Miracle-dz/UniFAR-FTUs huggingface dataset:
Habitat orientation alters the outcome of interspecific competition: A microcosm study with zooplankton grazers

Abstract Habitat orientation has recently been demonstrated to affect the foraging behavior, growth, and production of plankton grazers. Because the orientation effect may vary with species, we hypothesize that habitat orientation may alter interspecific interactions between animal species. We experimentally investigated how habitat orientation (placing cuboid chambers in three orientations with long, medium, and small side as the chamber height) affected the interaction between two common cladoceran species, Daphnia magna and Moina micrura, which competitively exploited green algae of Chlorella pyrenoidosa at two volume scales (64 and 512 ml). Results show that chamber orientation and volume additively affected the behavior and species performance of the grazers. Specifically, both grazer species generally decreased their average swimming velocity, grazing rate (on algal cells), body size, and survival and reproduction rates with increasing chamber height for both chamber volumes and with decreasing chamber volume regardless of chamber orientation. Nevertheless, the decrease magnitude was greater for M. micrura with increasing chamber height but was greater for D. magna with decreasing chamber volume. Correspondingly, when cocultured, the density ratio of D. magna to M. micrura increased with increasing chamber height but decreased with decreasing chamber volume. At the end of the experiment, none of D. magna individuals survived in the small and short (large‐based) chambers, and few M. micrura individuals survived in large and tall (small‐based) chambers. These results indicate that both habitat orientation and size affect the outcome of interspecific competition between grazer species. We suggest that variation in habitat orientation may improve community coexistence and species diversity in nature.
Solution of magnetohydrodynamic flow and heat transfer of radiative viscoelastic fluid with temperature dependent viscosity in wire coating analysis

Wire coating process is a continuous extrusion process for primary insulation of conducting wires with molten polymers for mechanical strength and protection in aggressive environments. In the present study, radiative melt polymer satisfying third grade fluid model is used for wire coating process. The effect of magnetic parameter, thermal radiation parameter and temperature dependent viscosity on wire coating analysis has been investigated. Reynolds model and Vogel’s models have been incorporated for variable viscosity. The governing equations characterizing the flow and heat transfer phenomena are solved analytically by utilizing homotopy analysis method (HAM). The computed results are also verified by ND-Solve method (Numerical technique) and Adomian Decomposition Method (ADM). The effect of pertinent parameters is shown graphically. In addition, the instability of the flow in the flows of the wall of the extrusion die is well marked in the case of the Vogel model as pointed by Nhan-Phan-Thien.
FGF-2 enhances intestinal stem cell survival and its expression is induced after radiation injury.

Fibroblast growth factors (FGFs) have mitogenic activity toward a wide variety of cells of mesenchymal, neuronal, and epithelial origin and regulate events in normal embryonic development, angiogenesis, wound repair, and neoplasia. FGF-2 is expressed in many normal adult tissues and can regulate migration and replication of intestinal epithelial cells in culture. However, little is known about the effects of FGF-2 on intestinal epithelial stem cells during either normal epithelial renewal or regeneration of a functional epithelium after injury. In this study, we investigated the expression of FGF-2 in the mouse small intestine after irradiation and determined the effect of exogenous FGF-2 on crypt stem cell survival after radiation injury. Expression of FGF-2 mRNA and protein began to increase at 12 h after γ-irradiation, and peak levels were observed from 48 to 120 h after irradiation. At all times after irradiation, the higher molecular mass isoform (∼24 kDa) of FGF-2 was the predominant form expressed in the small intestine. Immunohistochemical analysis of FGF-2 expression after radiation injury demonstrated that FGF-2 was predominantly found in the mesenchyme surrounding regenerating crypts. Exogenous recombinant human FGF-2 (rhFGF-2) markedly enhanced crypt stem cell survival when given before irradiation. We conclude that expression of FGF-2 is induced by radiation injury and that rhFGF-2 can enhance crypt stem cell survival after subsequent injury.
Development of Patch-Clamp Chips for Mammalian Cell Applications

