Miracle-dz/UniFAR-FTUs huggingface dataset:
The Use of Physarum for Testing of Toxicity/Mutagenicity

Abstract : Growing and differentiating cultures of the true slime mold, Physarum polycephalum, have been investigated for possible use in testing for toxicity of several fuels--hydrazine, ethanol and hydrocarbons. Testing protocols were based on several already in the literature. Effects on growth were studied via inhibition of microplasmodial growth (Becker et al., Cancer Res. 23, 1910, 1963) and effects on differentiation by inhibition of (or interference with) plasmodial sporulation (Sauer et al., Exptl, Cell Res. 57, 319; 1969) and of amoebal flagellation (Mir and Wright, Microbios. Lett. 5, 39, 1978). Effects on growth of microplasmodia were expressed as ED50 values, calculated from spectrophotometric measurements of while culture protein, DNA or pigment. ED50S (protein data) for hydrazine.2 HC1 and ethanol were 40 ug/ml and 1.5% (v/v), respectively. Short, straight chain, even numbered hydrocarbons (C6 - C10) at 1% completely stopped microplasmodial growth. The C12 - C16 hydrocarbons at the same concentration did not inhibit growth and may have served as a carbon source, since they seemed to have a glucose-sparing effect.
Chemocyanin, a small basic protein from the lily stigma, induces pollen tube chemotropism

In plant reproduction, pollination is an essential process that delivers the sperm through specialized extracellular matrices (ECM) of the pistil to the ovule. Although specific mechanisms of guidance for pollen tubes through the pistil are not known, the female tissues play a critical role in this event. Many studies have documented the existence of diffusible chemotropic factors in the lily stigma that can induce pollen tube chemotropism in vitro, but no molecules have been isolated to date. In this study, we identified a chemotropic compound from the stigma by use of biochemical methods. We purified a lily stigma protein that is active in an in vitro chemotropism assay by using cation exchange, gel filtration, and HPLC. Tryptic digestion of the protein yielded peptides that identified the protein as a plantacyanin (basic blue protein), and this was confirmed by cloning the cDNA from the lily stigma. Plantacyanins are small cell wall proteins of unknown function. The measured molecular mass by electrospray ionization ion source MS is 9,898 Da, and the molecular mass of the mature protein (calculated from the cDNA) is 9,900.2 Da. Activity of the lily plantacyanin (named chemocyanin) is enhanced in the presence of stigma/stylar cysteine-rich adhesin, previously identified as a pollen tube adhesin in the lily style.
Regenerative therapy of infrabony defects with or without systemic doxycycline. A randomized placebo-controlled trial.

AIM Comparison of regenerative therapy of infrabony defects with and without administration of postsurgical systemic doxycycline (DOXY). METHODS In each of 61 patients one infrabony defect was treated with enamel matrix derivative (EMD), EMD plus filler or membrane at two centres. By random assignment patients received either 200 mg DOXY per day or placebo (PLAC) for 7 days after surgery. Prior to and 6 months after surgery probing pocket depths (PPD) and vertical attachment level (PAL-V) were obtained. RESULTS Fifty-four patients (DOXY: 27; PLAC: 27) were re-examined after 6 months and had been treated exclusively with EMD. Seven to 8 days after surgery 81% of defects in both groups showed complete flap closure. In both groups significant (p < 0.001) PPD reduction (DOXY: 3.87 ± 1.44 mm; PLAC: 3.67 ± 1.30 mm) and PAL-V gain (DOXY: 3.11 ± 1.50 mm; PLAC: 3.32 ± 1.83 mm) were observed. However, the differences failed to be statistically significant (PPD: 0.20; p = 0.588; PAL-V: 0.21; p = 0.657). CONCLUSIONS Two hundred milligram systemic DOXY administered for 7 days after therapy of infrabony defects with EMD failed to result in better PPD reduction and PAL-V gain compared with PLAC which may be due to low power (50%) and, thus, random chance.
Beneficial effects of gfap/vimentin reactive astrocytes for axonal remodeling and motor behavioral recovery in mice after stroke

