Miracle-dz/UniFAR-FTUs huggingface dataset:
Genotypically unbalanced diploid<==>diploid foetal mouse chimaeras: possible relevance to human confined mosaicism.

Two series of mouse chimaeras were produced by aggregating pairs of eight-cell embryos that differed at the Gpi-1s locus, encoding glucose phosphate isomerase (GPI-1); the paired embryos were respectively homozygous Gpi-1sa/Gpi-1sa and Gpi-1sb/Gpi-1sb. Chimaeric blastocysts were transferred to pseudopregnant females, that were homozygous Gpi-1sc/Gpi-1sc and produced only GPI-1C enzyme. Quantitative electrophoresis of GPI-1 was used to estimate the contribution of each embryo (GPI-1A and GPI-1B enzyme activity) to the foetus, placenta and other extraembryonic tissues of 12 1/2 day chimaeric conceptuses. For both series of chimaeras, the distributions of %GPI-1A in different tissues were classified as (1) balanced and typical, (2) balanced but atypical or (3) unbalanced. One series of chimaeras was clearly unbalanced, so that the cells derived from the (C57BL x CBA/Ca)F2 embryo (Gpi-1sb/Gpi-1sb) predominated over those derived from the BALB/c inbred strain (Gpi-1sa/Gpi-1sa) in most foetuses. Two significant observations were made concerning this unbalanced series. Firstly, the mean composition of the placenta and other extraembryonic tissues was similar to that in the foetus, i.e. also unbalanced with (C57BL x CBA/Ca)F2 (abbreviated to BF2) cells predominating. Secondly, despite this generalized deficiency of BALB/c cells, there were differences in the frequency of non-chimaeric tissues between different developmental lineages. In 20/38 [corrected] chimaeric conceptuses in the unbalanced series only BF2 cells were detected in the foetus, whereas both BF2 and BALB/c cells were present in at least one of the extraembryonic tissues. This group of chimaeras, therefore, shows some similarities to human confined mosaicism. Although chimaerism occurred more often in the primitive endoderm (hypoblast) lineage (yolk sac endoderm and parietal endoderm) than in the placenta, this may also be the case in human mosaics. The mosaic status of the human yolk sac endoderm is usually unknown so it is possible that mosaicism often occurs in the yolk sac endoderm as well as the trophectoderm in human 'confined placental mosaicism'. The uniformly unbalanced phenotype seen in the mouse chimaeras may be a result of generalized cell selection against BALB/c cells in all tissues. As an alternative explanation, we propose that most of the BALB/c cells in the blastocyst are allocated to the mural trophectoderm, which has a limited mitotic potential and so contributes little to the mid-gestation conceptus. Further work is required to test these possibilities.
Identification of bacteria infecting Ixodes ricinus ticks by 16S rDNA amplification and denaturing gradient gel electrophoresis.

Ticks harbor a complex microbial population, which they acquire while feeding on a variety of mammalians and birds. Zoonotic diseases transferred by ticks are an increasing problem and have become a burden to the community. 16S rDNA amplification and denaturing gradient gel electrophoresis (DGGE) enables detection of the broad spectrum of bacteria that settles in the ticks. Profiling the complete microbial population in ticks may provide a better understanding of the ticks' potential to harbor and disperse pathogens. Separation of pathogenic species by DGGE is based on variation in %GC content within the 16S rDNA genetic region. Sequencing of these fragments allows identification of bacterial species. Present study identified some well-known tick-infecting bacteria, such as members of genus Borrelia, Rickettsiales, and Pseudomonas, but also less described tick-infecting bacteria such as Rhodococcus erythropolis, Spiroplasma spp. , and an endosymbiont of the microarthropod Folsomia candida. This is the first report of Segniliparus rugosus-infected Ixodes ricinus ticks. Also, it is the first report of several of these pathogens in the Norwegian tick population.
Energy Efficiency and Quality of Data Reconstruction Through Data-Coupled Clustering for Self-Organized Large-Scale WSNs

