Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA Damage and Cellular Stress Responses AktPromotesPost-IrradiationSurvival ofHumanTumorCells through Initiation , Progression , and Termination of DNA-PKcs – Dependent DNA Double-Strand Break Repair

Akt phosphorylation has previously been described to be involved in mediating DNA damage repair through the nonhomologous end-joining (NHEJ) repair pathway. Yet themechanism how Akt stimulates DNA-protein kinase catalytic subunit (DNA-PKcs)-dependent DNAdouble-strand break (DNA-DSB) repair has not been described so far. In the present study, we investigated themechanism bywhichAkt can interact withDNA-PKcs and promote its function during the NHEJ repair process. The results obtained indicate a prominent role of Akt, especially Akt1 in the regulation of NHEJ mechanism for DNA-DSB repair. As shown by pull-down assay of DNA-PKcs, Akt1 through its C-terminal domain interacts with DNA-PKcs. After exposure of cells to ionizing radiation (IR), Akt1 and DNA-PKcs form a functional complex in a first initiating step of DNA-DSB repair. Thereafter, Akt plays a pivotal role in the recruitment of AKT1/DNA-PKcs complex to DNA duplex ends marked by Ku dimers. Moreover, in the formed complex, Akt1 promotes DNA-PKcs kinase activity, which is the necessary step for progression of DNA-DSB repair. Akt1-dependent DNA-PKcs kinase activity stimulates autophosphorylation of DNA-PKcs at S2056 that is needed for efficient DNA-DSB repair and the release of DNA-PKcs from the damage site. Thus, targeting of Akt results in radiosensitization ofDNA-PKcs andKu80 expressing, but not of cells deficient for, either of these proteins. The data showed indicate for the first time that Akt through an immediate complex formation withDNA-PKcs can stimulate the accumulation ofDNA-PKcs at DNA-DSBs and promoteDNA-PKcs activity for efficient NHEJ DNA-DSB repair. Mol Cancer Res; 10(7); 945–57. 2012 AACR.
Non‐invasive ventilation during cycle exercise training in patients with chronic respiratory failure on long‐term ventilatory support: A randomized controlled trial

The role of non‐invasive ventilation (NIV) during exercise training (ET) in patients with chronic respiratory failure (CRF) is still unclear. The aim of this study was to test whether NIV during ET had an additional effect in increasing the 6‐min walking distance (6MWD) and cycle endurance time compared with ET alone.
The diurnal distribution of sleep propensity: experimental data about the interaction of the propensities for slow‐wave sleep and REM sleep

The aim of the present study was to assess the diurnal variation of sleep propensity by evaluating the temporal distribution of sleep onset latency (SOL) and REM‐ and slow‐wave sleep (SWS) parameters in systematically scheduled daytime naps for 12 young males. To reduce the effect of prior SWS on subsequent REM sleep, a double‐nap technique was used, i.e. two adjacent naps A and B, which were separated by a 10‐min break. Nap duration was adjusted in such a way that nap A allowed 30 min of sleep and nap B one complete NREM–REM cycle. EEG slow wave activity (SWA, power density from 0.5–4 Hz) was estimated from nap A and REM sleep parameters from nap B. The time span between 08.00 hours and 24.00 hours was covered by nine double‐naps at 2 h intervals. The order of the nap sessions was systematically varied within and across subjects. For each subject, the time between successive double‐nap recordings was at least three days. SOL was shortest in the time interval 12.00 hours to 16.00 hours and significantly longer between 20.00 hours and 24.00 hours. REM sleep duration and the percentage of sleep onset REM episodes decreased continuously from 08.00 hours to the interval 18.00–20.00 hours and increased thereafter, with a time course inversely related to the one of body temperature, which was also measured continuously. SWA showed a steady, threefold increase from 08.00 hours to 24.00 hours. The study offers new data on the diurnal variation of sleep propensity which seems to be a composite function of the drives for SWS and REM sleep.
Sequence memory for prediction, inference and behaviour

