Miracle-dz/UniFAR-FTUs huggingface dataset:
An engineering analysis of myocardial fiber orientation in pig's left ventricle in systole

The concept of discrete layers and bundles of muscle as a basic structural arrangement in left ventricular myocardium was tested by measuring the helix angles at 1 mm intervals from endocardium to epicardium, using pig's heart in the contracted state. A fixed coordinate system was established which permitted measurement of corresponding sites in hearts of different dimensions.
Reduced cellular cross-sectional area in the leaf elongation zone of wheat causes a decrease in dry weight deposition under saline conditions

Expansion and dry weight (DW) of wheat leaves are spatially distributed along the axis and affected by salinity. The objective of this study was to evaluate the effect of salinity on the spatial distribution of cellular cross-sectional area and DW in the elongating and mature leaf zones of leaf 4 of the main stem of spring wheat (Triticum aestivum L. cv. Lona) during its linear growth phase. Plants were grown in illitic–chloritic silt loam with 0 and 120 mM NaCl in a growth chamber. Cellular cross-sectional area and DW contents of leaves were determined on the 5–20-mm scale along the leaf axis. Spatial distribution of cellular cross-sectional area changed slightly with distance within the elongation zone in both treatments. The cellular cross-sectional area of the leaf at 120 mM NaCl was reduced by 32% at 5 mm, as compared with about 36% averaged from the region between 5 and 30 mm from the leaf base, indicating that the reduction in the cellular cross-sectional area by salinity occurred mainly at the leaf base when the leaf initiates. A slight decrease in the DW per leaf length at a given location in the elongation zone may be due to the strongly decreased cellular cross-sectional area by salinity. This suggests that the limitation of leaf growth by salinity may be due mainly to the effect of salinity on leaf expansion, but not due to the effect on the synthesis of dry matter.
Regime shifts observed in Lake Kasumigaura, a large shallow lake in Japan: Analysis of a 40‐year limnological record

Lake Kasumigaura, which is composed of the two basins (Nishiura and Kitaura), is a large, shallow, hypereutrophic lake. Phytoplankton and water quality records from the past forty years were analysed to elucidate whether or not, when, and what type of certain regime shifts may have occurred, based on using inferential regime shift detectors. Characteristics of the phytoplankton and water quality changes were similar at 6 sampling sites in the two basins, with 20 water quality parameters being classified into four groups, based on cluster analysis. Shifts in dominant plankton groups (DPGs) and water quality occurring almost concomitantly, concentration on the period from 1987 to 1992 (Shift A) and from 1997 to 2001 (Shift B), with those observed for the two basins usually being similar with small differences. Two types of inferential regime shift detectors (sequential t-test type; Rodionov's RSD and sequential F-test type: package strucchange in R) yielded similar timings and significances of the shifts. Furthermore, changes in skewness and conditional heteroskedasticity (package early warnings in R) usually represented early warning signals before the shifts. Correlation analysis and ratios of dissolved inorganic nitrogen (DIN) vs. total phosphorus (TP) supported the hypothesis that phosphorus was the phytoplankton biomass limiting nutrient, except for one period for the Nishiura basin. Neither the nitrogen:phosphorus (N/P) ratio hypothesis and ammonia–nitrate (NH4-N/NO3-N) hypothesis satisfactorily explain the DPGs before and after Shift A (Microcystis spp. and Planktothrix spp., respectively), although it may be possible that these ratios triggered the DPG change in this shift. A considerable increase in silicon was observed for Shift B when the DPGs changed from cyanobacteria to diatoms. Further studies on the accurate types and triggers of the regime shifts are necessary to better understand the interactions between ecosystem and water quality for this and similar lakes elsewhere.
A Miocene Relative of the Ganges River Dolphin (Odontoceti, Platanistidae) from the Amazonian Basin

