Miracle-dz/UniFAR-FTUs huggingface dataset:
The cis-Acting Family of Repeats Can Inhibit as well as Stimulate Establishment of an oriPReplicon

ABSTRACT Previously we have shown that the establishment of anoriP replicon is dependent on its epigenetic modification, which occurs in only 1 to 10% of proliferating cells (E. R. Leight and B. Sugden, Mol. Cell. Biol. 21:4149–4161, 2001). To gain insights into the cis-acting requirements for the establishment of oriP replicons, we monitored the replication of oriP plasmid derivatives for several weeks following their introduction into cells. In EBNA-1-positive 143B and H1299 cells, plasmids containing only the region of dyad symmetry (DS) of oriP replicated but were lost more rapidly from cells than were oriP plasmids, demonstrating that the family of repeats (FR) of oriP acts in cis to stimulate replication in these cells. Unexpectedly, we found that the DS plasmid was established efficiently in 293/EBNA-1 cells, being lost at a rate of only 8% per cell generation over 24 days posttransfection. However, plasmids containing the FR in addition to the DS of oriPreplicated but were lost at a rate of approximately 30% per cell generation in 293/EBNA-1 cells, indicating that the FR inhibitsoriP's establishment in this cell line. FR's enhancement of transcription of a promoter in cis and FR's ability to inhibit replication fork movement do not account solely fororiP's inefficient establishment. In addition, DNA looping between FR and DS neither stimulates nor inhibits replication. Deletion of 11 EBNA-1 binding sites in the FR or replacement of the FR with DS sequences, however, does overcome the inhibitory activity of the FR, thereby allowing efficient establishment of the oriPderivative in 293/EBNA-1 cells.
Biometrics in social grants: Separating myth from reality

The South African government provides a social assistance programme that pays out monetary grants to qualifying persons. In 2012, the South African Social Security Agency (SASSA) who manages these social grants, instituted a new form of identification that required the capturing of biometric features such as fingerprints and voice samples, to better identify the grant recipients in order to reduce fraud. This paper describes the development of a framework for an appropriate implementation of biometrics for the social grant programme taking into account the security requirements as well as the vulnerability of the grant recipients.
Shifting concepts in rectal cancer management

The management of rectal cancer has transformed over the last 3 decades and continues to evolve. Some of these changes parallel progress made with other cancers: refinement of surgical technique to improve organ preservation, selective use of neoadjuvant (and adjuvant) therapy, and emergence of criteria suggesting a role for individually tailored therapy. Other changes are driven by fairly unique issues including functional considerations, rectal anatomic features, and surgical technical issues. Further complexity is due to the variety of staging modalities (each with its own limitations), neoadjuvant treatment alternatives, and competing strategies for sequencing multimodal treatment even for nonmetastatic disease. Importantly, observations of tumor response made in the era of neoadjuvant therapy are reshaping some traditionally held concepts about tumor behavior. Frameworks for prioritizing and integrating complex data can help to formulate treatment plans for patients. CA Cancer J Clin 2012;. © 2012 American Cancer Society.
Statistical state dynamics-based analysis of the physical mechanisms sustaining and regulating turbulence in Couette flow

This paper describes a study of the self-sustaining process in wall-turbulence based on a second order statistical state dynamics (SSD) model of Couette flow. SSD models with this form are referred to as S3T models and self-sustain turbulence with a mean flow and second order perturbation structure similar to that obtained by DNS. The use of a SSD model to study the physical mechanisms underlying turbulence has advantages over the traditional approach of studying the dynamics of individual realizations of turbulence. One advantage is that the analytical structure of SSD isolates and directly expresses the interaction between the coherent mean flow and the incoherent perturbation components of the turbulence. Isolation of the interaction between these components reveals how this interaction underlies both the maintenance of the turbulence variance by transfer of energy from the externally driven flow to the perturbation components as well as the enforcement of the observed statistical mean turbulent state by feedback regulation between the mean and perturbation fields. Another advantage of studying turbulence using SSD models is that the analytical structure of S3T turbulence can be completely characterized. For example, turbulence in the S3T system is maintained by a parametric growth mechanism. Furthermore, the equilibrium statistical state of the turbulence can be demonstrated to be enforced by feedback regulation in which transient growth of the incoherent perturbations episodically suppresses coherent streak growth preventing runaway parametric growth of the incoherent turbulent component. Using S3T to isolate these parametric growth and feedback regulation mechanisms allows a detailed characterization of the dynamics of the self-sustaining process in S3T turbulence with compelling implications for understanding the mechanism of wall-turbulence.
Old Lineage on an Old Island: Pixibinthus, a New Cricket Genus Endemic to New Caledonia Shed Light on Gryllid Diversification in a Hotspot of Biodiversity

