Miracle-dz/UniFAR-FTUs huggingface dataset:
Construction and use of signal sequence selection vectors in Escherichia coli and Bacillus subtilis

To study the diversity and efficiency of signal peptides for secreted proteins in gram-positive bacteria, two plasmid vectors were constructed which were used to probe for export signal-coding regions in Bacillus subtilis. The vectors contained genes coding for extracellular proteins (the alpha-amylase gene from Bacillus licheniformis and the beta-lactamase gene from Escherichia coli) which lacked a functional signal sequence. By shotgun cloning of restriction fragments from B. subtilis chromosomal DNA, a great variety of different export-coding regions were selected. These regions were functional both in B. subtilis and in E. coli. In a number of cases where protein export had been restored, intracellular precursor proteins of increased size could be detected, which upon translocation across the cellular membrane were processed to mature products. The high frequency with which export signal-coding regions were obtained suggests that, in addition to natural signal sequences, many randomly cloned sequences can function as export signal.
The Potential for Circuit Reconstruction by Expanded Neural Precursor Cells Explored through Porcine Xenografts in a Rat Model of Parkinson's Disease

Neural precursors with the properties of neural stem cells can be isolated from the developing brain, can be expanded in culture, and have been suggested as a potential source of cells for neuronal replacement therapies in degenerative disorders such as Parkinson's disease (PD). Under such conditions an improved spectrum of functional benefit may be obtained through homotypic reconstruction of degenerated neural circuitry, and to this end we have investigated the potential of expanded neural precursor cells (ENPs) to form long axonal projections following transplantation in the 6-hydroxydopamine-lesioned rat model of PD. ENPs have been isolated from the embryonic pig, since implantation in a xenograft environment is thought to favor axonal growth. These porcine ENPs possessed similar properties in vitro to those described in other species: they proliferated in response to epidermal and fibroblast growth factor-2, expressed the neuroepithelial marker nestin, and differentiated into neurons, astrocytes, and occasional oligodendrocytes on mitogen withdrawal. The use of pig-specific markers following xenotransplantion into cyclosporin A-immunosuppressed rats revealed that many cells differentiated into neurons and displayed extensive axogenesis, such that when placed in the region of the substantia nigra fibers projected throughout the striatal neuropil. These neurons were not restricted in the targets to which they could project since following intrastriatal grafting fibers were seen in the normal striatal targets of the pallidum and substantia nigra. Staining for a pig-specific synaptic marker suggested that synapses were formed in these distant sites. A small number of these cells differentiated spontaneously to express a catecholaminergic phenotype, but were insufficient to mediate behavioral recovery. Our results suggest that when the efficiency of neurochemical phenotype induction is increased, ENP-derived neurons have the potential to be a uniquely flexible source of cells for therapeutic cell replacement where anatomical reconstruction is advantageous.
A quantitative method for detecting explosive materials using terahertz spectroscopy

Terahertz transmission spectroscopy offers simultaneous measuring capabilities for the spectral and depth information of the inspected materials. This enables effective determination of the species and amount of them, i.e., qualitative and quantitative detection. We have successfully applied this technique to quantitatively detect concealed explosives by an absorbance spectrum fitting method. Measurement of the amount of RDX sample covered with some barrier materials provides the experimental evidence for the validity of this quantitative method. Two factors relating to the detection accuracy are considered and analyzed, the fitting frequency range and the polynomial approximation of the unknown absorbance of the barrier.
Agents of newly recognized or infrequently encountered mycobacterial diseases

This paper reviews recent information on the systematics and clinical significance of potentially pathogenic environmental mycobacteria. A short history of these mycobacteria is given. Information on species for which clinical and systematic aspects have already been well documented, i.e., Mycobacterium kansasii, M. marinum, M. scrofulaceum, M. simiae, M. szulgai, M. ulcerans, M. xenopi, and members of the M. fortuitum complex, is updated. Although the M. avium complex was extensively reviewed in earlier literature, major new systematic and clinical information is presented in some detail. Species that have received very limited prior coverage, i.e., M. asiaticum, M. haemophilum, M. malmoense, and M. shimoidei, are the main subjects of this review and are discussed in detail. The rare infections attributed to species that are normally considered nonpathogenic, i.e., M. gastri, M. gordonae, the M. terrae complex, and most of the rapidly growing mycobacteria outside of the M. fortuitum complex, are critically reviewed. Finally, suggestions are offered for practical measures that can minimize the risk of failing to isolate or misidentifying some of the more obscure potentially pathogenic environmental mycobacteria that are only infrequently recognized.
Maker Gene Identification: a Multiple Kernel Support Vector Machine Approach