A Miocene relative of the Ganges River dolphin (Odontoceti, Platanistidae) from the Amazonian Basin Giovanni Bianucci a , Olivier Lambert b , Rodolfo Salas-Gismondi c , Julia Tejada c d , Francois Pujos d e , Mario Urbina c & Pierre-Olivier Antoine f a Dipartimento di Scienze della Terra , Universita di Pisa, via S. Maria, 53 , I-56126 , Pisa , Italy b Institut royal des Sciences naturelles de Belgique , Departement de Paleontologie , Rue Vautier, 29, B-1000 , Brussels , Belgium c Departamento de Paleontologia de Vertebrados , Museo de Historia Natural-UNMSM , Av. Arenales 1256, Lima 14 , Peru d Institut Francais d’Etudes Andines (IFEA) , Casilla 18-1217, Av. Arequipa 4595, Lima 18 , Peru e Departamento de Paleontologia , Instituto Argentino de Nivologia, Glaciologia y Ciencias Ambientales (IANIGLA), CCT-CONICET-Mendoza , Avda. Ruiz Leal s/n, Parque Gral. San Martin, 5500 , Mendoza , Argentina f Institut des Sciences de l’Evolution (CNRS-UMR 5554), CC064, Universite Montpellier 2 , Place Eugene Bataillon , F-34095 Montpellier Cedex 05, France Published online: 07 May 2013.
Genetic assessment of some phenotypic variants of rice (Oryza spp.) for some quantative characters under the Gangatic plains of West Bengal

Twenty two (22) recombinant inbreed lines (RIL’s) derived from interspecific cross derivative of Oryza sativa and Oryza rufipogon along with two local check varieties MTU 7029 and Ranjit were evaluated in randomized block design (RBD) with two replications at two different environments (1 st at Regional Research Station, New Alluvial Zone (NAZ), Bidhan Chandra Krishi Viswavidyalaya, Sub-Centre, Chakdah, Nadia, West Bengal during Kharif season 2009 and 2 nd at Instructional Farm, Bidhan Chandra Krishi Viswavidyalaya, Jaguli, Nadia, during Kharif season 2010), to study the polygenic variations in yield for yield and its attributing characters and their cause and effect relationship. The analysis of variances revealed the significant differences among the 24 genotypes against all the characters except panicle weight, grain length, grain breadth and grain L/B ratio. The magnitude of phenotypic coefficients of variation (PCV) was higher than genotypic coefficients of variation (GCV) for all the characters suggesting the influences of the environmental forces on the expression of these characters. High PCV and GCV values were observed in grain yield per plant, 1000 grain weight, L/B ratio, grain breadth and panicle weight. High heritability coupled with moderate to high genetic advance as percent of mean for plant height, panicle weight, grain length, grain L/B ratio, 1000 grain weight and yield per plant while low heritability estimates along with low genetic advance were observed for fertility percentage and florets number per panicle. In general, genotypic correlation coefficients were higher than their corresponding phenotypic correlation coefficients. Path coefficient analysis revealed that number of characters chosen was very much appropriate as evident from low value of residual effect. Maximum positive direct effect was imparted by number of gains per panicle followed by grain L/B ratio, days to 50% flowering and panicle length respectively. Florets number per panicle imparted the maximum negative direct effect followed by grain breadth, fertility percentage and panicle number per plant. Per se performance revealed that two lines viz; KS-7 and KS-13 were promising in respect of grain yield and some other yield related traits. Number of grains per panicle and floret number per panicle give significant positive correlation with yield. Key words: Correlation, genotypic coefficients of variation, genetic advance, heritability, phenotypic coefficients of variation, rice, recombinant inbreed lines.
IFN‐γ‐induced TNF‐α is a prerequisite for in vitro production of nitric oxide generated in murine peritoneal macrophages by IFN‐γ

The effect of IFN‐γ to stimulate formation of nitric oxide (NO) by normal murine peritoneal macrophages (Mϕ) has been found to be completely dependent on the ability of IFN‐γ to activate secretion of TNF‐α. The NO‐stimulatory effect of IFN‐γ was abolished by anti‐TNF‐α antibodies, the inhibitory intervention of which could be fully reversed by exogenously supplied TNF‐α. Accordingly, the failure of Mϕ from C3H/HeJ mice to secrete TNF‐α upon stimulation with IFN‐γ was associated with their complete incapability to generate NO, unless they were simultaneously treated with IFN‐γ + TNF‐α. Collectively, the data document that similar to the NO up‐regulatory action of other cytokines, the effect of IFN‐γ is not independent, but depends on a synergistic cooperation with the self‐produced TNF‐α. The findings thus indicate that a widespread opinion claiming that IFN‐γ per se is able to stimulate biosynthesis of NO needs revision.
NPR1 enhances the DNA binding activity of the Arabidopsis bZIP transcription factor TGA7This paper is one of a selection of papers published in a Special Issue from the National Research Council of Canada – Plant Biotechnology Institute.