Few studies have focused on the early colonization of New Caledonia by insects, after the re-emergence of the main island, 37 Myr ago. Here we investigate the mode and tempo of evolution of a new endemic cricket genus, Pixibinthus, recently discovered in southern New Caledonia. First we formally describe this new monotypic genus found exclusively in the open shrubby vegetation on metalliferous soils, named ‘maquis minier’, unique to New Caledonia. We then reconstruct a dated molecular phylogeny based on five mitochondrial and four nuclear loci in order to establish relationships of Pixibinthus within Eneopterinae crickets. Pixibinthus is recovered as thesister clade of the endemic genus Agnotecous, mostly rainforest-dwellers. Dating results show that the island colonization by their common ancestor occurred around 34.7 Myr, shortly after New Caledonia re-emergence. Pixibinthus and Agnotecous are then one of the oldest insect lineages documented so far for New Caledonia. This discovery highlights for the first time two clear-cut ecological specializations between sister clades, as Agnotecous is mainly found in rainforests with 19 species, whereas Pixibinthus is found in open habitats with a single documented species. The preference of Pixibinthus for open habitats and of Agnotecous for forest habitats nicely fits an acoustic specialization, either explained by differences in body size or in acoustic properties of their respective habitats. We hypothesize that landscape dynamics, linked to major past climatic events and recent change in fire regimes are possible causes for both present-day low diversity and rarity in genus Pixibinthus. The unique evolutionary history of this old New Caledonian lineage stresses the importance to increase our knowledge on the faunal biodiversity of ‘maquis minier’, in order to better understand the origin and past dynamics of New Caledonian biota.
Breastfeeding and wheeze prevalence in pre‐schoolers and pre‐adolescents: the Genesis and Healthy Growth studies

To date, extensive research has been undertaken on a potential link of breastfeeding (BF) to wheezing illnesses. Nevertheless, an association remains to be established, partly due to age‐dependent discrepancies and different definitions of exposures/outcomes across studies. We thus investigated the relation of diverse infantile feeding patterns with wheeze/asthma prevalence in two cohorts of children of different ages (preschool and preadolescent).
Efficacy of Nitazoxanide againstCryptosporidium parvum in Cell Culture and in Animal Models

ABSTRACT Nitazoxanide (NTZ), a drug currently being tested in human clinical trials for efficacy against chronic cryptosporidiosis, was assessed in cell culture and in two animal models. The inhibitory activity of NTZ was compared with that of paromomycin (PRM), a drug that is partially effective against Cryptosporidium parvum. A concentration of 10 μg of NTZ/ml (32 μM) consistently reduced parasite growth in cell culture by more than 90% with little evidence of drug-associated cytotoxicity, in contrast to an 80% reduction produced by PRM at 2,000 μg/ml (3.2 mM). In contrast to its efficacy in vitro, NTZ at either 100 or 200 mg/kg of body weight/day for 10 days was ineffective at reducing the parasite burden in C. parvum-infected, anti-gamma-interferon-conditioned SCID mice. Combined treatment with NTZ and PRM was no more effective than treatment with PRM alone. Finally, NTZ was partially effective at reducing the parasite burden in a gnotobiotic piglet diarrhea model when given orally for 11 days at 250 mg/kg/day but not at 125 mg/kg/day. However, the higher dose of NTZ induced a drug-related diarrhea in piglets that might have influenced its therapeutic efficacy. As we have previously reported, PRM was effective at markedly reducing the parasite burden in piglets at a dosage of 500 mg/kg/day. Our results indicate that of all of the models tested, the piglet diarrhea model most closely mimics the partial response to NTZ treatment reported to occur in patients with chronic cryptosporidiosis.
Disruptive natural selection predicts divergence between the sexes during adaptive radiation

Abstract Evolution of sexual dimorphism in ecologically relevant traits, for example, via resource competition between the sexes, is traditionally envisioned to stall the progress of adaptive radiation. An alternative view is that evolution of ecological sexual dimorphism could in fact play an important positive role by facilitating sex‐specific adaptation. How competition‐driven disruptive selection, ecological sexual dimorphism, and speciation interact during real adaptive radiations is thus a critical and open empirical question. Here, we examine the relationships between these three processes in a clade of salamanders that has recently radiated into divergent niches associated with an aquatic life cycle. We find that morphological divergence between the sexes has occurred in a combination of head shape traits that are under disruptive natural selection within breeding ponds, while divergence among species means has occurred independently of this disruptive selection. Further, we find that adaptation to aquatic life is associated with increased sexual dimorphism across taxa, consistent with the hypothesis of clade‐wide character displacement between the sexes. Our results suggest the evolution of ecological sexual dimorphism may play a key role in niche divergence among nascent species and demonstrate that ecological sexual dimorphism and ecological speciation can and do evolve concurrently in the early stages of adaptive radiation.
IMC control of combustion instability

