Miracle-dz/UniFAR-FTUs huggingface dataset:
mRNA Stability and Polysome Loss in Hibernating Arctic Ground Squirrels (Spermophilus parryii)

ABSTRACT All small mammalian hibernators periodically rewarm from torpor to high, euthermic body temperatures for brief intervals throughout the hibernating season. The functional significance of these arousal episodes is unknown, but one suggestion is that rewarming may be related to replacement of gene products lost during torpor due to degradation of mRNA. To assess the stability of mRNA as a function of the hibernation state, we examined the poly(A) tail lengths of liver mRNA from arctic ground squirrels sacrificed during four hibernation states (early and late during a torpor bout and early and late following arousal from torpor) and from active ground squirrels sacrificed in the summer. Poly(A) tail lengths were not altered during torpor, suggesting either that mRNA is stabilized or that transcription continues during torpor. In mRNA isolated from torpid ground squirrels, we observed a pattern of 12 poly(A) residues at greater densities approximately every 27 nucleotides along the poly(A) tail, which is a pattern consistent with binding of poly(A)-binding protein. The intensity of this pattern was significantly reduced following arousal from torpor and undetectable in mRNA obtained from summer ground squirrels. Analyses of polysome profiles revealed a significant reduction in polyribosomes in torpid animals, indicating that translation is depressed during torpor.
PRDM14 promotes active DNA demethylation through the Ten-eleven translocation (TET)-mediated base excision repair pathway in embryonic stem cells

Ten-eleven translocation (TET) proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). 5fC and 5caC can be excised and repaired by the base excision repair (BER) pathway, implicating 5mC oxidation in active DNA demethylation. Genome-wide DNA methylation is erased in the transition from metastable states to the ground state of embryonic stem cells (ESCs) and in migrating primordial germ cells (PGCs), although some resistant regions become demethylated only in gonadal PGCs. Understanding the mechanisms underlying global hypomethylation in naive ESCs and developing PGCs will be useful for realizing cellular pluripotency and totipotency. In this study, we found that PRDM14, the PR domain-containing transcriptional regulator, accelerates the TET-BER cycle, resulting in the promotion of active DNA demethylation in ESCs. Induction of Prdm14 expression transiently elevated 5hmC, followed by the reduction of 5mC at pluripotency-associated genes, germline-specific genes and imprinted loci, but not across the entire genome, which resembles the second wave of DNA demethylation observed in gonadal PGCs. PRDM14 physically interacts with TET1 and TET2 and enhances the recruitment of TET1 and TET2 at target loci. Knockdown of TET1 and TET2 impaired transcriptional regulation and DNA demethylation by PRDM14. The repression of the BER pathway by administration of pharmacological inhibitors of APE1 and PARP1 and the knockdown of thymine DNA glycosylase (TDG) also impaired DNA demethylation by PRDM14. Furthermore, DNA demethylation induced by PRDM14 takes place normally in the presence of aphidicolin, which is an inhibitor of G1/S progression. Together, our analysis provides mechanistic insight into DNA demethylation in naive pluripotent stem cells and developing PGCs.
Claiming Fatherhood: Race and the Dynamics of Paternal Involvement among Unmarried Men

In 1965, Daniel Patrick Moynihan argued that the black family was nearing “complete breakdown” due to high rates of out-of-wedlock childbearing. In subsequent decades, nonmarital childbearing rose dramatically for all racial groups and unwed fathers were often portrayed as being absent from their children's lives. The authors examine contemporary nonmarital father involvement using quantitative evidence from the Fragile Families and Child Wellbeing Study and qualitative evidence from in-depth interviews with 150 unmarried fathers. The authors find that father involvement drops sharply after parents' relationships end, especially when they enter subsequent relationships and have children with new partners. These declines are less dramatic for African American fathers, suggesting that fathers' roles outside of conjugal relationships may be more strongly institutionalized in the black community. The challenges Moynihan described among black families some forty years ago now extend to a significant minority of all American children.
The Role of the Vagus Nerve in Mediating the Long‐Term Anorectic Effects of Leptin