The functional role of reactive astrocytes after stroke is controversial. To elucidate whether reactive astrocytes contribute to neurological recovery, we compared behavioral outcome, axonal remodeling of the corticospinal tract (CST), and the spatio‐temporal change of chondroitin sulfate proteoglycan (CSPG) expression between wild‐type (WT) and glial fibrillary acidic protein/vimentin double knockout (GFAP–/–Vim–/–) mice subjected to Rose Bengal induced cerebral cortical photothrombotic stroke in the right forelimb motor area. A foot‐fault test and a single pellet reaching test were performed prior to and on day 3 after stroke, and weekly thereafter to monitor functional deficit and recovery. Biotinylated dextran amine (BDA) was injected into the left motor cortex to anterogradely label the CST axons. Compared with WT mice, the motor functional recovery and BDA‐positive CST axonal length in the denervated side of the cervical gray matter were significantly reduced in GFAP–/–Vim–/– mice (n = 10/group, P < 0.01). Immunohistological data showed that in GFAP–/–Vim–/– mice, in which astrocytic reactivity is attenuated, CSPG expression was significantly increased in the lesion remote areas in both hemispheres, but decreased in the ischemic lesion boundary zone, compared with WT mice (n = 12/group, P < 0.001). Our data suggest that attenuated astrocytic reactivity impairs or delays neurological recovery by reducing CST axonal remodeling in the denervated spinal cord. Thus, manipulation of astrocytic reactivity post stroke may represent a therapeutic target for neurorestorative strategies. GLIA 2014;62:2022–2033
CDC42 and FGD1 Cause Distinct Signaling and Transforming Activities

ABSTRACT Activated forms of different Rho family members (CDC42, Rac1, RhoA, RhoB, and RhoG) have been shown to transform NIH 3T3 cells as well as contribute to Ras transformation. Rho family guanine nucleotide exchange factors (GEFs) (also known as Dbl family proteins) that activate CDC42, Rac1, and RhoA also demonstrate oncogenic potential. The faciogenital dysplasia gene product, FGD1, is a Dbl family member that has recently been shown to function as a CDC42-specific GEF. Mutations within the FGD1 locus cosegregate with faciogenital dysplasia, a multisystemic disorder resulting in extensive growth impairments throughout the skeletal and urogenital systems. Here we demonstrate that FGD1 expression is sufficient to cause tumorigenic transformation of NIH 3T3 fibroblasts. Although both FGD1 and constitutively activated CDC42 cooperated with Raf and showed synergistic focus-forming activity, both quantitative and qualitative differences in their functions were seen. FGD1 and CDC42 also activated common nuclear signaling pathways. However, whereas both showed comparable activation of c-Jun, CDC42 showed stronger activation of serum response factor and FGD1 was consistently a better activator of Elk-1. Although coexpression of FGD1 with specific inhibitors of CDC42 function demonstrated the dependence of FGD1 signaling activity on CDC42 function, FGD1 signaling activities were not always consistent with the direct or exclusive stimulation of CDC42 function. In summary, FGD1 and CDC42 signaling and transformation are distinct, thus suggesting that FGD1 may be mediating some of its biological activities through non-CDC42 targets.
A breast cancer case—control study in Girona, Spain. Endocrine, familial and lifestyle factors

This study was designed to explore risk factors for breast cancer with emphasis on the detection of clinical markers of the hormonal imbalance during the perimenarche. Three hundred and thirty women diagnosed with breast cancer and 346 population controls were identified and interviewed in Girona, Spain between 1986 and 89. Cases were more likely than controls to have had long menstrual periods in the first 5 years after menarche [odds ratio (OR)=3.0], to experience menopause at a late age (OR=1.5) and to report acne during adolescence (OR=1.6). Family history of breast cancer was associated with an increased risk (OR=2.3). Cases reported a lower use of drug treatments for anxiety and sleep disorders than controls. Moderate alcohol drinkers and smokers were at lower risk for breast cancer. No statistically significant association with breast cancer was observed for number of children, age at last pregnancy, oral contraceptive use, hormonal treatment after menopause and weight perception during the teenage years. Hormonal changes in the years following menarche may be relevant to breast cancer risk. The roles of menstrual period length and acne during adolescence should be further explored.
MRS imaging using anatomically based K‐space sampling and extrapolation

