Miracle-dz/UniFAR-FTUs huggingface dataset:
AP2 transcription factor induces apoptosis in retinoblastoma cells

The underlying cause of human retinoblastoma is complete inactivation of both copies of the RB1 gene. Other chromosome abnormalities, with the most common being extra copies of chromosome arm 6p, are also observed in retinoblastoma. The RB protein has previously been shown to interact with TFAP2 transcription factors. Here, we show that TFAP2A and TFAP2B, which map to chromosome arm 6p, are expressed in the amacrine and horizontal cells of human retina. TFAP2A RNA can readily be detected in retinoblastoma cell lines and tumors; however, the great majority of retinoblastoma cell lines and tumors are completely devoid of TFAP2A protein and TFAP2B RNA/protein. Transfection of TFAP2A and TFAP2B expression constructs into retinoblastoma cells induces apoptosis and inhibits proliferation. Our results suggest that a consequence of loss of RB1 gene function in retinoblastoma cells is inactivation of TFAP2A and TFAP2B function. We propose that inability to differentiate along the amacrine/horizontal cell lineages may underlie retinoblastoma tumor formation. © 2010 Wiley‐Liss, Inc.
Differences in toxicity and outcome associated with circadian variations between patients undergoing daytime and evening radiotherapy for prostate adenocarcinoma

ABSTRACT This retrospective study tested the hypothesis that disease control and treatment-related toxicity in patients undergoing high-dose radiotherapy (HDRT) for prostate cancer varies in a circadian manner. Patients with localized prostate adenocarcinoma receiving HDRT (median 78 Gy) to the prostate and involved seminal vesicle(s) without elective pelvic irradiation were divided into a daytime treatment (before 5 PM) group (n = 267) and evening treatment (after 5 PM) group (n = 142). Biochemical failure (Phoenix definition), acute and late gastrointestinal (GI) and genitourinary toxicities (Common Terminology Criteria for Adverse Events version 4), biochemical failure-free survival (BFFS) and freedom from late toxicity were assessed. Analyses were performed by binary logistic regression and Cox proportional hazard regression. The median follow-up was 68 months, and 75% of patients were ≥70 years old. Evening HDRT was significantly associated with worse freedom from ≥grade 2 late GI complications (hazard ratio = 2.96; p < 0.001). The detrimental effect of evening HDRT was significant in patients older than 70 years old (p < 0.001) but not in younger patients (p = 0.63). In a subgroup of propensity score-matched cohort with T2b–T3 disease (n = 154), the 5-year BFFS was worse in the evening group than the daytime group (72% vs. 85%, hazard ratio = 1.95, p = 0.05). Our study indicates that evening HDRT may lead to more GI complications, especially in older patients, and worse BFFS in patients with T2b–T3 disease.
Circulation dynamics of Mediterranean precipitation variability 1948–98

Canonical correlation analysis is used to identify main coupled circulation–rainfall patterns and to relate recent variability and trends of Mediterranean precipitation to large‐scale circulation dynamics. Analyses are based on geopotential heights (500 and 1000 hPa levels) for the North Atlantic–European area (National Centers for Environmental Prediction–National Center for Atmospheric Research reanalysis) and on highly resolved (0.5° × 0.5° ) monthly rainfall grids (Climatic Research Unit, Norwich) selected for the Mediterranean area during the 1948–98 period. Combining monthly analyses with similar characteristics to seasonal samples yields winter (October–March), spring (April–May) and summer (June–September) types of coupled variability; a particular autumn type for the whole Mediterranean does not occur on the monthly time scale. Coupled patterns specifically linked to one or two seasons include an east Atlantic jet (EA‐Jet) related pattern for summer and a Mediterranean meridional circulation (MMC) pattern for winter and spring. The most important pattern recurring with dynamical adjustments throughout the whole year reflects the seasonal cycle of the Mediterranean oscillation (MO), which is linked (with seasonal dependence) to the Northern Hemisphere teleconnection modes of the Arctic oscillation (AO) and North Atlantic oscillation (NAO). Winter rainfall trends of the recent decades marked by widespread decreases in the Mediterranean area and by opposite conditions in the southeastern part are linked to particular changes over time in several of the associated circulation patterns. Thus, different regional rainfall changes are integrated into an overall interrelation between Mediterranean rainfall patterns and large‐scale atmospheric circulation dynamics. Copyright © 2003 Royal Meteorological Society
HYDRAULIC FRACTURING IN PORUS AND NONPORUS ROCK AND ITS POTENTIAL FOR DETERMINING IN-SITU STRESSES AT GREAT DEPTH.