: We have previously described the designs of two planar patch-clamp neurochips and their application to the electrophysiological study of molluscan neurons cultured on-chip. Neuron attachment and growth over apertures on the neurochip surface permitted the acquisition of whole-cell patch-clamp recordings. To broaden the application of these neurochips from molluscan to mammalian neurons, we conducted a study of cell-to-aperture interaction to optimize condi- tions for these smaller, more fragile cells. For this purpose, we designed a “sieve” chip having multiple apertures on its surface. Random growth of rat cortical neurons resulted in a 32% (n = 324) probability of cell growth over 2 μ m diameter apertures; larger diameters resulted in growth through the aperture. Based on these findings, single-aperture neurochips were fabricated having 2 μ m diameter aperture and preliminary electrophysiological recordings from cortical cultures at 14 DIV are presented. The implications of this study for the next-generation neurochips are discussed.
Contraction-stimulated muscle glucose transport and GLUT-4 surface content are dependent on glycogen content.

The influence of muscle glycogen content on basal and contraction-induced glucose transport and cell surface GLUT-4 content was studied in rat skeletal muscle. Wistar rats were preconditioned by a combination of swimming exercise and diet, resulting in 40% lower (LG) or threefold higher (HG) muscle glycogen content compared with nonexercised controls (NG). At rest and during contractions, 2-deoxy-d-glucose uptake in perfused fast-twitch muscle, but not slow-twitch muscle, was significantly lower in HG compared with LG. Cell surface GLUT-4 content in the fast-twitch plantaris was 994 ± 180, 1,173 ± 311, and 2,155 ± 243 dpm/g in the basal condition and increased ( P < 0.05) to 2,285 ± 239, 3,230 ± 464, and 4,847 ± 654 dpm/g during contractions with HG, NG, and LG, respectively, the increase being significantly smaller in HG compared with LG. The contraction-induced increments in glucose transport and in cell surface GLUT-4 content were negatively correlated with the initial glycogen content (P <0.01). In conclusion, glucose transport and cell surface GLUT-4 content in resting and contracting fast-twitch muscle are dependent on the muscle glycogen content.
Expression of rab11a N124I in gastric parietal cells inhibits stimulatory recruitment of the H+-K+-ATPase.

Stimulation of the gastric parietal cell results in a massive redistribution of H+-K+-ATPase from cytoplasmic tubulovesicles to the apical plasma membrane. Previous studies have implicated the small GTPase rab11 in this process. Using matrix-assisted laser desorption mass spectrometry, we confirmed that rab11 is associated with H+-K+-ATPase-enriched gastric microsomes. A stoichiometry of one rab11 per six copies of H+-K+-ATPase was estimated. Furthermore, rab11 exists in at least three forms on rabbit gastric microsomes: the two most prominent resemble rab11a, whereas the third resembles rab11b. Using an adenoviral expression system, we expressed the dominant negative mutant rab11a N124I in primary cultures of rabbit parietal cells under the control of the tetracycline transactivator protein (tTA). The mutant was well expressed with a distribution similar to that of the H+-K+-ATPase. Stimulation of these cultures with histamine and IBMX was assessed by measuring the aminopyrine (AP) uptake relative to resting cells (AP index). In experiments on six culture preparations, stimulated uninfected cells gave an AP index of 10.0 ± 2.9, whereas parallel cultures expressing rab11a N124I were poorly responsive to stimulation, with a mean AP index of 3.2 ± 0.9. Control cultures expressing tTA alone or tTA plus actin responded equally well to stimulation, giving AP index values of 9.0 ± 3.1 and 9.6 ± 0.9, respectively. Thus inhibition by rab11a N124I is not simply due to adenoviral infection. The AP uptake data were confirmed by immunocytochemistry. In uninfected cells, H+-K+-ATPase demonstrated a broad cytoplasmic distribution, but it was cleared from the cytoplasm and associated with apically derived membranes on stimulation. In cells expressing rab11a N124I, H+-K+-ATPase maintained its resting localization on stimulation. Furthermore, this effect could be alleviated by culturing infected cells in the presence of tetracycline, which prevents expression of the mutant rab11. We therefore conclude that rab11a is the prominent GTPase associated with gastric microsomes and that it plays a role in parietal cell activation.
Stochastic modelling of tree architecture and biomass allocation: application to teak (Tectona grandis L. f.), a tree species with polycyclic growth and leaf neoformation