In this paper, we propose a mechanism which the neocortex may use to store sequences of patterns. Storing and recalling sequences are necessary for making predictions, recognizing time-based patterns and generating behaviour. Since these tasks are major functions of the neocortex, the ability to store and recall time-based sequences is probably a key attribute of many, if not all, cortical areas. Previously, we have proposed that the neocortex can be modelled as a hierarchy of memory regions, each of which learns and recalls sequences. This paper proposes how each region of neocortex might learn the sequences necessary for this theory. The basis of the proposal is that all the cells in a cortical column share bottom-up receptive field properties, but individual cells in a column learn to represent unique incidences of the bottom-up receptive field property within different sequences. We discuss the proposal, the biological constraints that led to it and some results modelling it.
Understanding and Predicting Dynamical Behaviours in Financial Markets: Financial Application Research in CERCIA

In this paper, we shall very briefly present some of our research work in computational finance that has been carried out so far since the inception of CERCIA. Six research studies with different subjects are summarised here. The techniques that we employ in the studies vary from evolutionary computation approaches (e.g. genetic programming), signal processing techniques (e.g. the power spectrum, the wavelet analysis, the correlation) to fractal analysis methods (e.g. detrended fluctuation analysis, fractal geometry). The applied areas range from stock market predictions, stock picking, automatic trading strategies and financial market understanding, etc. Some of the studies have already been published, whilst some are still in the pipeline and others are just in their initial stages. Thus, the quality of work is varied.
Egg cortical granule N-acetylglucosaminidase is required for the mouse zona block to polyspermy

The mammalian egg must be fertilized by only one sperm to prevent polyploidy. In most mammals studied to date, the primary block to polyspermy occurs at the zona pellucida, the mammalian egg coat, after exocytosis of the contents of the cortical granules into the perivitelline space. The exudate acts on the zona, causing it to lose its ability to bind sperm and to be penetrated by sperm previously bound to the zona. However, the cortical granule components responsible for the zona block have not been identified. Studies described herein demonstrate that N-acetylglucosaminidase is localized in cortical granules and is responsible for the loss in sperm-binding activity leading to the zona block to polyspermy. Before fertilization, sperm initially bind to the zona by an interaction between sperm surface GalTase and terminal N-acetylglucosamine residues on specific oligosaccharides of the zona glycoprotein ZP3 (Miller, D. J., M. B. Macek, and B. D. Shur. 1992. Nature (Lond.). 357:589-593). These GalTase-binding sites are lost from ZP3 after fertilization, an effect that can be duplicated by N-acetylglucosaminidase treatment. Therefore, N-acetylglucosaminidase, or a related glycosidase, may be present in cortical granules and be responsible for ZP3's loss of sperm-binding activity at fertilization. Of eight glycosidases assayed in exudates of ionophore-activated eggs, N-acetylglucosaminidase was 10-fold higher than any other activity. The enzyme was localized to cortical granules using immunoelectron microscopy. Approximately 70 or 90% of the enzyme was released from cortical granules after ionophore activation or in vivo fertilization, respectively. The isoform of N- acetylglucosaminidase found in cortical granules was identified as beta- hexosaminidase B, the beta, beta homodimer. Inhibition of N- acetylglucosaminidase released from activated eggs, with either competitive inhibitors or with specific antibodies, resulted in polyspermic binding to the zona pellucida. Another glycosidase inhibitor or nonimmune antibodies had no effect on sperm binding to activated eggs. Therefore, egg cortical granule N-acetylglucosaminidase is released at fertilization, where it inactivates the sperm GalTase- binding site, accounting for the block in sperm binding to the zona pellucida.
Macrophage Inhibitory Cytokine 1 Biomarker Serum Immunoassay in Combination with PSA Is a More Specific Diagnostic Tool for Detection of Prostate Cancer