Abstract : The process of Hydraulic Fracturing as a method of determining in-situ stresses in brittle elastic formations at great depth is analyzed both theoretically and experimentally. Theoretically, it is found that in attempting to relate the recorded hydraulic fracturing pressures to tectonic stresses, it is essential to investigate whether the fluid used to induce and extend fracture penetrates and flows into the rock strata. This flow raises the pore fluid pressure and creates additional stresses and displacements which lower the critical pressure required to initiate fracture and reduce the width of the newly-formed fracture. Based on this additional stress field, a realistic evaluation of in-situ stresses in permeable strata is obtained. Experimentally, hollow cylindrical and cubical specimens of porous and nonporus rock were tested under constant triaxial external loading and increasing internal (borehole) fluid pressure. In the cubical samples, three uniform unequal principal stresses were induced to simulate general conditions at great depth. The experimental results show that hydraulic fracturing occurred when the internal pressure achieved a critical value that could usually be predicted by the theoretical criteria for fracture initiation. (Author)
Long-term Changes in Dwarf Pine (Pinus mugo) Cover in the High Tatra Mountains, Slovakia

The present article focuses on the distribution of Pinus mugo under conditions in the central Tatra Mountains, the main mountain range of the Western Carpathians. We analyze the response of P. mugo distribution to selected abiotic habitat conditions in the eastern Tatra Mountains. The study also compares data on the distribution of P. mugo in the higher central Tatras and in the hills of the western Tatras published in previous studies. The source data for this study were aerial photographs from 3 periods (1955, 1986, and 2002). Mountain areas covered by mountain pine were identified and analyzed by ArcGIS 10, and pine fields were classified with the help of the gray scale mode. A strip of mountain pine above the upper limit of the forest represents an easily identifiable boundary on the aerial photographs: 25 well-recognized localities were selected to examine the changes in the tree line in the eastern Tatras. The distribution of mountain pine increased in the central granite and eastern limestone Tatra Mountains from 1955 to 2002 at all monitored sites. The percentage of total surface area covered in P. mugo increased from 28.11% in 1955 to 34.74% in 1986 and to 39.01% in 2002. The study also analyzes the dispersal of mountain pine over 40 years in relation to elevation, slope, radiation aspect, flow accumulation, and vertical and horizontal curvature. The results of this study explain ongoing vegetation changes and are of importance as a contribution to monitoring of climate change in the mid-European mountain areas.
Dinoflagellate cyst assemblages as tracers of sea‐surface conditions in the northern North Atlantic, Arctic and sub‐Arctic seas: the new ‘n = 677’ data base and its application for quantitative palaeoceanographic reconstruction

The distribution of dinoflagellate cyst (dinocyst) assemblages in surface sediment samples from 677 sites of the northern North Atlantic, Arctic and sub‐Arctic seas is discussed with emphasis on the relationships with sea‐surface parameters, including sea‐ice cover, salinity and temperature of the coldest and warmest months. Difficulties in developing a circum‐Arctic data base include the morphological variation within taxa (e.g. Operculodinium centrocarpum, Islandinium? cezare and Polykrikos sp.), which probably relate to phenotypic adaptations to cold and/or low salinity environments. Sparse hydrographical data, together with large interannual variations of temperature and salinity in surface waters of Arctic seas constitute additional limitations. Nevertheless, the use of the best‐analogue technique with this new dinocyst data base including 677 samples permits quantitative reconstruction of sea‐surface conditions at the scale of the northern North Atlantic and the Arctic domain. The error of prediction calculated from modern assemblages is ±1.3 °C and ±1.8 °C for the temperature of February and August, respectively, ±1.8 for the salinity, and ±1.5 months yr−1 for the sea‐ice cover. Application to late Quaternary sequences from the western and eastern subpolar North Atlantic (Labrador Sea and Barents Sea) provide reconstructions compatible with those obtained using the previous dinocyst data base (n = 371), which mainly included modern data from the northern North Atlantic. Copyright © 2001 John Wiley & Sons, Ltd.
Manipulación por hormigas de semillas de Euphorbia Characias (Euphorbiaceae) dentro del hormiguero

