Miracle-dz/UniFAR-FTUs huggingface dataset:
The emerging roles of Oct 4 in tumor-initiating cells

Wang YJ, Herlyn M. The emerging roles of Oct4 in tumor-initiating cells. Am J Physiol Cell Physiol 309: C709–C718, 2015; doi:10.1152/ajpcell.00212. 2015. — Octamer-binding transcription factor 4 (Oct4), a homeodomain transcription factor, is well established as a master factor controlling the self-renewal and pluripotency of pluripotent stem cells. Also, a large body of research has documented the detection of Oct4 in tumor cells and tissues and has indicated its enrichment in a subpopulation of undifferentiated tumor-initiating cells (TICs) that critically account for tumor initiation, metastasis, and resistance to anticancer therapies. There is circumstantial evidence for low-level expression of Oct4 in cancer cells and TICs, and the participation of Oct4 in various TIC functions such as its self-renewal and survival, epithelial-mesenchymal transition (EMT) and metastasis, and drug resistance development is implicated from considerable Oct4 knockdown and overexpression-based studies. In a few studies, efforts have been made to identify Oct4 target genes in TICs of different sources. Based on such information, Oct4 in TICs appears to act via mechanisms quite distinct from those in pluripotent stem cells, and a main challenge for future studies is to unravel the molecular mechanisms of action of Oct4, particularly to address the question on how such low levels of Oct4 may exert its functions in TICs. Acquiring cells from their native microenvironment that are of high enough quantity and purity is the key to reliably analyze Oct4 functions and its target genes in TICs, and the information gained may greatly facilitate targeting and eradicating those cells.
UNIVERSITY OF BOLOGNA Ph . D . Program in “ Biodiversity and Evolution ” Cycle

III 1. THE NEOLITHIC IN GREECE AND EUROPE . 1 1.1 The origin of agriculture and birth of the first farming communities . 1 1.2 The spread of Neolithic in Europe: an archaeological overview . 3 1.2.1 The Neolithic in Western Mediterranean . 4 1.2.2 The Neolithic in the Balkan peninsula . 6 1.2.3 The Neolithic in Central Europe: the Linear BandKeramik Culture (LDK) . 7 1.3 A genetic overview on the spread of Neolithic in Europe . 8 1.4 Cultural or demic diffusion? An open question . 12 1.5 The Neolithic in Greece . 14 1.5. 1 The Neolithic migration into Greece . 17 2. AIMS OF THE STUDY . 22 3. MATERIALS AND METHODS . 24 3.1 Population analysed . 24 3.2 Laboratory analyses . 27 3.2.1 Dna extraction . 27 3.2.3 Y-Chromosome genotyping . 28 3.3 Statistical analyses . 34 3.3.1 Intra-population variation . 34 3.3.2 Inter-population variation . 36 3.3.2.1 Genetic distances . 36 3.3.2.2 Multidimensional scaling . 37 3.3.2.3 Phylogenetic reconstruction: Median-joining Network . 37 3.3.2.4 Principal components analysis . 38 3.3.3 Demographic inferences through coalescence Bayesian methods . 39 3.3. 4 Time of the most recent common ancestor (T.M.R.C.A.) estimate . 40 4. RESULTS . 42 4.1 Y-chromosome results . 42 4.1.1 Haplogroup frequencies and intra-population diversity . 42 4.1.2 Demographic inferences . 48 4.1.3 Inter-population diversity . 51
Dynamic Crowd Emotion Contagion Simulation with GPU Acceleration