Energy efficiency has been a leading issue in Wireless Sensor Networks (WSNs) and has produced a vast amount of research. Although the classic tradeoff has been between the quality of gathered data versus the lifetime of the network, most works gave preference to an increased network lifetime at the expense of the data quality. A common approach for energy efficiency is partitioning the network into clusters with correlated data, where the representative nodes simply transmit or average measurements inside the cluster. In this paper, we explore the joint use of in-network processing techniques and clustering algorithms. This approach seeks both high data quality with a controlled number of transmissions using an aggregation function and an energy efficient network partition, respectively. The aim of this combination is to increase energy efficiency without sacrificing the data quality. We compare the performance of the Second-Order Data-Coupled Clustering (SODCC) and Compressive-Projections Principal Component Analysis (CPPCA) algorithm combination, in terms of both the energy consumption and the quality of the data reconstruction, to other combinations of the state-of-the-art clustering algorithms and in-network processing techniques. Among all the considered cases, the SODCC + CPPCA combination revealed a perfect balance between data quality, energy expenditure, and ease of network management. The main conclusion of this paper is that the design of WSN algorithms must be processing-oriented rather than transmission-oriented, i.e., investing energy on both the clustering and in-network processing algorithms ensures both energy efficiency and data quality.
Heterologous Expression and Molecular and Cellular Characterization of CaPUB1 Encoding a Hot Pepper U-Box E3 Ubiquitin Ligase Homolog1[C]

The U-box motif is a conserved domain found in the diverse isoforms of E3 ubiquitin ligase in eukaryotes. From water-stressed hot pepper (Capsicum annuum L. cv Pukang) plants, we isolated C. annuum putative U-box protein 1 (CaPUB1), which encodes a protein containing a single U-box motif in its N-terminal region. In vitro ubiquitination and site-directed mutagenesis assays revealed that CaPUB1 possessed E3 ubiquitin ligase activity and that the U-box motif was indeed essential for its enzyme activity. RNA gel-blot analysis showed that CaPUB1 mRNA was induced rapidly by a broad spectrum of abiotic stresses, including drought, high salinity, cold temperature, and mechanical wounding, but not in response to ethylene, abscisic acid, or a bacterial pathogen, suggesting its role in the early events in the abiotic-related defense response. Because transgenic work was extremely difficult in hot pepper, in this study we overexpressed CaPUB1 in Arabidopsis (Arabidopsis thaliana) to provide cellular information on the function of this gene in the development and plant responses to abiotic stresses. Transgenic Arabidopsis plants that constitutively expressed the CaPUB1 gene under the control of the cauliflower mosaic virus 35S promoter had markedly longer hypocotyls and roots and grew more rapidly than the wild type, leading to an early bolting phenotype. Microscopic analysis showed that 35S∷CaPUB1 roots had increased numbers of small-sized cells, resulting in disordered, highly populated cell layers in the cortex, endodermis, and stele. In addition, CaPUB1-overexpressing plants displayed increased sensitivity to water stress and mild salinity. These results indicate that CaPUB1 is functional in Arabidopsis cells, thereby effectively altering cell and tissue growth and also the response to abiotic stresses. Comparative proteomic analysis showed that the level of RPN6 protein, a non-ATPase subunit of the 26S proteasome complex, was significantly reduced in 35S∷CaPUB1 seedlings as compared to the wild type. Pull-down and ubiquitination assays demonstrated that RPN6 interacted physically with CaPUB1 and was ubiquitinated in a CaPUB1-dependent manner in vitro. Although the physiological function of CaPUB1 is not yet clear, there are several possibilities for its involvement in a subset of physiological responses to counteract dehydration and high-salinity stresses in transgenic Arabidopsis seedlings.
Comparison of restriction endonuclease analysis, ribotyping, and pulsed-field gel electrophoresis for molecular differentiation of Clostridium difficile strains