Recently, gene expression profiling using DNA microarray technique has been shown as a promising tool to improve the diagnosis and treatment of cancer. Support vector machine has been successfully used to classify cancer tissue based on gene expression data. Besides performance, the ability to discover underlying principles will be a crucial point in the medical field. In this paper, we present a novel marker gene identification method based on multiple kernel support vector machine (MK-SVM). The main strength of this technique is the detection of gene groups that are strongly associated with specific types of cancer and maybe useful to the diagnosis and treatment. It achieves this by employing a two phases' framework. Firstly, a 1-norm based regularized cost function is used to enforce sparsity and obtain gene subset. Secondly, a support vectors based rule extraction algorithm is implemented to determine the final marker genes. The ALL-AML Leukemia dataset is used to demonstrate the promising performance of this approach.
Uterine Artery Remodeling and Reproductive Performance Are Impaired in Endothelial Nitric Oxide Synthase-Deficient Mice1

Abstract The progressive rise in uterine blood flow during pregnancy is accompanied by outward hypertrophic remodeling of the uterine artery (UA). This process involves changes of the arterial smooth muscle cells and extracellular matrix. Acute increases in blood flow stimulate endothelial production of nitric oxide (NO). It remains to be established whether endothelial NO synthase (eNOS) is involved in pregnancy-related arterial remodeling. We tested the hypothesis that absence of eNOS results in a reduced remodeling capacity of the UA during pregnancy leading to a decline in neonatal outcome. UA of nonpregnant and pregnant wild-type (Nos3+/+) and eNOS-deficient (Nos3−/−) mice were collected and processed for standard morphometrical analyses. In addition, cross sections of UA were processed for cytological (smoothelin, smooth muscle α-actin) and proliferation (Ki-67) immunostaining. We compared the pregnancy-related changes longitudinally and, together with the data on pregnancy outcome, transversally by analysis of variance with Bonferroni correction. During pregnancy, the increases in radius and medial cross sectional area of Nos3−/− UA was significantly less than those of Nos3+/+ UA. Smooth muscle cell dedifferentiation and proliferation were impaired in gravid Nos3−/− mice as deduced from the lack of change in the expression of smoothelin and smooth muscle α-actin, and the reduced Ki-67 expression. Until 17 days of gestation, litter size did not differ between both genotypes, but at birth the number of viable newborn pups and their weights were smaller in Nos3−/− than in Nos3+/+ mice. We conclude that absence of eNOS adversely affects UA remodeling in pregnancy, which may explain the impaired pregnancy outcome observed in these mice.
Comorbidity on disorders with loss of impulse-control: pathological gambling, addictions and personality disorders.

OBJECTIVES To analyze the comorbidity of pathological gamblers, mainly in disorders with loss of impulse-control as addictions and personality disorders (PD). Also, to discuss addictive and impulsive characteristics of pathological gambling (PG), and their implications in prognosis and treatment. MATERIAL AND METHOD Cross-sectional study on 162 patients with PG admitted for treatment in a specific residential unit. The SCID-I and II were used for the addiction and the PD diagnosis. For the diagnosis and evaluation of PG the SOGS, AGQ III and the Gambling Severity Index were also used. RESULTS The 61.1 % of the patients presented some PD, where the cluster B ones (impulsive group) were more frequent, followed by C and A ones. 63.3% of patients had had in their lives substance dependence criteria, where alcohol dependence was the most prevalent. The presence of PD is related to the gravity of the addiction by the dependence to more than one substance (chi2=7.15; p<0.008). DISCUSSION TP and substance-related disorders (SRD) are frequent comorbidities of the PG. Their co-presentation could mean worse prognosis of this patients. The PG as impulsive disorder could help to the understanding of the etiopathogenia of this disorder, but also of the prognosis. This hypothesis will add to the addictive one other treatment approaches that should be included in future studies of PG.
Inflammatory Breast Diseases during Lactation: Milk Stasis, Puerperal Mastitis, Abscesses of the Breast, and Malignant Tumors – Current and Evidence-Based Strategies for Diagnosis and Therapy