Background and aims For a given genotype, the observed variability of tree forms results from the stochasticity of meristem functioning and from changing and heterogeneous environmental factors affecting biomass formation and allocation. In response to climate change, trees adapt their architecture by adjusting growth processes such as pre- and neoformation, as well as polycyclic growth. This is the case for the teak tree. The aim of this work was to adapt the plant model, GreenLab, in order to take into consideration both these processes using existing data on this tree species. Methods This work adopted GreenLab formalism based on source-sink relationships at organ level that drive biomass production and partitioning within the whole plant over time. The stochastic aspect of phytomer production can be modelled by a Bernoulli process. The teak model was designed, parameterized and analysed using the architectural data from 2- to 5-year-old teak trees in open field stands. Key results Growth and development parameters were identified, fitting the observed compound organic series with the theoretical series, using generalized least squares methods. Phytomer distributions of growth units and branching pattern varied depending on their axis category, i.e. their physiological age. These emerging properties were in accordance with the observed growth patterns and biomass allocation dynamics during a growing season marked by a short dry season. Conclusions Annual growth patterns observed on teak, including shoot pre- and neoformation and polycyclism, were reproduced by the new version of the GreenLab model. However, further updating is discussed in order to ensure better consideration of radial variation in basic specific gravity of wood. Such upgrading of the model will enable teak ideotypes to be defined for improving wood production in terms of both volume and quality.
Plasma insulin rise precedes rise in ob mRNA expression and plasma leptin in gold thioglucose-obese mice.

Circulating leptin levels are strongly related to the degree of adiposity, with hyperleptinemia being associated with hyperinsulinemia. In the gold thioglucose-injected mouse (GTG), hyperinsulinemia is an early abnormality in the development of insulin resistance and obesity. In this study, hyperinsulinemia occurred 1 wk post-GTG [GTG, 199 ± 43; age-matched controls (CON), 53 ± 5 μU/ml; P < 0.001], with leptin levels not rising until 2 wk post-GTG (CON, 3.2 ± 0.3; GTG, 9.9 ± 1.7 ng/ml; P < 0.001) in parallel with increases in the size of different fat pads and increased expression of ob mRNA. The ratio of serum leptin to fat pad weight was significantly higher in GTG mice 12 wk postinjection. Starvation-induced reductions in serum leptin (50%), glucose (50%), and insulin (74%) were greater than decreases in fat pad weight (18%). Adrenalectomy decreased both adiposity and serum leptin within 1 wk in both CON and GTG and altered the serum leptin level-to-fat pad weight ratio in CON. Thus hyperinsulinemia preceded increased ob expression and hyperleptinemia, which occurred in parallel with increasing adiposity, consistent with the role of leptin as an indicator of energy supplies. Changes in hormonal and nutritional status may modify this relationship.
Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project

The goal of the 1000 Genomes Consortium is to characterize human genome structural variation (SV), including forms of copy number variations such as deletions, duplications, and insertions. Mobile element insertions, particularly Alu elements, are major contributors to genomic SV among humans. During the pilot phase of the project we experimentally validated 645 (611 intergenic and 34 exon targeted) polymorphic “young” Alu insertion events, absent from the human reference genome. Here, we report high resolution sequencing of 343 (322 unique) recent Alu insertion events, along with their respective target site duplications, precise genomic breakpoint coordinates, subfamily assignment, percent divergence, and estimated A-rich tail lengths. All the sequenced Alu loci were derived from the AluY lineage with no evidence of retrotransposition activity involving older Alu families (e.g., AluJ and AluS). AluYa5 is currently the most active Alu subfamily in the human lineage, followed by AluYb8, and many others including three newly identified subfamilies we have termed AluYb7a3, AluYb8b1, and AluYa4a1. This report provides the structural details of 322 unique Alu variants from individual human genomes collectively adding about 100 kb of genomic variation. Many Alu subfamilies are currently active in human populations, including a surprising level of AluY retrotransposition. Human Alu subfamilies exhibit continuous evolution with potential drivers sprouting new Alu lineages.
EEG-based emotion classification using deep belief networks