Leptin, the product of the obese (ob) gene, is mainly known for its regulatory role of energy balance by direct activation of hypothalamic receptors. Recently, its function in the acute control of food intake was additionally attributed to activation of the vagus nerve to regulate meal termination. Whether vagal afferent neurones are involved in longer term effects of leptin on food intake, however, remains undetermined. Using vagotomised (VGX) rats, we sought to clarify the contributions of vagal afferents in mediating the long‐lasting effect of leptin on appetite suppression. Intraperitoneal (i.p.) injection of leptin (3.5 mg/kg) attenuated food intake at 4, 6, 8 and 24 h and body weight at 24 h postinjection in SHAM‐operated rats; however, this response was not abrogated by vagotomy. In a separate study using immunohistochemistry, we observed leptin‐induced Fos expression in the nucleus tractus solitarii, a brain structure where vagal afferent fibres terminate. This signal was not attenuated in VGX animals compared to the SHAM group. Moreover, leptin treatment led to a similar level of nuclear STAT3 translocation, a marker of leptin signalling, in the hypothalami of SHAM and VGX animals. In addition to the effects of leptin, vagotomy surgery itself resulted in a decrease of 24 h food intake. Analyses of brains from saline‐treated VGX animals revealed a significant induction of Fos in the nucleus tractus solitarii and changes in agouti‐related peptide and pro‐opiomelanocortin mRNA expression in the hypothalamus compared to their SHAM counterparts, indicating that the vagotomy surgery itself induced a modification of brain activity in areas involved in regulating appetite. Collectively, our data suggest that vagal afferents do not constitute a major route of mediating the regulatory effect of leptin on food intake over a period of several hours.
Matrix Metalloproteinase Production by COOH-Terminal Heparin-Binding Fibronectin Fragment in Rheumatoid Synovial Cells

Fibronectin with IIICS region is present in rheumatoid synovium, and fibronectin fragments are increased in rheumatoid joints. We investigated the ability of COOH-terminal heparin-binding fibronectin fragment (COOH-HBFN-f) containing IIICS to induce matrix metalloproteinase (MMP) production and the role of mitogen-activated protein kinase (MAPK) pathway and CS-1 sequence that can bind α4β1 integrin in MMP induction by COOH-HBFN-f in rheumatoid synovial fibroblasts (RSF). When RSF in monolayer culture were incubated with COOH-HBFN-f, COOH-HBFN-f stimulated the production of MMP-1, MMP-3, and MMP-13 by RSF in association with activation of extracellular signal-regulated kinase, p38 MAPK, and c-Jun NH2-terminal kinase. Immunoprecipitation of cell lysates demonstrated the presence of α4 integrin in cultured RSF. Similar to COOH-HBFN-f, treatment with CS-1 synthetic peptide derived from IIICS resulted in increased MMP production and activation of the kinases, although the MMP levels were low. Preincubation of RSF with anti-α4 integrin antibody resulted in partial suppression of the COOH-HBFN-f–stimulated MMP production. Inhibition studies using protein kinase inhibitors (PD98059 and SB203580) showed that those MAPK pathways contributed to MMP up-regulation by COOH-HBFN-f and CS-1. Thus, the present results have clearly shown that COOH-HBFN-f and CS-1 stimulate MMP production in association with activation of MAPK pathways in RSF. Integrin α4β1 may be partially involved in the MMP induction by COOH-HBFN-f.
Phosphoproteomic Analysis of the Mouse Brain Cytosol Reveals a Predominance of Protein Phosphorylation in Regions of Intrinsic Sequence Disorder*S

We analyzed the mouse forebrain cytosolic phosphoproteome using sequential (protein and peptide) IMAC purifications, enzymatic dephosphorylation, and targeted tandem mass spectrometry analysis strategies. In total, using complementary phosphoenrichment and LC-MS/MS strategies, 512 phosphorylation sites on 540 non-redundant phosphopeptides from 162 cytosolic phosphoproteins were characterized. Analysis of protein domains and amino acid sequence composition of this data set of cytosolic phosphoproteins revealed that it is significantly enriched in intrinsic sequence disorder, and this enrichment is associated with both cellular location and phosphorylation status. The majority of phosphorylation sites found by MS were located outside of structural protein domains (97%) but were mostly located in regions of intrinsic sequence disorder (86%). 368 phosphorylation sites were located in long regions of disorder (over 40 amino acids long), and 94% of proteins contained at least one such long region of disorder. In addition, we found that 58 phosphorylation sites in this data set occur in 14-3-3 binding consensus motifs, linear motifs that are associated with unstructured regions in proteins. These results demonstrate that in this data set protein phosphorylation is significantly depleted in protein domains and significantly enriched in disordered protein sequences and that enrichment of intrinsic sequence disorder may be a common feature of phosphoproteomes. This supports the hypothesis that disordered regions in proteins allow kinases, phosphatases, and phosphorylation-dependent binding proteins to gain access to target sequences to regulate local protein conformation and activity.
Research on Look-Ahead Control Strategy Based on Turbo PMAC for Parallel Kinematics Mechanism