Background: Breast diseases during the lactation period are of high importance because they can be an essential cause for early cessation of breastfeeding. Methods: To provide a comprehensive overview on the current recommendations of diagnostics and therapies, a systematic literature research was performed on a variety of online medical databases. Results: The primary aim of all therapy is a quick reduction of pain to allow continued breastfeeding. Each particular form of breast disease requires a specific therapy. These can range from conservative measures to antibiotics and surgical procedures. All therapeutic measures, including pharmacotherapy, are normally not an indication for cessation of breastfeeding. Conclusion: Because the majority of breast diseases during the postnatal period occur only after the women have left the maternity clinics, all involved healthcare workers should educate women especially on preventive measures.
Chronic progressive cardiac dysfunction years after doxorubicin therapy for childhood acute lymphoblastic leukemia.

PURPOSE Cross-sectional studies show that cardiac abnormalities are common in long-term survivors of doxorubicin-treated childhood malignancies. Longitudinal data, however, are rare. METHODS Serial echocardiograms (N = 499) were obtained from 115 doxorubicin-treated long-term survivors of childhood acute lymphoblastic leukemia (median age at diagnosis, 4.8 years; median follow-up after completion of doxorubicin, 11.8 years). Results were expressed as z scores to indicate the number of standard deviations (SDs) above (+) or below (-) the normal predicted value. Median individual and cumulative doxorubicin doses were 30 mg/m2 per dose and 352 mg/m2, respectively. RESULTS Left ventricular fractional shortening was significantly reduced after doxorubicin therapy, and the reduction was related to cumulative dose. z scores for fractional shortening transiently improved before falling to -2.76 more than 12 years after diagnosis. Reduced fractional shortening was related to impaired contractility and increasing afterload, consequences of a progressive reduction of ventricular mass, and wall thickness relative to body-surface area. Left ventricular contractility fell significantly over time and was depressed at last follow-up in patients receiving more than 300 mg/m2 of doxorubicin. Systolic and diastolic blood pressures were below normal more than 9 years after diagnosis. Even patients receiving lower cumulative doxorubicin doses experienced reduced mass and dimension. Fractional shortening and dimension at the end of therapy predicted these parameters 11.8 years later. CONCLUSION Cardiac abnormalities were persistent and progressive after doxorubicin therapy. Inadequate ventricular mass with chronic afterload excess was associated with progressive contractile deficit and possibly reduced cardiac output and restrictive cardiomyopathy. The deficits were worst after highest cumulative doses of doxorubicin, but appeared even after low doses.
Seasonal dynamics and phylogenetic diversity of free-living and particle-associated bacterial communities in four lakes in northeastern Germany

The phylogenetic diversity and seasonal dynamics of free-living and particle-associated bacterial communities were investigated in the epilimnion of 4 lakes of the Mecklenburg Lake Dis- trict, northeastern Germany. All lakes differed in their limnological features, ranging from olig- otrophic to eutrophic and dystrophic. Bacterial community structure and seasonal dynamics were analyzed by denaturing gradient gel electrophoresis (DGGE) and clone libraries of 16S rRNA gene fragments. Communities of free-living and particle-associated bacteria greatly differed among the lakes. In addition, significant differences occurred between both bacterial fractions within each lake. Seasonal changes were more pronounced in free-living than in particle-associated bacterial commu- nities. Non-metric multidimensional scaling (NMDS) analyses revealed several strong correlations between bacterial communities (both free-living and particle-associated) and environmental vari- ables such as pH, dissolved organic carbon (DOC), phytoplankton biomasses, and primary produc- tion. Phylogenetically, all cloned and sequenced 16S rRNA gene fragments belonged to already known freshwater clusters. Clone libraries of free-living bacteria were dominated by sequences of Actinobacteria, Bacteroidetes, and Betaproteobacteria, whereas those of particle-associated bacteria predominantly consisted of Cyanobacteria and Bacteroidetes sequences. Other freshwater phyla such as Alpha- and Gammaproteobacteria, Verrucomicrobia, Planctomycetes, and members of Can- didate Division OP10 were found in low proportions. These differences may indicate an adaptation of distinct bacterioplankton communities to the respective environmental conditions of each lake.
Characterization of plasminogen activators from normal human breast and colon and from breast and colon carcinomas