espanolSe describe el proceso de manipuiacion por obreras de Pheidole pallidula, Tapinoma nigenimum, Aphaenogaster senilis y Messor barbam de las semilias de Eup\wrbia characias, especie mirmecocora mediterranea, dentro del hormiguero P.pallidula y Tnigehum consumen el eleosoma y la semilla sin eleosoma queda situada dentro del nido. A.senilis separa el eleosoma de la semilla, consumen la zona mas extema del eleosoma y posteriormente la seda y el eleosoma manipulado son hamportados fuera del nido. M.barba- rus, especie w'vora, dehe una relacion perjudicial para las semilias de E.characias ya que acaban siendo consumidos tanto el eleosoma como el resto de la seda. El tratarniento por hormigas tiene un efecto adi- cionai. Las sedas manipulada por P.pallidula, Tnigerrimum o A.senilis, sin eleosoma y con raspaduras en la cuticula, muestran una emergencia superior (82.7%, n=122 semilias sembrada) que las semilias con el eleosoma intacto (63.9%, n=172 semilias sembradas). Semilias sin eleosoma -eliminado con pinzas- tie- nen un mismo nivel de emergencia que las tratadas por hormigas (76.0%, n=142 semillas sembrada). La presencia de eleosoma tiene un efecto negativo en la emergencia de plantuias de E.characias catalaEs descriu el proces de manipulacio per obreres de Pheidole pallidula, Tapinoma nigerrimum, Aphaenogasier senilis i Messor barbarus de les granes d'Euphorbia characias, especie mirmeujcara meditenania, dintre del formiguer. P.pallidula i Tnigerrimum consumeixen l'eleosoma, i la grana sense eleosoma h abandonada dintre del formiguer. A.senilis separa l'eleosoma de la grana, consumeix la zona mes extema de l'eleosoma i posteriorment grana i eleosoma son transportats i abandonats fora del Nu. M.barbarus, espeie granivora, defineix una relacio perjudicial per a les granes de E.characias, ja que les obreres a the seed, without elaiosome, is left within the nest. Smaii and big (soldier) wor- kers of P.pallidula intewene in this process. Aphaeiwgaster senilis workers separate the elaiosome of the seed, consume the most extemai zone of elaiosome and, subsequently, the seed and the manipulated elaiosome are transported outside the nest. Messor barbarus, a granivorous ant, dennes a harmfd rela- tionship since the seeds of E.characias finish by being consumed. Ant treatment has an additional effect: seeds manipulated by P.palluiula, T.nigerrimum or A.senilis, deprived of the elaiosome and with scars on the seed cuticle have a higher emergence level (82.7%, n=122 sown seeds) than seeds with the elaiosome (63.9%, n=172 sown seeds). Seeds artificiaiiy deprived of the elaiosome but without scars do not show any difference in emergence as compared with ant-treated seeds (76.0%, n=142 sown seeds). The presence of the elaiosome has a negative effect on the emergence of seedlings of E.characias
Seasonal changes in meltwater storage and drainage characteristics of the Dokriani Glacier, Garhwal Himalayas (India)

Storage and drainage characteristics of the Dokriani Glacier (9.66 km2) located in the Garhwal Himalayas have been studied. In order to understand these characteristics, clear weather (non-rainy) days data for three ablation seasons (1996–1998) are used because discharge is melt-driven on such days. Moreover, diurnal variations in the discharge on clear days represent the true picture of glacier response to streamflow. Results indicate that meltwater storage characteristics of the glacier lead to high discharges in the stream during the night. Consequently, night-time discharges are comparable with those observed during daytime throughout the melt season. Meltwater storage characteristics of the glacier are much stronger in the early part of the melt season and they weaken as the melt season progresses. Diurnal variations in the discharge are observed to be clearer with advancement of the melt season providing variations in the timing of peak flow. Maximum discharge for different years was observed between 1700 and 1900 hours, showing a lag of 2 hours in the timing of maximum flow over the ablation period. The time to peak flow varied from 8.5 to 11 hours. For all the years, a strong seasonal trend towards increasing diurnal amplitude in discharge until August and thereafter a decreasing trend, was observed. The time lag between Qmax and Tmax varied from 3–6 hours over the ablation season and recession of melt water became faster with time. The time lag is higher at the beginning of the melt season and reduces as the melt season progresses. Recession trends of the hydrographs with time suggested a similar hydrological response of the glacier in June and September. The basin behaved like a single conceptual linear reservoir for these two months, while for July and August it behaved like two conceptual linear reservoirs, namely, accumulation and ablation reservoirs.
The Arabidopsis leucine-rich repeat receptor kinase MIK2/LRR-KISS connects cell wall integrity sensing, root growth and response to abiotic and biotic stresses