Pathogen-induced transcriptional reprogramming of the plant genome is mediated predominantly by the cofactor NPR1 (NON-EXPRESSOR OF PATHOGENESIS-RELATED GENES1). NPR1 lacks any known DNA-binding domain and is proposed to regulate transcription through interactions with TGA transcription factors that bind to as-1-like pro- moter elements. Previous studies have focused on the interaction of NPR1 with subgroup I (TGA1, TGA4) or subgroup II (TGA2, TGA5, TGA6) factors. Using the yeast two-hybrid system, we showed that a member of subgroup III (TGA7) in- teracts with wild-type NPR1 but not with mutants in the ankyrin repeats that are important for disease resistance. Muta- tions in the NPR1 BTB/POZ domain also greatly reduced interaction with TGA7. NPR1 substantially increased the binding of TGA7 to cognate promoter elements in vitro, including a salicylic-acid-inducible element of the PR-1 promoter. While TGA7 interacted with all TGA factors tested, interactions were not observed between TGA2 and subgroup I factors, indicating that cross-clade interaction is not a general property of the family. Transcripts from subgroup III TGA factors were weakly inducible by salicylic acid and pathogens, but only TGA3 expression was dependent on NPR1. These results suggest that NPR1-mediated DNA binding of TGA7 could regulate the activation of defense genes.
Potential allelopathic effects of Suregada multiflorum and the influence of soil type on its residue's efficacy

This experiment was conducted to determine the potential allelopathic effects of the aqueous extracts and dried leaf powder of Suregada multiflorum and to find the herbicidal effects of its granule on the weed species, barnyardgrass (Echinochloa crus-galli) and slender amaranth (Amaranthus viridis), in various growth media (germination paper, sand, and soil). Observations in this study demonstrated that the potential and magnitude of their inhibitory effects varied among the plant parts. The leaves and branches possessed the strongest inhibition levels, followed by the bark. The aqueous extract from the leaves of S. multiflorum had a remarkably stronger inhibitory effect on the germination and growth of slender amaranth, compared with barnyardgrass; when applied at the concentration of 100 g L–1, it completely inhibited the germination and initial seedling growth of slender amaranth. In addition, all the treatments of the dried leaf powder had stronger inhibition effects than the aqueous extract. Interestingly, the inhibitory effects of the dried leaf granule of S. multiflorum were stronger than the effects of the dried leaf powder at equal rates. The degree of inhibitory effect of the S. multiflorum granule, applied in various growing media, can be classified in order of decreasing inhibition as germination paper = sand > clay soil. The present study indicates that the S. multiflorum granule product that was developed in this research has the potential to provide a powerful organic herbicide for controlling slender amaranth.
Basal Cytokeratins and HER-2 Oncogene in Breast Cancer

10 INTRODUCTION . 12 REVIEW OF THE LITERATURE . 14 1. Human mammary gland epithelium . 14 1.1 Cytokeratin expression in normal human mammary gland. 16 1.2 Mammary gland stem/progenitor cells. 18 2. Breast cancer stem cells . 21 3. Basal phenotype breast cancer . 23 3.1 Identification of basal phenotype breast cancer with immunohistochemistry. 23 3.2 Identification of basal phenotype breast cancer with gene expression microarrays . 25 3.3 Prevalence of basal phenotype tumors in sporadic breast cancers . 26 3.4 Association of the basal phenotype with BRCA1 in hereditary and sporadic tumors. 27 3.5 Morphological features and histological type of basal phenotype breast cancer. 29 3.6 Clinicopathological and biological characteristics of basal phenotype breast cancer . 30 3.7 Association of basal phenotype breast cancer with HER-2 status. 32 3.8 Genetic alterations in basal phenotype tumors . 33 3.9 Prognosis of basal phenotype breast cancer . 33 3.10 Treatment of basal phenotype breast cancer . 35 4. HER-2 oncogene in breast cancer.36 4.1 Methods in the assessment of HER-2 status. 38 4.1.1 Detection of HER-2 gene amplification by FISH. 39 4.1.2 Detection of HER-2 gene amplification by CISH . 40 AIMS OF THE STUDY . 42 MATERIALS AND METHODS . 43 1. Tumor samples and cell lines . 43 1.1 Study I . 43 1.2 Study II. 43 1.3 Study III . 44 1.4 Study IV . 44 2. Immunohistochemistry (I,II,IV). 45 2.1 The optimization of basal phenotype breast cancer detection (I) . 46 2.2 Double immunostaining of CK5/14 and Ki-67 (IV) . 47 2.3 Interpretation of the immunohistochemical stainings (I,II,IV). 48 3. In situ hybridization (I-IV) . 48 3.1 Dual-color chromogenic in situ hybridization (dc-CISH, III) . 49 3.1.1 Pretreatment. 49 3.1.2 Hybridization. 49 3.1.3 Detection of the hybridized probes. 50 3.2 Fluorescence in situ hybridization (III) . 50 3.3 Scoring of dc-CISH and FISH samples (III) . 51 4. Statistical methods (I-IV). 51
Effect of water temperature and prey concentrations on initial development of Lophiosilurus alexandri Steindachner, 1876 (Siluriformes: Pseudopimelodidae), a freshwater fish