Background Prostate cancer (PCa) is the most common malignancy among men in the United States. Though highly sensitive, the often-used prostate-specific antigen (PSA) test has low specificity which leads to overdiagnosis and overtreatment of PCa. This paper presents results of a retrospective study that indicates that testing for macrophage inhibitory cytokine 1 (MIC-1) concentration along with the PSA assay could provide much improved specificity to the assay. Methods The MIC-1 serum level was determined by a novel p-Chip-based immunoassay run on 70 retrospective samples. The assay was configured on p-Chips, small integrated circuits (IC) capable of storing in their electronic memories a serial number to identify the molecular probe immobilized on its surface. The distribution of MIC-1 and pre-determined PSA concentrations were displayed in a 2D plot and the predictive power of the dual MIC-1/PSA assay was analyzed. Results MIC-1 concentration in serum was elevated in PCa patients (1.44 ng/ml) compared to normal and biopsy-negative individuals (0.93 ng/ml and 0.88 ng/ml, respectively). In addition, the MIC-1 level was correlated with the progression of PCa. The area under the receiver operator curve (AUC-ROC) was 0.81 providing an assay sensitivity of 83.3% and specificity of 60.7% by using a cutoff of 0.494 for the logistic regression value of MIC-1 and PSA. Another approach, by defining high-frequency PCa zones in a two-dimensional plot, resulted in assay sensitivity of 78.6% and specificity of 89.3%. Conclusions The analysis based on correlation of MIC-1 and PSA concentrations in serum with the patient PCa status improved the specificity of PCa diagnosis without compromising the high sensitivity of the PSA test alone and has potential for PCa prognosis for patient therapy strategies.
MORPHOMETRIC CORRELATION PATTERNS OF ADULT BIRDS (FRINGILLIDAE: PASSERIFORMES AND COLUMBIFORMES) MIRROR THE EXPRESSION OF DEVELOPMENTAL CONTROL GENES

Stimulated by the rapid progress in developmental genetics, recent approaches to evolutionary theory focus on the interface function of developmental processes in the study of genotype‐phenotype mapping. From this viewpoint, the main result of the present analysis is that the expression patterns of developmental control genes are reflected in the infraspecific correlation patterns of phenotypic characters in the adult stage. The study is based on 42 logarithmically scaled skeletal measurements of two avian clades, finches (43 species, n = 313) and pigeons (27 species, n = 219). First, for each clade an “observed correlation matrix” was calculated by computing a bias‐reduced pooled‐species correlation matrix based on the clade‐specific pooled within‐species variance‐covariance matrix between measurements. Second, the expression domains of diverse developmental control genes, that is, Hox, Msx, Pax, Mhox, Shh, Bmp, and Gdf, in characters were represented by “theoretical matrices. ” Finally, the observed and the theoretical matrices were compared by Mantel's test to test hypotheses about pattern similarities between phenotypic correlations and the expression of developmental control genes. Seventeen percent of the single matrix comparisons revealed significant (P ≤ 0.05) pattern correspondences in finches, whereas 63% were significant in pigeons. The multiple comparisons revealed correspondences at the highest significance level (P ≤ 0.001) in both clades and disclosed that 15% of the observed matrix patterns are explained in finches versus 22% in pigeons. Presumably, as finches have less pronounced correspondences between gene expression and phenotypic correlation, they are more derived than pigeons. Out of the significant single matrix comparisons, four correspondences are common to both clades: one of them is connected with the Gdf gene expression concerning limb length relations and also harmonizes with the dominant pattern within the infraspecific correlation matrices. The general implication is that the significant correspondences detected here between observed and theoretical matrices are based on a correspondence between phenotypic and genetic modules. Because the phenotypic modules are potential candidates for a direct impact of selection, the important role of genotype‐phenotype mapping in molding the body plan becomes apparent.
Pollutants Increase Song Complexity and the Volume of the Brain Area HVC in a Songbird

Environmental pollutants which alter endocrine function are now known to decrease vertebrate reproductive success. There is considerable evidence for endocrine disruption from aquatic ecosystems, but knowledge is lacking with regard to the interface between terrestrial and aquatic ecosystems. Here, we show for the first time that birds foraging on invertebrates contaminated with environmental pollutants, show marked changes in both brain and behaviour. We found that male European starlings (Sturnus vulgaris) exposed to environmentally relevant levels of synthetic and natural estrogen mimics developed longer and more complex songs compared to control males, a sexually selected trait important in attracting females for reproduction. Moreover, females preferred the song of males which had higher pollutant exposure, despite the fact that experimentally dosed males showed reduced immune function. We also show that the key brain area controlling male song complexity (HVC) is significantly enlarged in the contaminated birds. This is the first evidence that environmental pollutants not only affect, but paradoxically enhance a signal of male quality such as song. Our data suggest that female starlings would bias their choice towards exposed males, with possible consequences at the population level. As the starling is a migratory species, our results suggest that transglobal effects of pollutants on terrestrial vertebrate physiology and reproduction could occur in birds.
Diffusion Dynamics of Games on Online Social Networks