Plants actively perceive and respond to perturbations in their cell walls which arise during growth, biotic and abiotic stresses. However, few components involved in plant cell wall integrity sensing have been described to date. Using a reverse-genetic approach, we identified the Arabidopsis thaliana leucine-rich repeat receptor kinase MIK2 as an important regulator of cell wall damage responses triggered upon cellulose biosynthesis inhibition. Indeed, loss-of-function mik2 alleles are strongly affected in immune marker gene expression, jasmonic acid production and lignin deposition. MIK2 has both overlapping and distinct functions with THE1, a malectin-like receptor kinase previously proposed as cell wall integrity sensor. In addition, mik2 mutant plants exhibit enhanced leftward root skewing when grown on vertical plates. Notably, natural variation in MIK2 (also named LRR-KISS) has been correlated recently to mild salt stress tolerance, which we could confirm using our insertional alleles. Strikingly, both the increased root skewing and salt stress sensitivity phenotypes observed in the mik2 mutant are dependent on THE1. Finally, we found that MIK2 is required for resistance to the fungal root pathogen Fusarium oxysporum. Together, our data identify MIK2 as a novel component in cell wall integrity sensing and suggest that MIK2 is a nexus linking cell wall integrity sensing to growth and environmental cues.
Wind-stress variability over the Benguela upwelling system

Regional wind-stress variability over the Benguela Upwelling System is described using 16 months (01 August 1999 29 November 2000) of satellite derived QuikSCA T wind data. The QuikSCA T data are compared to the climatologies presented by Kamstra (1985) and Bakun and Nelson (1991), as well as the long-term climatology (1968-1996) of the surface vector wind speed field off the coast of southern Africa, as derived from the 2.5° resolution NCEPINCAR reanalysis dataset. Broad scale similaritie"s are found between the QuikSCA T and the long-term NCEPINCAR climatology (1968-1996) data sets. This allows one to have confidence in using this scatterometer data to investigate details of spatial and temporal variability over the Benguela System. 3 During summer, wind-stress maxima are found at approximately 17, 29 and 34°S. These maxima strengthen in late summer. The seasonal northward migration of the South Atlantic Anticyclone becomes apparent in late autumn, when the strongest wind-stress occurs north of 28°S. A significant wind-stress minimum is observed to develop slightly north of Cape Columbine (33°S) during autumn. To the north (1023.5°S) the Benguela is characterised by relatively strong south-easterly wind-stress during winter. To the south (24-35°S) the Benguela is characterised by relatively weak westerly to south-westerly wind-stress during winter. A southward migration of southeasterly wind-stress is observed during early spring. By November the entire Benguela Upwelling System is once again characterised by southerly to south-easterly wind stress. Wind-stress variability is investigated using both a type of artificial neural network, known as the Kohonen Self Organising Map (SOM), as well as a wavelet analysis. Two independent SOM studies are conducted. The first study produced a 6x4 SOM output array, which is used to examine seasonal variability as well as the temporal evolution of two synoptic-scale wind events. For the second study both a SOM and a wavelet analysis are applied to an extracted data set to find that the system can be divided into six discrete wind regimes, 10-15°S; 15.5-18.5°S; 19-23.5°S; 2428.5°S; 29-32.5°S; and 33-35°S. The wavelet power spectra for these wind cells span a range of frequencies from 4 to 64 days, with each region appearing to contain distinct periodicities. To the north, 10-23.5°S, the majority of the power occurs during winter, with a 6-16 day periodicity. Further south, 24-35°S, the majority of the power occurs in the summer. Here a bi-modal distribution occurs, with peaks of 6-16 and 35-40 days. Lastly a case study sequence of the spatial distribution of wind-stress, windstress curl and SST, at a location off the west coast of southern Africa (25-30 S and 12-17°E), is discussed in relation to an intense, upwelling favourable, wind event that occurred from 11-20 February 2000. Un ive rsi ty of Ca pe To wn
Characterization of the genome and transcriptome of the blue tit Cyanistes caeruleus: polymorphisms, sex‐biased expression and selection signals