A novel realtime look-ahead velocity control strategy, which was based on Turbo PMAC for parallel kinematics mechanism, was proposed to avoid gouging and mechanical vibration that caused by kinematics calculation failure in virtual axis machine tool machining. In terms of configuration of look-ahead control strategy, the basic is acceleration and deceleration algorithm. Then according to the ultiformity and practicality of polynomial, the acceleration and deceleration construction algorithm of polynomial were proposed. Finally, it was confirmed by experiment that the impact was reduced, which was account for the application of look-ahead control strategy and the performance of the control strategy was improved.
Interleukin Regulation of Asymmetric Antibody Synthesized by Isolated Placental B Cells

Canellada A, Färber A, Zenclussen AC, Gentile T, Dokmetjian J, Keil A, Blois S, Miranda S, Berod L, Gutiérrez G, Markert UR, Margni RA. Interleukin regulation of asymmetric antibody synthesized by isolated placental B cells. AJRI 2002; 48: 275–282 © Blackwell Munksgaard, 2002
Can a ‘living wage’ springboard human capability? An exploratory study from New Zealand

ABSTRACT ‘Living’ wage campaigns are more than calls for higher basic minima rates of pay. They are predicated on the notion that there is a discrete income below which people risk further deprivation, but above which there should be a qualitative upward shift in human capability. Problematically, however, the theory of diminishing marginal returns predicts that the function linking freedom from deprivation with income will form a smooth curve with no clear pivot (i.e. no discrete ‘living’ wage at all). Living wages thus remain controversial in that tests of these competing views are rare. A cross-sectional online survey of over 1000 working adults in New Zealand was undertaken to explore these two competing propositions. Household income was compared with measures of life and work capability. It emerged that the function linking life and work capabilities to household income was ‘spiked’ rather than continuous; the spike traversed scalar midpoints (e.g. from job dissatisfaction to satisfaction), making the shift qualitative (because dissatisfaction is qualitatively different from satisfaction) and the pivot point coincided with more people reporting having enough (versus insufficient) incomes to meet their basic needs. These findings are consistent with the arguments that there is a wage above which workers can begin to develop their capabilities rather than their being no such income point as suggested by the theory of diminishing marginal returns. Its existence has implications for public policy makers, and for wage theory.
Strategy detection of noncooperative dynamic games

This paper is a continuation of [4,13], and considers a different fundamental problem that is called strategy detection. Specifically, we consider an infinitely repetitive noncooperative game between a human and a machine, where the machine updates its strategy according to the previous strategies and payoffs of the machine and the human, the update rule of the machine is known to the human, but the strategies played by the machine are unknown to the human. We formulate the process of obtaining the strategy of the machine by observing its payoffs as the strategy detection problem. By defining a graph called weighted pair graph, and using the theories of finite automata and formal languages, we give an equivalent condition for the existence of the solution to the problem, and design algorithms for finding the solution and detecting the strategy of the machine.
Café life in the digital age: augmenting information flow in a café-work-entertainment space

In this report we detail our experience of designing and installing a large-screen public, interactive community board, the eyeCanvas, in a neighbourhood café and art gallery in San Francisco. Features of the community board include the ability to display content related to the café, including menus, nightly events and artists' work; the possibility of signing up for the cafe's email newsletter; and a touch-screen, "finger scribble" application that allows comments to be left. We describe the café, the eyeCanvas interactive display, the contents that are posted to the display comment on the adoption, use and impact of the eyeCanvas display.
Mixed-linkage ( 1 fi 3 ) , ( 1 fi 4 )-bD-glucan is not unique to the Poales and is an abundant component of Equisetum arvense cell walls