A comprehensive strategy for the acquisition, reconstruction, and postprocessing of MR spectroscopic images is presented. The reconstruction algorithm is the most critical component of this strategy. It is assumes that the desired image is spatially bounded, meaning that the desired image contains an object that is surrounded by a background of zeros. The reconstruction algorithm relies on prior knowledge of the background zeros for k‐space extrapolation. This algorithm is a good candidate for proton MR spectroscopic image reconstruction because these images are often spatially bounded and prior knowledge of the zeros is easily obtained from a rapidly acquired high resolution conventional MRI. Although the reconstruction algorithm can be used with the standard 3DFT k‐space distribution, a distribution that relies on anatomical features that are likely to occur in the spectroscopic image can produce better results. Prior knowledge of these anatomical features is also obtained from a conventional MRI. Finally, the postprocessing component of this strategy is valuable for reducing subcutaneous lipid contamination. Overall, the comprehensive approach presented here produces images that are better resolved than standard approaches without increasing acquisition time or reducing SNR. Examples using NAA data are provided.
A framework for ontology-based question answering with application to parasite data

Research in life sciences requires a sophisticated and integrated platform to query and analyze a large volume of data represented in various data. Two major challenges exist in this regard: integrating heterogeneous data sources and providing intuitive methods of accessing and querying data.In this regard, the semantic problem solving environment (SPSE) is created for parasite immunology research. SPSE utilizes semantic Web approaches to integrate and manage heterogeneous data in a knowledge-base called parasite experiment repository (PKR). This dissertation proposes two ontology-based question answering approaches to provide facilities to access and query annotated data. The first approach is an ontology-driven query answering system that guides users in exploring ontology schemas and generating queries in the form of RDF-triples – Cuebee. Significant enhancements are introduced to the preliminary version of Cuebee to extend its key functionalities and make it more user-friendly and useful. A comprehensive study evaluates ontology-driven querying with conventional DBMS-based querying approaches for life sciences data. The second approach proposes a natural way of obtaining answers from annotated data by introducing a general framework for ontology-based natural language question answering – OntoNLQA. A key characteristic of OntoNLQA is its capability in capturing semantics of the question and mapping it to the semantics of the annotated data model (ontology and RDF-triples) in order to create computational queries. This framework consists of five components each of which proposes different strategies and methods. This dissertation instantiates OntoNLQA in the context of parasite immunology and develops a system called AskCuebee. This system allows parasitologists to pose genomic, proteomic and pathway questions in natural language form related to the parasite T. cruzi. AskCuebee demonstrates the utility and usefulness of the OntoNLQA by implementing and evaluating its components. Index words: Question Answering, Natural language Processing, Ontology, Data Integration, Parasite Immunology A Framework for Ontology-Based Question Answering with Application to Parasite Data
The Interrogator model

The Interrogator is a protocol security analysis tool implemented in Prolog and based on a communicating-machine message transformation model with message modification threats. It supports a large and extendible class of symbolic encryption and data transformation operators with a novel equation-solving approach in the context of equational theories. The operator representation and equation-solving capability has a simple interface to the protocol and threat model. <<ETX>>
Cytogenetic studies in mice treated with the jet fuels, Jet-A and JP-8

The genotoxic potential of the jet fuels, Jet-A and JP-8, were examined in mice treated on the skin with a single dose of 240 mg/mouse. Peripheral blood smears were prepared at the start of the experiment (t = 0), and at 24, 48 and 72 h following treatment with jet fuels. Femoral bone marrow smears were made when all animals were sacrificed at 72 h. In both tissues, the extent of genotoxicity was determined from the incidence of micronuclei (MN) in polychromatic erythrocytes. The frequency of MN in the peripheral blood of mice treated with Jet-A and JP-8 increased over time and reached statistical significance at 72 h, as compared with concurrent control animals. The incidence of MN was also higher in bone marrow cells of mice exposed to Jet-A and JP-8 as compared with controls. Thus, at the dose tested, a small but significant genotoxic effect of jet fuels was observed in the blood and bone marrow cells of mice treated on the skin.
El poder de mercado o eficiencia: origen de las utilidades del sistema bancario mexicano de 1995