Triton X‐100 and NaSCN extracts of 18 normal breast and colon tissues and of 20 breast and colon carcinomas were fractionated by SDS‐PAGE and plasminogen activators (PA) revealed by a zymographic method. Four different lysis bands, corresponding to MWs of 54,000, 68,000, 95,000 and 110,000 were observed. Using immunoadsorption with specific antisera against urokinase (UK) and tissue PA (t‐PA), we found that all normal tissue extracts contained free t‐PA (68 kd). Some of these revealed, in addition, a complex (110 kd) of t‐PA with a 40‐kd component. The latter presumably represents the fastacting specific inhibitor of t‐PA and UK. Most carcinoma extracts contained, in addition to the two t‐PA‐related lysis bands, the UK‐related 54 kd PA, and some a 95 kd complex of UK with the 40 kd component For each extractant, mean total fibrinolytic activity of normal and tumor tissue was comparable when measured on conventional fibrin plates, but breast and colon carcinomas contained higher concentrations of UK‐related PA. PA activity was higher in normal and carcinoma NaSCN extracts than in the corresponding Triton X‐100 extracts. In general, Triton X‐100 but not NaSCN extracts of malignant tissue contained a high concentration of fibrinolytic inhibitors. Mixing experiments revealed that the inhibitory activity was mainly directed against UK. It was abolished by acidification of the carcinoma extracts. The anti‐UK inhibitory activity was absent in extracts of normal breast or colon and appears to be different from the 40 kd fast‐acting PA inhibitor. These studies show that malignant transformation of breast and colon is accompanied by important changes of the production of a UK‐related PA and of an inhibitory activity directed against UK.
Characterization of the Interleukin-4 Nuclear Activated Factor/STAT and Its Activation Independent of the Insulin Receptor Substrate Proteins (*)

The activation of a latent DNA binding factor by interleukin-4 (IL-4), the IL-4 nuclear activated factor (IL-4 NAF), occurs within minutes of IL-4 binding to its receptor. Molecular characterization of IL-4 NAF by ultraviolet light cross-linking experiments revealed a single protein of 120-130 kDa in contact with the DNA target site. Glycerol gradient sedimentation analysis indicated a molecular mass of IL-4 NAF consistent with a monomer that is capable of binding DNA. The IL-4 NAF target site is a palindromic sequence that is also recognized by the interferon-induced transcription factor, p91/STAT1α. However, IL-4 NAF and p91/STAT1α display distinguishable DNA binding specificities that may generate one level of specificity in the expression of target genes. Previous studies suggested the involvement of the insulin receptor substrate-1 (IRS-1) in the IL-4 signal transduction pathway. Although IRS-1 is involved in the stimulation of mitogenesis, our results demonstrate that activation of IL-4 NAF is independent of IRS-signaling proteins. The results of this study indicate that IL-4 stimulates bifurcating signal pathways that can direct mitogenesis via the IRS-signaling proteins and specific gene expression via the IL-4 NAF.
Genetic gains in annual egg production from selection on part-record percent production in the fowl.