A combined clinical and molecular epidemiologic analysis of 46 strains of Clostridium difficile, including 16 nosocomial isolates from one ward (outbreak ward) plus 17 other nosocomial isolates and 13 community-acquired isolates, was performed. HindIII digests of total cellular DNA were analyzed by restriction enzyme analysis (REA) and ribotyping; SmaI digests were analyzed by pulsed-field gel electrophoresis (PFGE). Isolates were assigned to typing groups on the basis of the profiles detected; isolates with closely related profiles were assigned to subgroups. The 16 isolates from the outbreak ward were resolved by both REA and PFGE into five distinct groups; 13 isolates represented two REA groups and three PFGE groups and two isolates were resolved as distinct groups by both techniques. DNA obtained from one isolate was persistently partially degraded, precluding analysis by PFGE. Seventeen sporadic nosocomial isolates were resolved by REA and PFGE into comparable numbers of groups (i.e., nine groups) and subgroups (i.e., 15 and 14 subgroups, respectively), with two isolates not evaluable by PFGE. The 13 epidemiologically unrelated community-acquired isolates were assigned to 11 groups by REA and to 12 groups by PFGE. Overall, ribotyping identified only nine groups among the 46 isolates. We conclude that REA and PFGE have comparable discriminatory powers for epidemiologic typing of C. difficile isolates and that ribotyping is appreciably less discriminatory. For a few isolates, partial DNA degradation prevented analysis by PFGE but not by REA or ribotyping; the cause of the degradation is unknown.
Long-Term Prospective Evaluation of Offspring of Diabetic Mothers

We have suggested that altered maternal metabolism may affect the subsequent anthropometrie and neuropsychological development of children who were in utero during disturbances in maternal fuel economy. This study reports the physical growth through 8 yr of age and the neuropsychological development through 4 yr of age in offspring of diabetic mothers (ODM). At birth, 50% of infants had weights >90th percentile for gestational age. By 12 mo, length and weight were similar to the general population. Height remained normal until 7 yr of age, when it became slightly greater than average. After 5 yr of age, relative weight increased dramatically, and by 8 yr of age, half of the ODM had weights >90th percentile. This childhood obesity in ODM is correlated with maternal prepregnant weight and independently with amniotic fluid insulin at 32–38 wk gestation. The Brazelton Neonatal Behavioral Assessment Scale (BNBAS) was administered to 185 newborn ODM. Significant correlations were found between poorer second- and third-trimester glycemie regulation and lower scores in three of four newborn BNBAS dimensions. The Stanford-Binet Intelligence Scale was measured in 102 ODM at 4 yr of age. We found an inverse correlation between childhood IQ and second- and third-trimester maternal lipid metabolism (serum free fatty acids and β-hydroxybutyrate). This correlation is not explained by adverse perinatal events, socioeconomic status, maternal IQ, ethnicity, or diabetes type. These long-range associations between altered maternal metabolism and childhood growth and development continue to support Freinkel's hypothesis of fuel-mediated teratogenesis.
Primary cloud assessment in THEOS imagery using k-means clustering and morphological transformation algorithms

THEOS is the earth observation satellite system, which acquires earth images via its optical instruments. As its instruments consists of passive type CCD sensors, the instruments require sunlight reflected from the Earth surface for imaging. Then, cloud presence above imaging area directly affects the image usability, image interpretation, image classifying accuracy, calibration activity and so on. As THEOS mainly focuses on country needs, imaging over Thailand and Asian countries has been main priority since its launch. These countries are in the equatorial region and subjected to heavy cloud throughout the year. Thus, cloud cover assessment plays important role in assessing image usability. This study aims to develop algorithms which will be applied to the images for automatic identification and estimation of cloud content for each image. The algorithms are separated into 2 steps. Firstly, using the k-means clustering for specific cloud threshold value detection. Pixels with digital number ( DN) value above cloud threshold are marked as cloud pixels. Secondly, morphological transformation is subsequently applied to the data consisting of individual steps, erosion, dilation, closing and opening for reassessing and double-checking the non-cloud pixel. The results after implementing the cloud mask investigation indicates that this approach is capable of providing accurate cloud coverage assessment for THEOS images.
Cloning, localization and functional properties of a cGMP‐gated channel in photoreceptor cells from fish pineal gland