Iben Sørensen, Filomena A. Pettolino, Sarah M. Wilson, Monika S. Doblin, Bo Johansen, Antony Bacic and William G. T. Willats Department of Biology, The University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark, Plant Cell Biology Research Centre, School of Botany, University of Melbourne, Melbourne, Vic. 3010, Australia, Department of Biology, The University of Copenhagen, Østerfarimagsgade 2D, Copenhagen DK-1353, Denmark, and Australian Centre for Plant Functional Genomics, School of Botany, University of Melbourne, Melbourne, Vic. 3010, Australia
Empirical Study on Spatial Distribution and Dynamic Mechanism of Retail Industry in China

By applying the retail industry panel data of 31 provinces in China from 2005-2009,spatial distribution character of retail industry in China were analyzed by employing the Moran' I index,non-equilibrium index.The empirical relationship between density of retail enterprise and sales of goods per capita,population,GDP per capita,urbanization,market index were estimated by econometric analysis methods.Empirical results showed that,spatial distribution density of China's retail industry is obviously gradient,highest density in eastern area,followed by middle area,lowest in western,but the spatial distribution of retail industry is coordination with population.Study also found out,areas with the high economic development level,high population density,big retail goods sales amount per person,high urbanization rate,are more likely attracting the enter of retail enterprises,industry concentration will be more apparent because of the strong market demand and consumer purchasing power.In short term,the increasing of urbanization rate will promote the retail development,but in the long run,excessive urbanization is unfavorable.
Direct Aorta Ascending Approach in Transcatheter Aortic Valve Implantation

Objective Direct aorta ascending approach [transaortic approach (TAo)] is a new access way for transcatheter aortic valve implantation (TAVI) to be used in patients with peripheral vascular disease and as an alternative to transapical approach. Methods Both the Edwards SAPIEN and CoreValve systems were used. Depending on the position of the ascending aorta, the relation to the sternum, the brachiocephalic vein, vein grafts, and left and right internal mammary artery grafts from previous heart surgery, either right minithoracotomy or left ministernotomy was selected. Computed tomographic scan with reconstruction was applied for this decision making. A hybrid operating room was used with echocardiographic and fluoroscopy guidance. Results We have done 30 procedures via the aorta ascendens. The mean age of the patients was 80 years, and 18 were men. The mean Logistic EuroSCORE of 33 reflects the comorbidities. More than half of the patients had coronary vessel disease and had undergone coronary artery bypass graft; 20% had abdominal aortic aneurysm. The mean ejection fraction was 41%, and the patients were in New York Heart Association class III to IV. The mean gradient was 50 mm Hg, and the mean valve area was 0.7 cm2. The mean valve size was 28 mm. The use of Edwards SAPIEN versus CoreValve was 50%/50%, and thoracotomy versus sternotomy was 9 versus 21. All procedures were done successfully, but one patient had a periprocedural valve-in-valve implantation. Twenty-two patients were extubated in the operation room. The patients stayed in the intensive care unit for one night. Six patients were reoperated on. One patient had a postoperative balloon aortic valvuloplasty. The overall survival was 81% (follow up, 1–18 months). Conclusions Access design is an important issue in TAVI. When central approach is needed, TAVI-TAo is safe. For patients with low ejection fraction, the TAVI-TAo is preferred to the TAVI-transapical. The cannulation technique of the aorta is well known for cardiothoracic surgeons, and the method is feasible both for the Medtronic CoreValve and the Edwards SAPIEN valve, either via right minithoracotomy or ministernotomy to obtain the best coaxial alignment. It seems easier to position the bigger valves more precisely via this central approach.
Somatic cell hybrids between human lymphoma cell lines. V. IdUrd inducibility and P3HR‐1 superinfectability of Daudi/HeLa (DAD) and Daudi/P3HR‐1 (DIP‐1) cell lines