Es comun observar que a medida que el grado de concentracion de una industria disminuye, sus empresas presentan resultados cada vez menos atractivos, en terminos de ganancias. El debate se centra en la explicacion de dicha relacion positiva, pues, por un lado, el paradigma Estructura-Conducta-Desempeno (SCP) senala que las ganancias son mayores debido al poder de mercado que ejercen las empresas, mientras que la hipotesis de eficiencia destaca que la ventaja se da porque las empresas grandes pueden trabajar con costos menores. Utilizando datos para el sistema bancario mexicano en el periodo 1995–1999, ambas hipotesis son puestas a prueba para tratar de explicar el origen de las ganancias de los bancos en el pais. En particular, se encuentra evidencia que apoya el punto de vista que sostiene el paradigma SCP.
Assessment of functional gastrointestinal disorders using the gastro-questionnaire

The purpose was to investigate the reliability and factorial structure of the Gastro-Questionnaire for the screening and psychometric measurement of functional gastrointestinal disorders (FGDs). The questionnaire contains 27 gastrointestinal symptom items drawn from the Rome—II criteria, which are rated by frequency and severity, as well as some items to exclude organic diseases. The questionnaire was administered to 259 normal participants and to 69 participants of the annual German meeting of patients with irritable bowel syndrome. Reliability was good (Cronbach’s alpha for frequency and severity items: α = .86 and α = .87). Factor analysis yielded a six-factor solution explaining 60.7% of the variance. Diagnostic frequencies ranged from 32.8%to100% for FGDs in general, from 1.3% to 76.8% for irritable bowel syndrome, and from 7.0% to 100% for functional dyspepsia, depending on samples and symptom definitions. The Gastro-Questionnaire is a very economic, reliable, and content-valid instrument for the assessment of FGDs.
Prevention of gastrointestinal infection using immunobiological methods with milk fermented with Lactobacillus casei and Lactobacillus acidophilus

Summary The protective effect of feeding milk fermented with a mixture of Lactobacillus casei sp. and Lb. acidophilus sp. against Salmonella typhimurium infection in mice was compared with that obtained feeding milks fermented with these microorganisms individually. The survival rate obtained after oral infection with Sal. typhimurium was 100% in mice pretreated by feeding during 8 d with the mixture of Lb. casei and Lb. acidophilus fermented milks. Similar treatments with the individual milks were ineffective. Moreover, mice became more susceptible to infection with Sal. typhimurium after such treatment. The colonization of liver and spleen with the pathogen was markedly inhibited by the pretreatment with the mixture of fermented milk, while such inhibition was not observed using the Lb. casei and Lb. acidophilus milks. The highest levels of anti-salmonellae antibodies in serum and in intestinal fluid were found in the group of mice fed with the mixture and with Lb. casei fermented milk respectively. However, this latter milk was not effective in protecting against Sal. typhimurium. When the mice were first infected with Sal. typhimurium and then fed with the mixture of fermented milks, pathogen colonization was not prevented. The results suggest that the augmentation of resistance to salmonellae caused by the treatment with Lb. casei-+Lb. acidophilus-fermented milk was due to the anti-salmonellae protective immunity mainly mediated by the mucosal tissue. Milk fermented with this mixture could be used as an immunobiological method to prevent gastrointestinal infection.
Racial differences in occupational status and income in South Africa, 1880 and 1881

Using data on employed men from the 1980 and 1991 South African Censuses, we analyze the determinants of occupational status and income. Whites are found to have much higher occupational status, and especially income, than members of other racial groups. Most of the racial differentials in occupational status can be explained by racial differences in the personal assets that determine occupational attainment (especially education), but only a much smaller fraction of the White/non-White income differential can be so explained. Despite a modest reduction between 1980 and 1991 in the role of race in socioeconomic attainment, the overall picture shows more stability than change.
Adaptive polynomial neural networks for times series forecasting

Time series prediction involves the determination of an appropriate model, which can encapsulate the dynamics of the system, described by the sample data. Previous work has demonstrated the potential of neural networks in predicting the behaviour of complex, non-linear systems. In particular, the class of polynomial neural networks has been shown to possess universal approximation properties, while ensuring robustness to noise and missing data, good generalisation and rapid learning. In this work, a polynomial neural network is proposed, whose structure and weight values are determined with the use of evolutionary computing. The resulting networks allow an insight into the relationships underlying the input data, hence allowing a qualitative analysis of the models' performance. The approach is tested on a variety of non-linear time series data.
The variation of scattered x-rays with density in an irradiated body.