Abstract: The perception of photic information and its translation into a rhythmic melatonin signal differ considerably among vertebrates. In the fish pineal gland, melatonin biosynthesis is controlled directly by the natural light/dark cycle. There are indications that the mechanisms of phototransduction are similar in the retinal and pineal photoreceptor cells. Here we report the molecular cloning of a novel ionic cyclic guanosine monophosphate (cGMP)‐gated channel from trout pineal photoreceptors. The deduced amino acid sequence exhibits a high sequence homology to cyclic nucleotide‐gated‐3 (CNG) channels from retinal cones. In situ hybridization with sections of trout pineal gland revealed the expression of CNG channel in photoreceptor cells of the pineal organ. Electrophysiological studies by means of patch‐clamp technique indicated that the native channel in photoreceptor cells and the expressed channel in a human cell line (HEK 293 cells) have properties similar to those of cone‐CNG (cCNG)‐3 channels. They are activated by cGMP, insensitive to cyclic adenosine monophosphate (cAMP) and blocked by intracellular Mg2+ ions at positive voltage values. They have a single‐channel conductance close to 42 pS in negative voltage range. In transfected HEK cells loaded with the calcium indicator dye Fura 2, direct activation of CNG channels by 8‐Br‐cGMP increased fluorescence. The signal was blocked by the addition of Mg2+ ions. From these results, it is suggested that the pineal cyclic nucleotide‐gated channel is a good candidate for mediating calcium entry into the pineal photoreceptors. It is most probably a key element in the signalling pathways that control the rhythmic production of melatonin.
General practitioners’ knowledge and approach to chronic kidney disease in Karachi, Pakistan

Due to lack of adequate number of formally trained nephrologists, many patients with chronic kidney disease (CKD) are seen by general practitioners (GPs). This study was designed to assess the knowledge of the GPs regarding identification of CKD and its risk factors, and evaluation and management of risk factors as well as complications of CKD. We conducted a cross-sectional survey of 232 randomly selected GPs from Karachi during 2011. Data were collected on a structured questionnaire based on the kidney disease outcomes and quality initiative recommendations on screening, diagnosis, and management of CKD. A total of 235 GPs were approached, and 232 consented to participate. Mean age was 38.5 ± 11.26 years; 56.5% were men. Most of the GPs knew the traditional risk factors for CKD, i.e., diabetes (88.4%) and hypertension (80%), but were less aware of other risk factors. Only 38% GPs were aware of estimated glomerular filtration rate in evaluation of patients with CKD. Only 61.6% GPs recognized CKD as a risk factor for cardiovascular disease. About 40% and 29% GPs knew the correct goal systolic and diastolic blood pressure, respectively. In all, 41% GPs did not know when to refer the patient to a nephrologist. Our survey identified specific gaps in knowledge and approach of GPs regarding diagnosis and management of CKD. Educational efforts are needed to increase awareness of clinical practice guidelines and recommendations for patients with CKD among GPs, which may improve management and clinical outcomes of this population.
Performance analysis of sparse recovery models for bad data detection and state estimation in electric power networks

This paper investigates the sparse recovery models for bad data detection and state estimation in power networks. Two sparse models, the sparse L1-relaxation model (L1-R) and the multi-stage convex relaxation model (Capped-L1), are compared with the weighted least absolute value (WLAV) in the aspects of the bad data processing capacity and the computational efficiency. Numerical tests are conducted on power systems with linear and nonlinear measurements. Based on numerical tests, the paper evaluates the performance of these robust state estimation models. Furthermore, suggestion on how to select parameter of sparse recovery models is also given when they are used in electric power networks.
Stability of Ferromagnetic Patterns Inscribed on Arrays of Multisegmented Magnetic Nanocylinders