The emotion contagion is an important research point in the crowd simulation field. However, as the positions of crowd usually change dynamically, computing the contagion process becomes a challenge. There exists a solution for a similar problem, the N-body problem, but it's too time consuming to be adapted in crowd simulation as it needs to calculate the reactions between every two objects. In order to solve this problem, we provided a fast adjacent test and contagion computing algorithm with GPU acceleration. Firstly individuals' affection fields were set and projected onto two dimensional ground and represented by squares of the same size; secondly the whole ground was divided into squares as the same size as those for the affection projection; thirdly, adjacent squares were tested to generate the nearer neighbors and the contagion results were calculated. All these steps were processed in parallel by GPU.
Interactive comment on “ An overview of regional and local characteristics of aerosols in South Africa using satellite , ground , and modeling data ” by S

ter (PM2.5 and PM10) concentrations, but suffers from a lack of clarity in the discussion and in the figures. For these reasons, I think the paper requires Major Revisions before being published. I do think the core message – that column AOD from satellite data is not a useful proxy for surface PM2.5 in South Africa – is a publishable finding that builds on a body of research that stemmed from or led to the SAFARI 1992 and 2000 field campaigns.
Palm and Finger Print Characteristics in Nonfamilial Cleft Lip and Palate Patients and their Parents

AbstractThe aim of this study was to investigate if Iranian individuals with nonfamilial cleft lip and palate (CLP) and their unaffected parents display more dermatoglyphic asymmetry than the normal population.The study group included 55 patients with nonfamilial CLP and their unaffected parents (38 fathers and 47 mothers). The control group included 60 healthy children and their parents (37 fathers and 50 mothers). Total ridge counts of each finger (TRC), atd angles, a-b ridge counts, and finger print pattern types of all participants were recorded. Asymmetry between the right and left hands of each individual was determined. Dissimilarity between pattern types on homologous fingers was compared using chi-square test. Asymmetry of other parameters was statistically analyzed using the Mann-Whitney U test.There were no significant differences between the groups in terms of their asymmetry of atd angle, a-b ridge count, and pattern dissimilarity score. However, significant differences in mean TRC between CLP patients and control children were found for the right ring digit (P = 0.023), right little digit (P = 0.032), and left index digit (P = 0.005). Also, there were significant differences among CLP patients and control children (P = 0.022) as well as unaffected fathers of CLP patients and their control group (P = 0.020) in terms of type of finger print pattern.No enhanced fluctuating asymmetry was found in most of the dermatoglyphic traits in the population studied, which indicated a low degree of developmental instability of the sporadic cases of cleft deformity.
Two-step human–environmental impact history for northern New Zealand linked to late-Holocene climate change

Following resolution of a long-standing debate over the timing of the initial settlement of New Zealand from Polynesia (late 13th century), a prevailing paradigm has developed that invokes rapid transformation of the landscape, principally by fire, within a few decades of the first arrivals. This model has been constructed from evidence mostly from southern and eastern regions of New Zealand, but a more complicated pattern may apply in the more humid western and northern regions where forests are more resilient to burning. We present a new pollen record from Lake Pupuke, Auckland, northern New Zealand, that charts the changing vegetation cover over the last 1000 years, before and after the arrival of people. Previous results from this site concurred with the rapid transformation model, although sampling resolution, chronology and sediment disturbance make that interpretation equivocal. Our new record is dated principally by tephrochronology together with radiocarbon dating and includes a cryptotephra deposit identified as Kaharoa tephra, a key marker for first settlement in northern New Zealand. Its discovery and stratigraphic position below two Rangitoto-derived tephras enables a clearer picture of environmental change to be drawn. The new pollen record shows an early phase (step 1) of minor, localised forest clearance around the time of Kaharoa tephra (c. 1314 AD) followed by a later, more extensive deforestation phase (step 2) commencing at around the time of deposition of the Rangitoto tephras (c. 1400–1450 AD). This pattern, which needs to be corroborated from other well-resolved records from northern New Zealand, concurs with an emerging hypothesis that the ‘Little Ice Age’ had a significant impact on pre-European Māori with the onset of harsher conditions causing a consolidation of populations and later environmental impact in northern New Zealand.
Tetrodotoxin Concentrations in Pleurobranchaea maculata: Temporal, Spatial and Individual Variability from New Zealand Populations