Combustion instability is a phenomenon that happens in a gas turbine when the lean premixed combustion mode is used to reduce the NOx emissions. The process is unstable and thus difficult to control. This paper applies the internal model control (IMC) method in the control of the combustion instability, with the aim of finding effective control structures and methods for this kind of system, and preparing for the study of wide-range robust control. Design results show that the IMC controller has good disturbance rejection capability, but the method should be improved to achieve better performance for the active control of combustion instability.
“Drugs on oxygen”: an update and perspective on the role of cytochrome P450 testing in pharmacology

Low hit rates for lead compounds and high attrition remain a major problem for drug development. The reasons for compound failure range from poor pharmacokinetics to toxic metabolites and adverse drug interactions; all of which are frequently mediated by cytochrome P450-dependent monooxygenases (CYPs). However, despite some 30 years of assay development and refinement, CYP metabolism remains a critical issue during drug development. While current testing strategies succeed in characterizing single substance toxicity, they are challenged by practical issues such as assay standardization or complex scenarios such as multidrug usage. This editorial summarizes where we stand and highlights the major challenges we face with CYPs in drug development today. The article also tries to spell out the future direction of CYP testing. The latter will depend on the extended inclusion of polypharmacy into testing strategies, as well as on our capability to make use of upcoming complex in vitro test systems and their inclusion into tiered testing strategies.
Logic optimization of QCA circuits using ant colony optimization

Implementation of logic circuits using Quantum-dot Cellular Automata (QCA) technology due to the proper features, e.g. high device density, fast switching time and extremely low power, is an intense research area. Boolean primitives in QCA circuits are the majority gate and inverter. Recently, evolutionary algorithms, especially Genetic Algorithm (GA), have been used for implementing a given Boolean function with the minimum number of required primitives. In this paper, a novel method for optimal implementation of three variable Boolean functions by using Ant Colony Optimization (ACO) algorithm is presented. Simulation results demonstrate that the proposed method outperforms GA-based methods in the average number of required gates and levels for implementing three variable Boolean functions.
Allometry of Sexual Size Dimorphism in Dioecious Plants: Do Plants Obey Rensch’s Rule?

Rensch’s rule refers to a pattern in sexual size dimorphism (SSD) in which SSD decreases with body size when females are the larger sex and increases with body size when males are the larger sex. Many animal taxa conform to Rensch’s rule, but it has yet to be investigated in plants. Using herbarium collections from New Zealand, we characterized the size of leaves and stems of 297 individuals from 38 dioecious plant species belonging to three distantly related phylogenetic lineages. Statistical comparisons of leaf sizes between males and females showed evidence for Rensch’s rule in two of the three lineages, indicating SSD decreases with leaf size when females produce larger leaves and increases with leaf size when males produce larger leaves. A similar pattern in SSD was observed for stem sizes. However, in this instance, females of small-stemmed species produced much larger stems than did males, but as stem sizes increased, SSD often disappeared. We hypothesize that sexual dimorphism in stem sizes results from selection for larger stems in females, which must provide mechanical support for seeds, fruits, and dispersal vectors, and that scaling relationships in leaf sizes result from correlated evolution with stem sizes. The overall results suggest that selection for larger female stem sizes to support the weight of offspring can give rise to Rensch’s rule in dioecious plants.
Complement and the Antiglobulin Test *

To study the specificity of antiglobulin reactions which are dependent upon C‘ uptake by the sensitized erythrocytes, “antisera to C’” were prepared by immunizing animals with washed specific precipitates containing bound C‘. These antisera, as well as antisera to whole human serum, agglutinated the red cells of cold hemolytic anemia, Lea sensitized red cells, and sensitized sheep erythrocytes exposed to sublytic doses of C’. Antisera to GAhuC‘ (specific precipitate with bound human complement) and antisera to whole human serum, were assayed for complement antiglobulin reactions by cross‐titration with sensitized sheep cells (EA) exposed to decreasing sublytic amounts of human C’ (EAhuC‘). Because EAhuC’ red cells are agglutinable with anti‐human γ globulin sera, reagents for cross‐titration should first be freed of such antibodies by specific precipitation with human y globulin. In addition, heterophile (anti‐sheep cell) antibodies should be absorbed from reagents and sources of C‘, and controls maintained to ensure absence of “rheumatoid” effect.
Étude d'un analyseur de surface de la langue naturelle : application à l'indexation automatique de textes