Magnetic nanocylinders (MNs) can be grown inside of longitudinal nanoporous produced in alumina membranes by means of different techniques. In a similar way, multisegmented MNs (m-MNs) can be obtained by alternating magnetic and nonmagnetic materials during the fabrication process. In both cases, nanocylinders result axially parallel and forming triangular arrays immerse themselves within the membrane used to produce them. Due to shape anisotropy, each magnetic segment presents its magnetization pointing along the cylinder axis either inward or outward of the membrane plane. The as-grown system presents no global magnetization. A strong enough localized magnetic field can revert the magnetization of small groups of neighboring m-MNs. This feature can be used to inscribe ferromagnetic patterns (FP) over either membrane surface to store fixed information (security codes or firmware). Here, we study the total energy per cylinder for the case of a disc shaped FP inscribed over a circular membrane containing a huge amount of m-MNs. To try to prevent spontaneous magnetization reversion due to thermal effects we test for m-MNs a stabilization mechanism proposed previously for homogeneous MNs: an opposite ferromagnetic band (OFB) inscribed inside the FP. We have compared inscription and stabilization of FP over arrays of homogenous and multisegmented MNs.
Determination of the best model for estimating heritability of economic traits and their genetic and phenotypic trends in Iranian native fowl

Abstract. The objective of the present study was to estimate the heritability and to assess the existence of maternal effects for economic traits in Iranian native fowl. Variance components were estimated for body weight at hatch (BW0), 8 (BW8) and 12 (BW12) weeks of age, age at sexual maturity and weight at sexual maturity, egg number and average egg weight at 28th, 30th and 32nd weeks using restricted maximum likelihood method and six animal models. The best model was determined using the Akaike information criterion for each trait. For age at sexual maturity, the basic model consisting of direct genetic effects was superior. For weight at sexual maturity and egg number, a model consisting of maternal permanent environmental effects in addition to direct genetic effects was the best. For average egg weight at 28th, 30th and 32nd weeks, the model with direct and maternal genetic effects assuming no covariance between them was the best. For BW0, BW8 and BW12, the model including maternal genetic and permanent environmental effects in addition to direct genetic effects was the most appropriate. The estimates of direct heritability ranged from 0.05 (BW0) to 0.35 (weight at sexual maturity). Direct genetic variance and heritability were overestimated if maternal effects were ignored in the statistical model for all traits except ASM. The results indicated that the evaluation of direct and maternal genetic and phenotypic trends based on the best model for each trait was carried out. Maternal genetic trends for BW0, BW8, BW12 and average egg weight at 28th, 30th and 32nd weeks were significantly positive. Present results indicated favourable effects of the performed breeding program for all traits except BW0, during generations.
Microbial Pathogenesis in Cystic Fibrosis: Pulmonary Clearance of Mucoid Pseudomonas aeruginosa and Inflammation in a Mouse Model of Repeated Respiratory Challenge

ABSTRACT Chronic endobronchiolitis compounded by recurring Pseudomonas aeruginosa infections is the major cause of morbidity and mortality in patients with cystic fibrosis (CF). In this study, a mouse model of repeated respiratory exposure to P. aeruginosa was established to facilitate investigations of factors contributing toP. aeruginosa persistence and associated inflammatory processes in the lung. While a single exposure to P. aeruginosa aerosols resulted in only mild histopathological changes, repeated exposure caused significant lung pathology in C57BL/6J mice. The peak of histopathological changes and inflammation in C57BL/6J mice was characterized by subacute lymphohistiocytic bronchopneumonia and persistent elevation of tumor necrosis factor alpha and macrophage inflammatory protein 2 in the lung but not in the serum. When isogenic nonmucoid (mucA+) and mucoid (mucA22) P. aeruginosa strains were compared, the mucoid cells were cleared several-fold less efficiently than the parental nonmucoid strain during the initial stages of the aerosol exposure regimen. However, the microscopic pathology findings and proinflammatory cytokine levels were similar in mice exposed to nonmucoid and mucoid P. aeruginosa throughout the infection. We also tested lung histopathology and proinflammatory cytokines in interleukin 10 (IL-10)-deficient transgenic (IL-10T) mice. Significant mortality was seen in IL-10T mice on initial challenge withP. aeruginosa, although no histopathological differences could be observed in the lungs of C57BL/6J and surviving IL-10T mice after a single exposure. However, increased pathology was detected in IL-10T mice relative to C57BL/6J after repeated challenge with P. aeruginosa. This observation supports the proposals that anti-inflammatory cytokines may play a role in suppressing P. aeruginosa-induced tissue damage during chronic infection.