In recent years, there are many great successes in using deep architectures for unsupervised feature learning from data, especially for images and speech. In this paper, we introduce recent advanced deep learning models to classify two emotional categories (positive and negative) from EEG data. We train a deep belief network (DBN) with differential entropy features extracted from multichannel EEG as input. A hidden markov model (HMM) is integrated to accurately capture a more reliable emotional stage switching. We also compare the performance of the deep models to KNN, SVM and Graph regularized Extreme Learning Machine (GELM). The average accuracies of DBN-HMM, DBN, GELM, SVM, and KNN in our experiments are 87.62%, 86.91%, 85.67%, 84.08%, and 69.66%, respectively. Our experimental results show that the DBN and DBN-HMM models improve the accuracy of EEG-based emotion classification in comparison with the state-of-the-art methods.
Temporal responses of oxidative vs. glycolytic skeletal muscles to K+ deprivation: Na+ pumps and cell cations.

When K+ output exceeds input, skeletal muscle releases intracellular fluid K+ to buffer the fall in extracellular fluid (ECF) K+. To investigate the mechanisms and muscle specificity of the K+ shift, rats were fed K+-deficient chow for 2-10 days, and two muscles at phenotypic extremes were studied: slow-twitch oxidative soleus and fast-twitch glycolytic white gastrocnemius (WG). After 2 days of low-K+ chow, plasma K+ concentration ([K+]) fell from 4.6 to 3.7 mM, and Na+-K+-ATPase α2 (not α1) protein levels in both muscles, measured by immunoblotting, decreased 36%. Cell [K+] decreased from 116 to 106 mM in soleus and insignificantly in WG, indicating that α2 can decrease before cell [K+]. After 5 days, there were further decreases in α2 (70%) and β2 (22%) in WG, not in soleus, whereas cell [K+] decreased and cell [Na+] increased by 10 mM in both muscles. By 10 days, plasma [K+] fell to 2.9 mM, with further decreases in WG α2 (94%) and β2 (70%); cell [K+] fell 19 mM in soleus and 24 mM in WG compared with the control, and cell [Na+] increased 9 mM in soleus and 15 mM in WG; total homogenate Na+-K+-ATPase activity decreased 19% in WG and insignificantly in soleus. Levels of α2, β1, and β2 mRNA were unchanged over 10 days. The ratios of α2 to α1 protein levels in both control muscles were found to be nearly 1 by using the relative changes in α-isoforms vs. β1- (soleus) or β2-isoforms (WG). We conclude that the patterns of regulation of Na+ pump isoforms in oxidative and glycolytic muscles during K+ deprivation mediated by posttranscriptional regulation of α2β1 and α2β2 are distinct and that decreases in α2-isoform pools can occur early enough in both muscles to account for the shift of K+ to the ECF.
Phosphoinositide 3-kinase is required for aldosterone-regulated sodium reabsorption.

Aldosterone, a steroid hormone, regulates renal Na+ reabsorption and, therefore, plays an important role in the maintenance of salt and water balance. In a model renal epithelial cell line (A6) we have found that phosphoinositide 3-kinase (PI 3-kinase) activity is required for aldosterone-stimulated Na+reabsorption. Inhibition of PI 3-kinase by the specific inhibitor LY-294002 markedly reduces both basal and aldosterone-stimulated Na+ transport. Further, one of the products of PI 3-kinase, phosphatidylinositol 3,4,5-trisphosphate, is increased in response to aldosterone in intact A6 monolayers. This increase occurs just before the manifestation of the functional effect of the hormone and is also inhibited by LY-294002. With the use of blocker-induced noise analysis, it has been demonstrated that inhibition of phosphoinositide formation causes an inhibition of Na+ entry in both control and aldosterone-pretreated cultures by reducing the number of open functional epithelial Na+ channels (ENaCs) in the apical membrane of the A6 cells. These novel observations indicate that phosphoinositides are required for ENaC expression and suggest a mechanism for aldosterone regulation of channel function.
Determination of low-molecular-mass antioxidant concentrations in human respiratory tract lining fluids.