Nous presentons l'etude et la realisation d'un analyseur de surface de la langue naturelle, dans le contexte des systemes de recherche d'informations. Cette analyse morpho-syntaxique a pour objet la reconnaissance des concepts vehicules par les syntagmes nominaux (groupes conceptuels) presents dans les textes, en vue de leur indexation automatique. Pour cela nous avons defini: 1) une analyse morphologique utilisant un dictionnaire de racines organise en arbre lexicographique, un ensemble de desinences et des modeles de composition morphologique; 2) une analyse syntaxique partielle basee d'une part, sur un filtrage utilisant une matrice de precedente qui exploite les relations positionnelles de la langue et certaines contraintes grammaticales, et d'autre part sur une resolution des ambiguites grammaticales par l'application de schemas predefinis; 3) un enrichissement automatique du vocabulaire base sur une interpretation des formes inconnues en fonction de l'orthographe et du contexte immediat. L'architecture de cet analyseur est presentee en detail, ainsi que des resultats d'experimentation obtenus pour des textes de differents corpus
Detection of Toxoplasma gondii in cerebrospinal fluid from AIDS patients by polymerase chain reaction

The polymerase chain reaction (PCR) was used to detect Toxoplasma gondii DNA in cerebrospinal fluid (CSF) from 14 patients with AIDS by amplification of the repetitive B1 gene. Positive PCRs were obtained in CSF from four of nine patients with toxoplasmic encephalitis. CSF samples from five control patients were negative for T. gondii DNA by PCR.
Towards a framework for evaluating investments in data warehousing

Data warehousing technology offers organizations the potential for much greater exploitation of informational assets. However, the evaluation of potential investments in this technology poses problems for organizations as traditional evaluation methods are constrained when dealing with strategic IT applications. Nevertheless, many organizations are procedurally obliged to use such methods for evaluating data warehousing investments. This paper identifies five problems with using such methods in these circumstances: evaluating intangible benefits; making the relationship between IT and profitability explicit; dealing with the vanishing status quo; dealing with the extended investment time frame; and evaluating infrastructural investments. The authors studied how four organizations in the UK and Ireland attempted to overcome these problems when introducing data warehousing, and propose a framework for evaluating data warehousing investments. This framework consists of a high-level analysis of the economic environment and of the information intensity of the relationship between the organization and its customers. Based on the outcome of this analysis, the authors propose four factors that have to be managed during the evaluation process in order to ensure that the limitations of the traditional evaluation techniques do not adversely affect the evaluation process. These factors are: commitment and sponsorship; the approach to evaluation; the time scale of benefits; and the appraisal techniques used.
On death and dying.

Dr. J. Russell Little, Chief, Division of Infectious Disease, the Jewish Hospital of St. Louis and Associate Professor of Medicine and Microbiology, Washington University School of Medicine: Our guest this morning is Elisabeth Kubler-Ross, MD. Dr. Ross has become something of a celebrity since the feature story inLifemagazine (Nov 21, 1969, p 36) concerning her and her work and the appearance of her recent book entitledOn Death and Dying.1The book provides a fascinating account of an experiment in teaching and therapy concerned with the emotional problems of seriously ill and dying patients. We have decided to dispense with the traditional case presentation today even though Dr. Ross could discuss any of our hospitalized patients with a terminal disease. Instead we shall turn over the entire hour to her discussion of her approach to the emotional problems of dying patients. Dr. Elisabeth Kubler-Ross, Medical Director, South
Direct Detection of Sabin Poliovirus Vaccine Strains in Stool Specimens of First-Dose Vaccinees by a Sensitive Reverse Transcription-PCR Method

ABSTRACT A multiplex reverse transcription-PCR method was optimized to monitor the duration of excretion of Sabin poliovirus strains in stools of vaccinees following administration of the first dose of the trivalent oral vaccine. The assay detected approximately 1 50% tissue culture infective dose of each poliovirus serotype spiked into cell culture media. Although PCR inhibitors were frequently encountered in the stool specimens, a 1:20 dilution of the extracted RNA was sufficient to obtain a positive PCR result. Analysis of 195 stool specimens collected from 26 vaccinees showed that poliovirus types 1, 2, and 3 were identified more frequently by PCR than by tissue culture isolation. The percentages of specimens positive by PCR for poliovirus types 1, 2, and 3 were 67.2, 82.6, and 53.8, respectively. In contrast, the culture method identified types 1, 2, and 3 virus in 55.4, 64.1, and 27.7% of the samples, respectively. Poliovirus type 2 excretion was detected by PCR in practically all of the oral poliovirus vaccine recipients for 4 to 8 weeks following vaccination. In contrast, excretion of type 1 and 3 viruses was more variable, with a range of 1 to 8 weeks. Shedding of type 3 virus ceased in ∼70% of vaccinees within a week after immunization. In addition to an enhanced sensitivity for the detection of poliovirus, this PCR method permits the direct characterization of virus in stool specimens without further passage in culture, which may select for genetic variants that may not accurately reflect the virus composition in the original specimen.