Tetrodotoxin (TTX) is a potent neurotoxin that has been identified in a range of phylogenetically unrelated marine and terrestrial organisms. Tetrodotoxin was recently detected in New Zealand in Pleurobranchaea maculata (the grey side-gilled sea slug). From June 2010 to June 2011 wild specimens were collected from 10 locations around New Zealand. At one site (Narrow Neck Beach, Auckland) up to 10 individuals were collected monthly for 6 months. Attempts were also made to rear P. maculata in captivity. Tetrodotoxin was detected in samples from eight of the ten sites. The highest average (368.7 mg kg−1) and maximum (1414.0 mg kg−1) concentrations were measured in samples from Illiomama Rock (Auckland). Of the toxic populations tested there was significant variability in TTX concentrations among individuals, with the highest difference (62 fold) measured at Illiomama Rock. Tetrodotoxin concentrations in samples from Narrow Neck Beach varied temporally, ranging from an average of 184 mg kg−1 in June 2010 to 17.5 mg kg−1 by December 2010. There was no correlation between TTX levels and mass. The highest levels correspond with the egg laying season (June–August) and this, in concert with the detection of high levels of TTX in eggs and early larval stages, suggests that TTX may have a defensive function in P. maculata. Only one larva was successfully reared to full maturation and no TTX was detected.
A Component System for Spontaneous Virtual Networks

In this paper, we propose a framework and a component system, which can be used to dynamically create modularized network services. A composer can automatically compose such services from a library of available components, taking into account dependencies among components and the possibility of sharing components by different services. In addition to group communication and publish/subscribe functionalities, which are implemented as components already, it is very easy to extend the library with third-party components or own implementations. The framework performs the calculation of a suitable service composition and its deployment among all participating nodes. Each composition can take into account different application requirements or incorporate new components without changing the host application. Since the system is also highly modularized itself, it allows to flexibly choose alternative composition or deployment algorithms, or develop new ones.
Prediction of the structure of the replication initiator protein DnaA

The secondary structure of DnaA protein and its interaction with DNA and ribonucleotides has been predicted using biochemical, biophysical techniques, and prediction methods based on multiple‐sequence alignment and neural networks. The core of all proteins from the DnaA family consists of an “open twisted α/β structure,” containing five α‐helices alternating with five β‐strands. In our proposed structural model the interior of the core is formed by a parallel β‐sheet, whereas the α‐helices are arranged on the surface of the core. The ATP‐binding motif is located within the core, in a loop region following the first β‐strand. The N‐terminal domain (80 aa) is composed of two α‐helices, the first of which contains a potential leucine zipper motif for mediating protein‐protein interaction, followed by a β‐strand and an additional α‐helix. The N‐terminal domain and the α/β core region of DnaA are connected by a variable loop (45–70 aa); major parts of the loop region can be deleted without loss of protein activity. The C‐terminal DNA‐binding domain (94 aa) is mostly α‐helical and contains a potential helix‐loop‐helix motif. DnaA protein does not dimerize in solution; instead, the two longest C‐terminal α‐helices could interact with each other, forming an internal “coiled coil” and exposing highly basic residues of a small loop region on the surface, probably responsible for DNA backbone contacts. © 1997 Wiley‐Liss Inc.
Partial logistic artificial neural networks (PLANN) for flexible modeling of censored survival data

Linear and non-linear flexible regression analysis techniques, such as those based on splines and feed forward artificial neural networks (FFANN), have been proposed for the statistical analysis of censored survival time data, to account for the presence of non linear effects of predictors. Among survival functions, the hazard has a biological interest for the study of the disease dynamics, moreover it allows for the estimation of cumulative incidence functions for predicting outcome probabilities over follow-up. Therefore, specific error functions and data representation have been introduced for FFANN extensions of generalized linear models, in the perspective of modelling the hazard function of censored survival data. These techniques can be applied to account for the prognostic contribution of new biomarkers in addition to the traditional ones.
Detection of hepatitis C virus RNA by a combined reverse transcription-polymerase chain reaction assay