Antioxidants present within lung epithelial lining fluids (ELFs) constitute an initial line of defense against inhaled environmental oxidants such as ozone, nitrogen oxides, and tobacco smoke, but the antioxidant composition of human ELFs is still incompletely characterized. We analyzed ELF concentrations of the low-molecular-mass antioxidants ascorbate, urate, glutathione (GSH), and α-tocopherol by obtaining bronchoalveolar lavage (BAL) and nasal lavage fluids from healthy nonsmoking volunteers and compared two different BAL procedures. ELF dilution by the lavage procedures was estimated by measurement of urea in recovered BAL fluids in comparison with those in blood plasma from the same subjects. The results indicated that a recently developed single-cycle BAL procedure minimizes influx of non-ELF urea into the instilled fluid and thus allows for a more accurate determination of ELF antioxidant concentrations. Using this procedure, we determined that bronchoalveolar ELF contains 40 ± 18 (SD) μM ascorbate, 207 ± 167 μM urate, 109 ± 64 μM GSH, and 0.7 ± 0.3 μM α-tocopherol ( n = 12 subjects). Similar analysis of nasal lavage fluid yielded nasal ELF levels of 28 ± 19 μM ascorbate and 225 ± 105 μM urate ( n = 12 subjects), whereas GSH was undetectable (<0.5 μM). Our results demonstrate that ascorbate and urate are major low-molecular-mass ELF antioxidants in both the upper and lower respiratory tract, whereas GSH is present at significant concentrations only in bronchoalveolar ELF.
Signatures of anti-Thomsen - Friedenreich antigen antibody diversity in colon cancer patients.

AIM To determine whether the structural and functional diversities of naturally occurring antibodies to the Thomsen - Friedenreich (TF) antigen may be of diagnostic and prognostic value in colon cancer. MATERIALS AND METHODS Serum samples were taken from patients with colon cancer (n = 94) and healthy controls (n = 64). The level of TF-specific antibody isotypes and their sialylation were determined using ELISA and lectin-ELISA with synthetic TF-polyacrylamide conjugate as an antigen and a sialic acid-specific Sambucus nigra agglutinin (SNA). The avidity was determined using ammonium thiocyanate as a chaotrope. The accuracy of diagnostics was evaluated using the receiver operator characteristic curve analysis and the survival analysis employing the Kaplan - Meier method. RESULTS Compared to healthy controls, patients with colon cancer exhibited a lower level of anti-TF IgG antibodies, significantly lower ratios of TF-specific IgG/IgM and IgG/IgA, an increased SNA reactivity of anti-TF antibodies, mostly on account of IgG, and a lower avidity of TF-specific antibodies, especially their SNA-reactive subset. An increased SNA reactivity of anti-TF IgG was observed already at the early stages of cancer (p = 0.0004). The decrease of the ratio of IgG/IgM and IgG/IgA showed a good accuracy of diagnostics with about 60% sensitivity at 90% specificity. A similar potential was found for the SNA binding/IgG level index. The high level of TF-specific IgA antibodies was associated with a lower survival rate (hazard ratio = 0.34). CONCLUSION This is the first report ever on the colon cancer-related signatures of anti-TF antibody diversity which show diagnostic potential, including in early cancer, and prognostic value. The hypersialylation of TF-specific antibodies appeared to be a common phenomenon in cancer. The signatures may be used as non-invasive antibody-based markers for colon cancer.
SpeedSeq: Ultra-fast personal genome analysis and interpretation

SpeedSeq is an open-source genome analysis platform that accomplishes alignment, variant detection and functional annotation of a 50× human genome in 13 h on a low-cost server and alleviates a bioinformatics bottleneck that typically demands weeks of computation with extensive hands-on expert involvement. SpeedSeq offers performance competitive with or superior to current methods for detecting germline and somatic single-nucleotide variants, structural variants, insertions and deletions, and it includes novel functionality for streamlined interpretation.