Decoding genomic sequences and determining their variation within populations has potential to reveal adaptive processes and unravel the genetic basis of ecologically relevant trait variation within a species. The blue tit Cyanistes caeruleus – a long‐time ecological model species – has been used to investigate fitness consequences of variation in mating and reproductive behaviour. However, very little is known about the underlying genetic changes due to natural and sexual selection in the genome of this songbird. As a step to bridge this gap, we assembled the first draft genome of a single blue tit, mapped the transcriptome of five females and five males to this reference, identified genomewide variants and performed sex‐differential expression analysis in the gonads, brain and other tissues. In the gonads, we found a high number of sex‐biased genes, and of those, a similar proportion were sex‐limited (genes only expressed in one sex) in males and females. However, in the brain, the proportion of female‐limited genes within the female‐biased gene category (82%) was substantially higher than the proportion of male‐limited genes within the male‐biased category (6%). This suggests a predominant on‐off switching mechanism for the female‐limited genes. In addition, most male‐biased genes were located on the Z‐chromosome, indicating incomplete dosage compensation for the male‐biased genes. We called more than 500 000 SNPs from the RNA‐seq data. Heterozygote detection in the single reference individual was highly congruent between DNA‐seq and RNA‐seq calling. Using information from these polymorphisms, we identified potential selection signals in the genome. We list candidate genes which can be used for further sequencing and detailed selection studies, including genes potentially related to meiotic drive evolution. A public genome browser of the blue tit with the described information is available at http://public-genomes-ngs.molgen. mpg.de.
AN ODYSSEY INTO LOCAL REFINEMENT AND MULTILEVEL PRECONDITIONING I: OPTIMALITY OF THE BPX PRECONDITIONER

In this article, we examine the Bramble-Pasciak-Xu (BPX) preconditioner in the setting of local 3D mesh refinement. While the available optimality results for the BPX preconditioner have been constructed primarily in the setting of uniformly refined meshes, a notable exception is the 2D result due to Dahmen and Kunoth, which established BPX optimality on meshes produced by a local 2D red-green refinement. The purpose of this article is to extend this original 2D optimality result to the local 3D red-green refinement procedure introduced by Bornemann-Erdmann-Kornhuber (BEK). The extension is reduced to establishing that locally enriched finite element subspaces allow for the construction of a scaled basis which is formally Riesz stable. This construction turns out to rest not only on shape regularity of the refined elements, but also critically on a number of geometrical properties we establish between neighboring simplices produced by the BEK refinement procedure. We also show that the number of degrees of freedom used for smoothing is bounded by a constant times the number of degrees of freedom introduced at that level of refinement, indicating that a practical implementable version of the resulting BPX preconditioner for the BEK refinement setting has provably optimal (linear) computational complexity per iteration, as well as having a uniformly bounded condition number. The theoretical framework supports arbitrary spatial dimension d ≥ 1, and we indicate clearly which geometrical properties established here must be re-established to show BPX optimality for spatial dimension d ≥ 4. The proof techniques require no coefficient smoothness assumptions beyond those required for well-posedness in H1.
Any Given Sunday: How Season Ticket Holders' Time of Stadium Entrance Is Influenced by Outcome Uncertainty

This paper constitutes a unique micro-level exploration of the relation between game outcome uncertainty and the behavior of highly committed season ticket holders of a major Bundesliga soccer team. Specifically, we look at 3,113 season ticket holders attending all 17 home games in the 2012-13 season and explore whether outcome uncertainty had an impact on their stadium arrival time. We find strong evidence that increased uncertainty about the expected outcome prompts these spectators to enter the stadium earlier. Moreover, season ticket holders travelling from outside the hosting city or paying higher season ticket prices exhibit a stronger reaction to uncertainty compared with season ticket hold ers in the standing section. We also find that younger spectators are less likely to arrive late when uncertainty increases.