Amplification of RNA by the polymerase chain reaction (PCR) is normally a two-step process requiring separate enzymes and buffer conditions. We describe a combined reverse transcription-PCR (RT-PCR) assay for hepatitis C virus (HCV) RNA amplification in which a single enzyme and buffer condition are used. In this assay, both the RT and PCR steps are carried out with the thermoactive DNA polymerase of Thermus thermophilus. A transcription vector containing HCV sequences has also been constructed to generate quantifiable HCV RNA templates that can be used to optimize reaction conditions and to assess the efficiency of amplification. Amplification from < or = 100 copies of RNA was detected reproducibly by gel electrophoresis. The assay sensitivity was increased to 10 RNA copies by hybridization to a probe. The patterns of viremia in three individuals infected with HCV were examined by amplification of HCV RNA from plasma samples collected serially over a period of 1 year. These results were correlated with the times of seroconversion and the onset of rise in levels of alanine aminotransferase in serum. In all three subjects, HCV RNA was detected prior to seroconversion and the initial rise in levels of alanine aminotransferase in serum. Upon seroconversion, HCV RNA fell to a level below the detection limit of the assay. This pattern of transient viremia appears to be characteristic of acute, resolving HCV infections. The combined RT-PCR assay is a sensitive method which circumvents the problems associated with PCR amplification of RNA. Using this assay, we demonstrated that three donors infected by the same index case all have similar patterns of viremia.
Downscaling Satellite Precipitation Estimates With Multiple Linear Regression, Artificial Neural Networks, and Spline Interpolation Techniques

Satellite precipitation estimates (SPEs) have been widely used in various applications. However, when applied to small basins and regions, the spatial resolution of SPEs is too coarse. In this study, we present three downscaling algorithms based upon the relationships between SPEs and cloud optical and microphysical properties in northeast Austria. Different downscaling techniques, namely, multiple linear regression, artificial neural networks, and spline interpolation, were adopted for the downscaling of Integrated Multi‐satellitE Retrievals for GPM (IMERG) precipitation data. In this respect, linear and nonlinear relationship among IMERG data and different cloud variables, such as cloud effective radius, cloud optical thickness, and cloud water path, was evaluated. Downscaled SPEs, as well as the original IMERG product, were subsequently validated using 54 rain gauges at a daily timescale. According to the results, all downscaled products were more accurate than the original IMERG data. Furthermore, all downscaling techniques captured the spatial patterns of precipitation reasonably well with more detailed information when compared with the original IMERG precipitation. However, the spline interpolation slightly outperformed the other techniques, followed by multiple linear regression and artificial neural network, respectively. Moreover, the proposed methods, which consistently showed increased correlation (e.g., from 0.30 to 0.56 for spline interpolation) and reduced mean absolute error and root‐mean‐square error (e.g., from 10.14 to 6.55 mm and 13.5 to 8.76 mm, respectively) for average of all events, can more accurately produce downscaled precipitation data.
Effects of Salinity on Soil Properties of Coastal Areas of (Babuganj, Bakerganj, Gournadi and Kalapara) in Bangladesh