Social games, being embedded in and drawing upon existing social networks, have the potential to spread virally. In this paper, we examine two popular social games, each having millions of Facebook users, to understand the role that users play individually and collectively in propagating social applications. At the individual level, the users' invitation behavior significantly outweighs their demographic and social network properties in predicting invitation success rate. At the collective level, we demonstrate that social games that encourage group formation tend to rapidly assimilate dense network cliques. Finally, engagement in a social game is closely tied with the ability to recruit friends.
New pieces of the pathogenetic mosaic in inflammatory bowel disease

Ulcerative colitis is a lifelong disease with an elevated risk of colorectal neoplasia New hypotheses such as the defensin concept are available concerning the ongoing inflammatory reaction It is known that telomere length is related to neoplasia In this issue of EJGH it is speculated as to whether the telomere length of fibroblasts is related to the age of onset of chronic inflammatory bowel disease It is questionable whether the length of telomeres in fibroblasts is related directly to neoplasia but indirectly via variable age of onset and duration of disease Ulcerative colitis (UC) is a lifelong disease. Patients with UC have an approximately 20% risk of developing colorectal cancer. The risk of neoplasia increases with the duration of the disease. Why some patients develop colorectal cancer and others do not is still poorly understood. UC patients who develop cancer have an underlying process of genetic and epigenetic instability in the inflamed mucosa, as indicated previously using several experimental techniques. Rapid cell turnover and oxidative injury observed in UC mucosa is associated with accelerated telomere shortening, followed by an increased potential for the chromosomal ends to fuse, ending in chromatin damage and chromosomal instability. It has been reported that chromosomal losses are greater and telomeres are shorter in the biopsies of patients with long-standing UC. Telomere length is correlated with chromosomal instability in a variety of epithelial preneoplastic lesions. In the case of an inflammatory context for UC mucosa, this genetic (and also epigenetic) damage may be associated with cellular transformation and tumour progression. However, almost all studies have focussed on the hypothesis that the epithelial cells are the primary target in this scenario, leading to epithelial types of cancer. The elongated lifespan of fibroblasts, as reported in the paper by Getliffe et al. in this issue of European Journal of Gastroenterology and Hepatology, is probably indirectly connected to a lesser frequency of colorectal neoplasia in UC as part of a different immune response in these patients compared with individuals with early-onset UC.
New Osseodensification Implant Site Preparation Method to Increase Bone Density in Low-Density Bone: In Vivo Evaluation in Sheep

Purpose:The aim of this study was to evaluate a new surgical technique for implant site preparation that could allow to enhance bone density, ridge width, and implant secondary stability. Materials and Methods:The edges of the iliac crests of 2 sheep were exposed and ten 3.8 × 10-mm Dynamix implants (Cortex) were inserted in the left sides using the conventional drilling method (control group). Ten 5 × 10-mm Dynamix implants (Cortex) were inserted in the right sides (test group) using the osseodensification procedure (Versah). After 2 months of healing, the sheep were killed, and biomechanical and histological examinations were performed. Results:No implant failures were observed after 2 months of healing. A significant increase of ridge width and bone volume percentage (%BV) (approximately 30% higher) was detected in the test group. Significantly better removal torque values and micromotion under lateral forces (value of actual micromotion) were recorded for the test group in respect with the control group. Conclusion:Osseodensification technique used in the present in vivo study was demonstrated to be able to increase the %BV around dental implants inserted in low-density bone in respect to conventional implant drilling techniques, which may play a role in enhancing implant stability and reduce micromotion.
MOTION BLUR DETECTION IN AERIAL IMAGES SHOT WITH CHANNEL-DEPENDENT EXPOSURE TIME

This paper presents a simple yet efficient approach for automatic blur detection in aerial images prov ided by a multi-channel digital camera system. The blur in consideration is due to the airplane motion and causes anisotropy in the Fo urier Transform of the image. This anisotropy can be detected and estimated to re cover the characteristics of the motion blur, but o ne cannot disambiguate the anisotropy produced by a motion blur from the possi ble spectral anisotropy of the underlying sharp ima ge. The proposed approach uses a camera with channel-dependent exposure times to address this issue. Under this multi-exposure s etting, the motion blur kernel is scaled proportionally to the exposure-time, wher eas the phase differences between the underlying sh arp colour channels are assumedly negligible. We show that considering the phase of the ratio of the Fourier Transforms of two channels enhances blur detection. Results obtained on 2000 images confirm the operational efficiency of our method.
Differences between gingivitis and periodontitis associated microbial flora in the beagle dog. Relationship of plaque parameters to histological parameters of periodontal disease.