HE use of early partial egg production records as a selection criterion for Timproving annual egg production was proposed by DEMPSTER and LERNER (1947). Their proposal was based on the contention of DICKERSON and HAZEL (19%) that genetic gain should be based on a unit of time, and that under certain conditions the genetic gain per unit of time could be increased by reducing the age of the parents. Further theoretical confirmation that the special case of selection on partial records to improve annual egg production met the required conditions was presented by LERNER and CRUDEN (1948), MADDISON (1954) and MORRIS (1956) based on parameter estimates in different populations. Further support for this hypothesis was provided by ERASMUS (1962) from what appear to be phenotypic correlation effects, and VAN VLECK and DOOLITTLE (1964) from genetic parameter estimates in the Cornel1 control population. Parameters estimated from still another population by OLIVER, BOHREN and ANDERSON (1957) indicated that this population should also gain more rapidly in annual record by selection on partial egg records to January 1 (approximately 40 weeks of age), than from selection on annual record. Furthermore, the parameter estimates obtained led to the conclusion that even greater gains in annual record could be achieved in that population by selecting on percent production to a fixed age (a measure of rate) rather than on number of eggs to a fixed age, which is influenced by both rate of production and age at maturity, Empirical evaluations of the hypothesis are difficult. MORRIS ( 1963) found that selection on part record egg numbers yielded direct response in part record for 12 generations, but that response in annual record ceased to increase after about four generations. Similar results from 10 and 11 generations of selection on number of eggs to 275 days of age in two strains were reported by GOWE and STRAIN (1963). MORRIS (1964) obtained parameter estimates in one of his populations which led to his suggestion that selection on percent production to a fixed age as pro-
Autour de nouvelles notions pour l'analyse des algorithmes d'approximation : formalisme unifié et classes d'approximation

The main objective of the polynomial approximation is the development of polynomial time algorithms for NP-hard problems, these algorithms guaranteeing feasible solutions lying as near as possible to the optimal ones. This work is the fist part of a couple of papers where we introduce the key-concepts of the polynomial approximation and present the main lines of a new formalism. Our purposes are, on the one hand, to present this theory and its objectives and, on the other hand, to discuss the appropriateness and the pertinence of its constitutive elements, as people knew them until now, and to propose their enrichment. Henceforth, these papers are addressed to both domain researchers and non-specialist readers. We particularly quote the great theoretical and operational interest in constructing an internal structure for the class NPO (of the optimization problems in NP). In this fist part, we focus on some basic tools allowing the individual evaluation of the approximability properties of any NP-hard problem. We present and discuss notions as algorithmic chain, approximation level, hardness threshold and two notions of limits (with respect to algorithmic chains and with respect to problems instances). The notions dealt in the paper are presented together with several illustrative examples. Cet article est le premier d'une serie de deux articles ou nous presentons les principales caracteristiques d'un nouveau formalisme pour l'approximation polynomiale (algorithmique polynomiale a garanties de performances pour les problemes NP-difficiles). Ce travail est l'occasion d'un regard critique sur ce domaine et de discussions sur la pertinence des notions usuelles. Il est aussi l'occasion de se familiariser avec l'approximation polynomiale, de comprendre ses enjeux et ses methodes. Ces deux articles s'adressent donc autant aux specialistes qu'aux non specialistes de ce domaine. Nous insistons tout particulierement sur l'interet, tant theorique qu'operationnel, de mettre en evidence une structure au sein de la classe NPO des problemes d'optimisation de NP. Dans ce premier article, nous nous interessons aux outils qui permettent d'evaluer, dans l'absolu, les proprietes d'approximation de problemes difficiles. Nous discutons notamment les notions de chaines d'approximation, de niveau d'approximation, d'ordre de difficulte ainsi que deux notions de limites (par rapport a une suite d'algorithmes et par rapport aux instances). Chaque notion est largement discutee et illustree par de nombreux exemples choisis essentiellement pour leur valeur pedagogique.
Analysis of Japanese national consumer price index using fuzzy autocorrelation model with fuzzy confidence intervals

Management systems and economic systems are complex because they involve human behaviors and are affected by many factors. When a system includes uncertainty such as those concerning human behaviors, a fuzzy system approach plays a pivotal role in its analysis. Therefore, many results concerning their work have been reported. Yabuuchi et al. have proposed a fuzzy autocorrelation model which uses the concept of soft computing for the Box-Jenkins model. Moreover, fuzzy random variables have been used for the fuzzy autocorrelation model and a predictive accuracy of the model improved. In this work, an improved fuzzy autocorrelation model by using fuzzy random variables will be compared with a fuzzy autocorrelation model by Japanese national consumer price index. And we will be confirmed the proposed model can be with high accuracy.