Bangladesh is highly vulnerable to sea level rise and salinity became a serious problem for agriculture all over the world. Soil salinity affects the parameters in soil and it is one of the major causes of decrease in the organic matter and nitrogen level in the southwestern part of Bangladesh. So, a field study was conducted to determine the effects of salinity on soil properties at Babuganj, Bakerganj, Gournadiupazilas of Barisal and Kalaparaupazilaof Patuakhali district of Bangladesh during the period of July to September 2016. Soil sampling was done by random sampling method at 0–50 cm and 50–100 cm depth. The dominant soil textural classes in the saline areas were silty clay. The soils pH of the surface horizon was slightly lower than those of the subsoil. Cation Exchange Capacity (CEC) of all these soils varied from 12.83 to 20.92 meq 100 g-1 soil. Electrical conductivity (EC) varied from 1.23 dS/m to 6.6 dS/m at Babuganj, Bakergnaj and Gournadi and moderately saline at Kalapara. The organic matter content was medium to high (0.62 to 1.6)% at Kalapara and Bakerganj but pretty low (0.39 to 1.03)% at Babuganj and Gournadi. Nutrient deficiencies for total nitrogen were quite dominant in the study areas. It was found that the clay content was the most fundamental property to control chemical properties of soils. From the correlation matrix it was found that organic matter showed significant negative relationship with CEC and Exchangeable Na, K, Ca and Mg showed mostly significant negative relationship with OM. Exchangeable sodium, potassium, calcium and magnesium were in high level and the dominant water soluble anions were Cland SO4 2-.
A Trouble Shared Is a Trouble Halved: Social Context and Status Affect Pain in Mouse Dyads

In mice behavioral response to pain is modulated by social status. Recently, social context also has been shown to affect pain sensitivity. In our study, we aimed to investigate the effects of interaction between status and social context in dyads of outbred CD-1 male mice in which the dominance/submission relationship was stable. Mice were assessed for pain response in a formalin (1% concentration) test either alone (individually tested-IT), or in pairs of dominant and subordinate mice. In the latter condition, they could be either both injected (BI) or only one injected (OI) with formalin. We observed a remarkable influence of social context on behavioral response to painful stimuli regardless of the social status of the mice. In the absence of differences between OI and IT conditions, BI mice exhibited half as much Paw-licking behavior than OI group. As expected, subordinates were hypoalgesic in response to the early phase of the formalin effects compared to dominants. Clear cut-differences in coping strategies of dominants and subordinates appeared. The former were more active, whereas the latter were more passive. Finally, analysis of behavior of the non-injected subjects (the observers) in the OI dyads revealed that dominant observers were more often involved in Self-grooming behavior upon observation of their subordinate partner in pain. This was not the case for subordinate mice observing the pain response of their dominant partner. In contrast, subordinate observers Stared at the dominant significantly more frequently compared to observer dominants in other dyads. The observation of a cagemate in pain significantly affected the observer's behavior. Additionally, the quality of observer's response was also modulated by the dominance/submission relationship.
Test of mindfulness and hope components in a psychological intervention for women with cancer recurrence.

OBJECTIVE Psychological interventions can attenuate distress and enhance coping for those with an initial diagnosis of cancer, but there are few intervention options for individuals with cancer recurrence. To address this gap, we developed and tested a novel treatment combining Mindfulness, Hope Therapy, and biobehavioral components. METHOD An uncontrolled, repeated measures design was used. Women (N = 32) with recurrent breast or gynecologic cancers were provided 20 treatment sessions in individual (n = 12) or group (n = 20) formats. On average, participants were middle aged (M = 58) and Caucasian (81%). Independent variables (i.e., hope and mindfulness) and psychological outcomes (i.e., depression, negative mood, worry, and symptoms of generalized anxiety disorder) were assessed pre-treatment and 2, 4, and 7 months later. Session-by-session therapy process (positive and negative affect, quality-of-life) and mechanism (use of intervention-specific skills) measures were also included. RESULTS Distress, anxiety, and negative affect decreased, whereas positive affect and mental-health-related quality-of-life increased over the course of treatment, as demonstrated in mixed-effects models with the intent-to-treat sample. Both hope and mindfulness increased, and use of mindfulness skills was related to decreased anxiety. CONCLUSIONS This treatment was feasible to deliver and was acceptable to patients. The trial serves as preliminary evidence for a multi-component intervention tailored to treat difficulties specific to recurrent cancer. The blending of the components was novel as well as theoretically and practically consistent. A gap in the literature is addressed, providing directions for testing interventions designed for patients coping with the continuing stressors and challenges of cancer recurrence.
human erythroid cells Hydroxyurea nitrosylates and activates soluble guanylyl cyclase in

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