We have studied two types of somatic cell hybrid with regard to expression of the Epstein‐Barr virus (EBV) cycle and its regulation. The first, DIP‐1, a hybrid formed between two human lymphoma EBV producers (Daudi and P3HR‐1), contained EBV DNA, expressed the virus‐determined nuclear antigen (EBNA), and was a producer of the EBV‐associated antigens EA (early antigen) and VCA (viral capsid antigen). The second, DAD, a hybrid series of clones formed between Daudi and a HeLa cell derivative (D98), differed with regard to the expression of EBNA, EA, VCA and the content of EBV DNA. EA was regularly induced in the EBV DNA‐containing hybrids following treatment with iododeoxyuridine (IdUrd). This induction was greater in lines spontaneously expressing EA. In two hybrids, DIP‐1 and DAD10, VCA and virus DNA synthesis were also induced in the presence of IdUrd, the latter being detected by in situ hybridization with P3HR‐1 EBV complementary RNA. Finally, while DIP‐1 was superinfectable by the P3HR‐1 EBV strain, the DAD series of hybrids were refractory to P3HR‐1 superinfection and lacked EBV receptors.
A Polysaccharide Utilization Locus from an Uncultured Bacteroidetes Phylotype Suggests Ecological Adaptation and Substrate Versatility

ABSTRACT Recent metagenomic analyses have identified uncultured bacteria that are abundant in the rumen of herbivores and that possess putative biomass-converting enzyme systems. Here we investigate the saccharolytic capabilities of a polysaccharide utilization locus (PUL) that has been reconstructed from an uncultured Bacteroidetes phylotype (SRM-1) that dominates the rumen microbiome of Arctic reindeer. Characterization of the three PUL-encoded outer membrane glycoside hydrolases was performed using chromogenic substrates for initial screening, followed by detailed analyses of products generated from selected substrates, using high-pressure anion-exchange chromatography with electrochemical detection. Two glycoside hydrolase family 5 (GH5) endoglucanases (GH5_g and GH5_h) demonstrated activity against β-glucans, xylans, and xyloglucan, whereas GH5_h and the third enzyme, GH26_i, were active on several mannan substrates. Synergy experiments examining different combinations of the three enzymes demonstrated limited activity enhancement on individual substrates. Binding analysis of a SusE-positioned lipoprotein revealed an affinity toward β-glucans and, to a lesser extent, mannan, but unlike the two SusD-like lipoproteins previously characterized from the same PUL, binding to cellulose was not observed. Overall, these activities and binding specificities correlated well with the glycan content of the reindeer rumen, which was determined using comprehensive microarray polymer profiling and showed an abundance of various hemicellulose glycans. The substrate versatility of this single PUL putatively expands our perceptions regarding PUL machineries, which so far have demonstrated gene organization that suggests one cognate PUL for each substrate type. The presence of a PUL that possesses saccharolytic activity against a mixture of abundantly available polysaccharides supports the dominance of SRM-1 in the Svalbard reindeer rumen microbiome.
Effects of Combined Strength and Endurance Training on Treadmill Load Carrying Walking Performance in Aging Men

Holviala, J, Häkkinen, A, Karavirta, L, Nyman, K, Izquierdo, M, Gorostiaga, EM, Avela, J, Korhonen, J, Knuutila, V-P, Kraemer, WJ, and Häkkinen, K. Effects of combined strength and endurance training on treadmill load carrying walking performance in aging men. J Strength Cond Res 24(6): 1584-1595, 2010-The present study examined the effects of twice weekly total body strength training (ST), endurance cycling (ET), and combined ST and ET (2 + 2 times a week) (SET) training on the load carrying walking test performance on the treadmill (TM) and changes in neuromuscular and endurance performance during a 21-week training period in aging men. Forty healthy men (54.8 ± 8.0 years) were divided into 3 training groups (ET n = 9, ST n = 11, SET n = 11) and a control group (C, n = 9). Peak oxygen uptake (&OV0312;o2peak), heart rate, and blood lactate concentration were measured before and after a 21-week training program using a graded TM and maximal incremental bicycle ergometer (BE) tests. Isometric forces, vertical jump, and electromyographic activity of leg extensor and/or forearm flexor (F) muscles were measured before and after training and the TM tests. Increases of 20-21% in strength and of 7-12% in cycling BE &OV0312;o2peak occurred in the training groups, whereas the changes of C remained minor. &OV0312;o2peak was associated, both before and after training, with TM exercise time in all groups (from r = 0.65, p = 0.030 to r = 0.93, p < 0.001). Only SET showed a significant training-induced increase (p = 0.011) in exercise time of the TM walking with no significant increase in TM &OV0312;o2peak. The present data suggest that in older men ET and SET induced specific increases in BE &OV0312;o2peak and ST and SET in strength. However, only SET increased walking exercise time indicating improved load carrying walking performance because of large individual differences in the magnitude of the development of either strength or endurance capacities.