The predominant dental plaque flora was compared between two groups of adult beagle dogs, (1) ten with gingivitis and (2) ten with advanced periodontitis. Plaque from a maxillary third premolar was cultured under strict anaerobic conditions. Specimens comprising the marginal periodontal tissues were taken at the plaque sampling site and analyzed for some histological parameters of periodontal disease. The periodontitis dogs scored significantly higher for crevice depth, length of ulcerated crevice epithelium, area of inflamed connective tissue, and loss of attachment. Supragingival periodontitis plaque had significantly higher anaerobic to aerobic ratio, proportions and CFU of esculin negative streptococci, but lower proportions of Actinomyces viscosus. Subgingival periodontitis plaque had significantly higher anaerobic to aerobic ratio, microscopic counts of spirochetes, total viable CFU, proportions and CFU of esculin negative streptococci and Fusobacterium nucieatum, as well as CPU of Bacteroides asaccharolyticus, Gram negative bacilli and coccobacilli, but significantly lower proportions of A. viscosus and unspeciated actinomycetes. The total viable CFU, proportions and CFU of esculin negative streptococci correlated with all four histological parameters of periodontal disease. The CFU of B. asaccharolyticus, bacilli, and coccobacilli correlated with the length of ulcerated crevice epithelium and loss of attachment, but F. nucleatum only with the area of inflamed connective tissue and loss of attachment.
A Time-Consistent Video Segmentation Algorithm designed for Real-Time Implementation

In this paper, we propose a time consistent video segmentation algorithm designed for real-time implementation. Our segmentation algorithm is based on a region merging process that combines both spatial and motion information. The spatial segmentation takes benefit of an adaptive decision rule and a specific order of merging. Our method has proven to be efficient for the segmentation of natural images (at or textured regions) with few parameters to be set. Temporal consistency of the segmentation is ensured by incorporating motion information through the use of an improved change detection mask. This mask is designed using both illumination differences between frames, and region segmentation of the previous frame. By considering both pixel and region levels, we obtain a particularly efficient algorithm at a low computational cost, allowing its implementation in real-time on the TriMedia processor for CIF image sequences.
Mycobacterial lipoprotein activates autophagy via TLR2/1/CD14 and a functional vitamin D receptor signalling

In human monocytes, Toll‐like receptor (TLR) 2/1 activation leads to vitamin D3‐dependent antimycobacterial activities, but the molecular mechanisms by which TLR2/1 stimulation induces antimicrobial activities against mycobacteria remain unclear. Here we show that TLR2/1/CD14 stimulation by mycobacterial lipoprotein LpqH can robustly activate antibacterial autophagy through vitamin D receptor signalling activation and cathelicidin induction. We found that CCAAT/enhancer‐binding protein (C/EBP)‐β‐dependent induction of 25‐hydroxycholecalciferol‐1α‐hydroxylase (Cyp27b1) hydroxylase was critical for LpqH‐induced cathelicidin expression and autophagy. In addition, increases in intracellular calcium following AMP‐activated protein kinase (AMPK) activation played a crucial role in LpqH‐induced autophagy. Moreover, AMPK‐dependent p38 mitogen‐activated protein kinase (MAPK) activation was required for LpqH‐induced Cyp27b1 expression and autophagy activation. Collectively, these data suggest that TLR2/1/CD14‐Ca2+‐AMPK‐p38 MAPK pathways contribute to C/EBP‐β‐dependent expression of Cyp27b1 and cathelicidin, which played an essential role in LpqH‐induced autophagy. Furthermore, these results establish a previously uncharacterized signalling pathway of antimycobacterial host defence through a functional link of TLR2/1/CD14‐dependent sensing to the induction of autophagy.