inhibitor, potently suppressed the anchorage‐independent growth of c‐Src‐transformed cells, indicating that the activation of CDKs contributes to the c‐Src transformation. We also found that purvalanol A suppressed the c‐Src activity as effectively as the Src‐selective inhibitor PP2, and that it reverted the transformed morphology to a nearly normal shape with less cytotoxicity than PP2. Purvalanol A induced a strong G2‐M arrest, whereas PP2 weakly acted on the G1‐S transition. Furthermore, when compared with PP2, purvalanol A more effectively suppressed the growth of human colon cancer HT29 and SW480 cells, in which Src family kinases and CDKs are activated. These findings demonstrate that the coordinated inhibition of cell cycle progression and tyrosine kinase signaling by the multi‐selective purvalanol A is effective in suppressing cancer progression associated with c‐Src up‐regulation.