The aim of this study was to investigate the effects of water temperature and prey concentrations (Artemia nauplii) on the initial development of Lophiosilurus alexandri larvae. The experiment was conducted using a 4 x 2 factorial design, with four water temperatures (23, 26, 29 and 32 °C), two different initial prey concentrations (P700 and P1,300) and three replicates. Feeding was increased during the fifteen-day experiment. At the end of the experiment, the survival and condition factor were affected only by prey concentrations, with elevated numbers of Artemia nauplii leading to higher averages of these variables. The total length (TL) and specific growth rate were separately influenced by temperature and prey concentration, without interaction between them, and weight showed an interaction with these factors. In general, an increase of temperature (23 to 32 °C) improved the growth and nitrogen gain in L alexandri larvae. For TL, the optimal temperatures estimated were 31.4 and 31.0 °C for P700 and P1,300, respectively. Similar mean body weight larvae and nitrogen gain were observed at 23 °C for both levels of prey concentrations. For other temperatures, the P1,300 level provided greater weight gain for L. alexandri. Therefore, it is suggested that temperatures between 29-32 °C combined with a higher level of prey concentration maximise the development and nitrogen gain in L. alexandri larvae. Moreover, this is the first result about nitrogen incorporation in neotropical fish larvae.
Crazy wasps: when parasites manipulate the Polistes phenotype

The infection of Polistes dominulus wasps by the strepsipteran Xenos vesparum provides a suitable case study for exploring parasitic manipulation. One aim of this review is to summarize the life cycle of X. vesparum: from infection of immature wasps to the "stylopization" of adults, and from its mating at summer aberrant aggregations of infected wasps to the overwintering of fertilized Xenos inside the abdomen of hibernating wasps. The second aim of this review it to highlight how this parasite manipulates the flexible phenotype of the wasp to maximize its own reproductive success.
Lords of the fly: Drosophila genetics and the experimental life.

The common fruit fly, Drosophila, has long been one of the most productive of all laboratory animals. From 1910 to 1940, the centre of Drosophila culture in America was the school of Thomas Hunt Morgan and his students, Alfred Sturtevant and Calvin Bridges. They first created "standard" flies through inbreeding and by organizing a network for exchanging stocks of flies which spread their practices around the world. In "Lords of the Fly", Robert E. Kohler argues that fly laboratories are a special kind of ecological niche in which the wild fruit fly is transformed into an artificial animal with a distinctive natural history. He shows that the fly was essentially a laboratory tool whose startling productivity opened many new lines of genetic research. Kohler also explores the moral economy of the "Drosophilists": the rules for regulating access to research tools, allocating credit for achievements, and transferring authority from one generation of scientists to the next. By closely examining the Drosophilists' culture and customs, Kohler reveals essential features of how experimental scientists do their work.
Comparison of Four Methods Calculating the Seasonal Pattern of Plant Growth Efficiency of a Kiwifruit Berry

Le cout pour la croissance du fruit du kiwi est calcule grâce a l'utilisation de plusieurs methodes. Celles-ci sont comparees tout au long de la croissance du fruit grâce a la mesure des differents composants du fruit, de la floraison a la maturite. Il ressort de cette etude que deux des methodes sur les quatre utilisees sont preferables
Transmission Electron Microscopy of Protein Bodies in the Amaranthus cruentus Seed Embryo

The ultrastructure of protein bodies in embryonic cells of the Amaranthus cruentus seed was examined by transmission electron microscopy. Most of the protein bodies of 2-5μm in diameter were densely electron-stained, containing phytin globoid inclusions but not protein crystalloid. Numerous small lipid bodies (spherosomes) of various sizes and shapes surrounded these protein bodies and filled the cytoplasm. No ER-bound polysomes were detectable around these protein bodies, suggesting that Amaranthus seed protein bodies are morphologically similar to the globulin type of legumes, quinoa (Chenopodium quinoa Willd.), and buckwheat (Fagopyrum esculentum Moench), the last two of which are taxonomically close to Amaranthaceae.
Striking a balance between retaining populations of protected seahorses and maintaining swimming nets