It is shown that, provided the effective atomic number remains constant, there is a general relationship between the variation of scatter with density and the variation with geometry of the system. A simplified analysis of the scatter contribution in water equivalent bodies is presented. This analysis leads to the definition of relative scatter absorption factors and the values of these factors in water equivalent materials are found by experiment for radiation with a half-value layer of 1·5 mm Cu. By the application of the general relationship between density of the body and geometry of the system values of the relative scatter absorption factors in bodies of other than unit density are deduced. These values may be employed in the calculation of the scatter dose delivered to points which lie in an inhomogeneous body. The practical importance of the results obtained is discussed with particular reference to the use of Transit Dose techniques.
Improving the Accuracy of Inverse Iteration

The EISPACK routine TINVIT is an implementation of inverse iteration for computing eigenvectors of real symmetric tridiagonal matrices. Experiments have shown that the eigenvectors computed with TINVIT are numerically less accurate than those from implementations of Cuppen’s divide-and-conquer method (TREEQL) and of the QL method (TQL2). The loss of accuracy can be attributed to TINVIT’s choice of starting vectors and to its iteration stopping criterion.This paper introduces a new implementation of TINVIT that computes each eigenvector from a different random starting vector and performs an additional iteration after the stopping criterion is satisfied. A statistical analysis and the results of numerical experiments with matrices of order up to 525 are presented to show that the numerical accuracy of this new implementation is competitive with that of the implementations of the divide-and-conquer and QL methods. The extension of this implementation to larger order matrices is discussed, albeit in less detail.
10 V programmable Josephson voltage standard and its application in direct comparison with conventional Josephson voltage standard

This paper briefly describes the working principle of the 10 V programmable Josephson voltage standard (PJVS) that was developed at the National Institute of Standards and Technology (NIST) and how to use it in a direct comparison with a conventional Josephson voltage standard (JVS). Manual and automatic comparison methods were investigated to verify the agreement between the two types of Josephson standards. The 10 V PJVS will be used as a transfer standard in the 2014 JVS Interlaboratory Comparison (ILC) that is organized by the National Conference of Standard Laboratories International (NCSLI).
SpaceClimber: Development of a Six-Legged Climbing Robot for Space Exploration

In this paper, we present the SpaceClimber integration study, a six-legged, bio-inspired, energy-efficient, and adaptable free-climbing robot for mobility in steep gradients. The long-term vision is to provide a system for the purpose of extraterrestrial surface exploration missions paying special attention to mobility in lunar craters in order to retrieve or analyze scientific samples from the interior of these craters. We present an envisaged mission for SpaceClimber and give a description of the system's morphology and the design steps. Apart from hardware design, parts of the control software as well as the utilization of evolutionary algorithms for both morphology design and locomotion control are presented.
Isolation and expression of the gene encoding mitochondrial ADP/ATP carrier (AAC) from the pathogenic yeast Candida parapsilosis

A gene homologous to Saccharomyces cerevisiae AAC genes coding for mitochondrial ADP/ATP carriers has been cloned from the pathogenic yeast Candida parapsilosis. A probe obtained by PCR amplification from C. parapsilosis DNA, using primers derived from the conserved transmembrane region of yeast ADP/ATP carriers, was used for screening of the C. parapsilosis genomic library. The cloned gene was sequenced and found to encode a polypeptide of 303 amino acids that shows homology with other yeast and fungal mitochondrial ADP/ATP carriers. The gene was designated CpAAC1 and was able to complement the growth phenotypes of S. cerevisiae double deletion mutant (Δaac2; Δaac3). The expression of the CpAAC1 gene was reduced under semi‐anaerobic conditions and it was affected at normal aerobic conditions by the nature of carbon sources used for growth. Hybridization experiments indicate that C. parapsilosis possesses a single gene encoding a mitochondrial ADP/ATP carrier. The GenBank Accession No. for the C. parapsilosis CpAAC1 gene is AF085429. Copyright © 1999 John Wiley & Sons, Ltd.