1. The fish family Syngnathidae (seahorses, pipefish, pipehorses and seadragons) is fully protected in New South Wales, Australia, but in some countries certain species are threatened by unsustainable collecting, capture as incidental bycatch, and habitat degradation. 2. Within Sydney Harbour, two species of seahorses (Hippocampus abdominalis and Hippocampus whitei) have been found to colonize artificial structures such as jetty pylons and protective netted swimming enclosures. These protective nets are subject to fouling from epibiotic growth (algae, ascidians, bryozoans, etc.) and rubbish, which causes the nets to collapse from the additional weight. Local authorities employ diving contractors on an ad hoc basis to remove the epibiota from nets. 3. Surveys showed a significant decline in the numbers of both seahorse species at one site following the replacement of a net, and recovery of the H. whitei population took more than 15 months. 4. A manipulative experiment tested the importance of epibiotic growth for seahorses. H. whitei, tagged with individual marks, were allocated to sections of a net that had undergone different cleaning procedures. Seahorse size, position on the net and total population abundance were recorded every 2 weeks over a 3 month period. It was demonstrated that seahorses have a significant positive association with epibiotic growth and proximity to the sea floor. Seahorse populations also showed seasonal variation in abundance with increased numbers on the net during the breeding season (spring–summer). 5. This project has led to the development of best practice net cleaning procedures for local authorities in Sydney Harbour to manage growth on the nets while minimizing impacts on seahorse populations. Copyright © 2009 John Wiley & Sons, Ltd.
Potential for increasing early vigour and total biomass in spring wheat. I. Identification of genetic improvements

Increased early vigour and vegetative biomass at anthesis should lead to yield improvements in wheat. Fifteen introductions were compared with five standard cultivars in Western Australia at Wongan Hills in 1988, and Wongan Hills, Merredin and Esperance in 1989 to identify useful parents for their early vigour and biomass production. Two times of sowing were included at Wongan Hills in 1989. Dry matter production was measured at all sites except Esperance at the early vegetative stage (49 to 55 days after sowing), late vegetative stage (56 to 75 days after sowing), and at anthesis. Some introductions were more vigorous in the vegetative stages, and produced more biomass at anthesis than the standard cultivars. Experiments under irrigated, non-stress conditions showed these lines produced leaves and tillers more quickly than the standard cultivars. The full growth potential of these lines may not have been expressed fully due to environmental limitations. While variation for dry matter production existed within the standard cultivars, it was not adequate or consistent enough to be of value in breeding. Dry matter production at the vegetative and anthesis stages was correlated significantly with grain yield in 1989, but not in 1988. Broad sense heritabilities for dry matter production at the three stages were generally high, averaging 72, 73 and 69% for early vegetative, late vegetative and anthesis dry matter production respectively. The importance of assessing the value of early vigour and biomass in breeding populations is discussed.
In Vitro Development Potentiality of Expanded Bovine Blastocysts Subsequent to Cryotop Vitrification

Embryo cryopreservation is a promising area of study in the field of reproductive research. One of the issues that have recently arisen is the discovery that the growing ability of embryos after cryopreservation varies depending on the culture period of the embryo prior to its cryopreservation. Therefore, the present study was designed to explore the in vitro development potentiality of bovine embryos at day 7 and day 8, as well as their survivability and hatchability after Cryotop vitrification. The blastocyst rate at day 8 (28.1%) was higher than that of day 7 (19.1%). Grade 1 (G1) and grade 2 (G2) expanded blastocysts at day 7 and day 8 were vitrified by Cryotop device using 20% (v/v) DMSO, 20% (v/v) EG and 0.5M. Except for the G2 expanded blastocysts at day 8, we found that the survival rates of vitrified G1 and G2 expanded blastocysts were not significantly different from the control group in both day 7 and day 8. However, the day 7 vitrified embryos showed superior rates of hatchability than those of day 8. In a curve estimation of correlation regressions, the hatching rate of day 7 G1 expanded blastocysts at 48 h showed a strong correlation (R 2 =0.914) with their survival rate. Therefore, we concluded that the day 7 culture period is the most suitable for vitrification of IVF derived blastocysts.