Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporal separation of replication and transcription during S-phase progression

Transcriptional events during S-phase are critical for cell cycle progression. Here, by using a nascent RNA capture assay coupled with high-throughput sequencing, we determined the temporal patterns of transcriptional events that occur during S-phase. We show that genes involved in critical S-phase-specific biological processes such as nucleosome assembly and DNA repair have temporal transcription patterns across S-phase that are not evident from total RNA levels. By comparing transcription timing with replication timing in S-phase, we show that early replicating genes show increased transcription late in S-phase whereas late replicating genes are predominantly transcribed early in S-phase. Global anti-correlation between replication and transcription timing was observed only based on nascent RNA but not total RNA. Our data provides a detailed view of ongoing transcriptional events during the S-phase of cell cycle, and supports that transcription and replication are temporally separated.
Influence of Polymorphisms in DNA Repair Genes XPD, XRCC1 and MGMT on DNA Damage Induced by Gamma Radiation and its Repair in Lymphocytes In Vitro

Abstract Rzeszowska-Wolny, J., Polanska, J., Pietrowska, M. , Palyvoda, O. , Jaworska, J., Butkiewicz, D. and Hancock, R. Influence of Polymorphisms in DNA Repair Genes XPD, XRCC1 and MGMT on DNA Damage Induced by Gamma Radiation and its Repair in Lymphocytes In Vitro. Radiat. Res. 164, 132– 140 (2005). DNA single-strand breaks (SSBs) were quantified by single-cell gel electrophoresis and micronucleated and apoptotic cells were quantified by microscopic assays in peripheral blood lymphocytes after irradiation on ice with 2 Gy of 60Co γ radiation, and their association with polymorphisms of genes that encode proteins of different DNA repair pathways and influence cancer risk (XPD codon 312Asp → Asn and 751Lys → Gln, XRCC1 399Arg → Gln, and MGMT 84Leu → Phe) was studied. In unirradiated lymphocytes, SSBs were significantly more frequent in individuals older than the median age (52 years) (P = 0.015; n = 81), and the frequency of apoptotic or micronucleated cells was higher in individuals with alleles coding for Asn at XPD 312 or Gln at 751 (P = 0.030 or 0.023 ANOVA, respectively; n = 54). The only polymorphism associated with the background SSB level was MGMT 84Phe (P = 0.04, ANOVA; n = 66). After irradiation, SSB levels and repair parameters did not differ significantly with age or smoking habit. The SSB level varied more than twofold and the repair rate and level of unrepaired SSBs more than 10-fold between individuals. The presence of variant alleles coding for Asn at XPD 312 was associated with more radiation-induced SSBs (P = 0.014) and fewer unrepaired SSBs (P = 0.008), and the phenotype (>median induced SSBs/<median unrepaired SSBs) was seen in the majority of XPD 312Asn/Asn homozygotes; the odds ratio for variant homozygotes to show this phenotype was 5.2 (95% confidence interval 1.4–19.9). The hypothesis is discussed that XPD could participate in repair of ionizing radiation-induced DNA damage. While it cannot be excluded that the effects observed are due to cosegregating polymorphisms or that the responses of lymphocytes are not typical of other cell types, the results suggest that polymorphism of DNA repair genes, particularly XPD, is one factor implicated in the variability of responses to ionizing radiation between different individuals.
Development of the Home Pregnancy Test

Abstract: The home pregnancy testworks by measuring human chorionic gonadotropin (hCG) hormone in urine. This hormone was initially studied in NICHD intramural laboratories as a reliable marker of certain tumors. Refinement of the assay for hCG detection to enhance specificity enabled its ready application to pregnancy detection.
Assessing the completeness and agreement of variables of the Information Systems on Live Births and on Mortality in Recife-PE, Brazil, 2010-2012.

OBJECTIVE to assess the information completeness and agreement on infant deaths. METHODS this was an evaluation study with descriptive design using data of the Information System on Live Births (Sinasc) and Mortality Information System (SIM) of residents in Recife-PE, Brazil, in 2010-2012; the deterministic records linkage was used to combine the data on infant deaths and live births. RESULTS of the 837 infant deaths registered on SIM, 811 (96.9%) were linked; the completeness obtained was above 95% on SIM and 98% on Sinasc; the agreement varied from 0.762 (substantial) to 0.997 (excellent) for the intraclass correlation coefficient, and it was excellent for Kappa index (>0.80). CONCLUSION Sinasc and SIM presented excellent completeness and agreement for most of the variables analyzed. The relationship between the databases is a tool that can be used by the health services of the municipalities to improve the vital statistics information systems.
A Feature-based Analysis of Open Source Tools for Enterprise 2.0 - Open Source Tools for Team Collaboration in SMEs

The marketplace of Enterprise 2.0 tools that support knowledge workers within companies to work together on cognitive tasks and share information and knowledge is diversified and offers commercial systems of varying complexity and functional range as well as open source software. Like commercial systems, open source tools for Enterprise 2.0 provide a broad range of functionality and offer a good alternative for organisations – especially for SMEs. This paper presents a study of the growing market for Enterprise 2.0 systems and focuses entirely on ones that are available under an open source license. We introduce a set of 97 individual features and criteria to assess a representative sample of open source Enterprise 2.0 tools. Our results show that the marketplace of open source tools for Enterprise 2.0 offers technically mature solutions with a broad range of functionality.
Mathematical Modeling of Longitudinal Dynamic Pressure Distribution on Planing Hulls

In the present paper, a mathematical model is used in order to predict the longitudinal distribution of dynamic pressure on planing hulls. The present model is based on the empirical equations resulted from multitude of experiments that have been carried out over the years on planing boats. These empirical equations are able to predict a longitudinal section of the pressure distribution. The obtained pressure field is then used to evaluate the dynamic pressure behind the stagnation line. A computer code is developed for the modeling purposes and the obtained results are validated against experimental data. In this regard, the effects of the trim angle, dead-rise angle and the wetted length on the longitudinal distribution of the dynamic pressure for the planing hulls are studied.
Human tumour clonality assessment—flawed but necessary

One of the premises of the somatic mutation theory of carcinogenesis is that tumours are clonal lesions derived from a single mutated stem cell progenitor. This theory spawned a proliferation of clonality studies, using a variety of different molecular markers to try to determine tumour clonality in multiple organs. In order to establish true clonality, it is necessary to identify the original founding mutation that occurred at the initiation of the progenitor clone. Use of other lesions may only serve to identify sub‐clones. As founding mutations have not been properly established in many organ systems, human clonality assessments carry this caveat. However it is only through clonality and mutation burden assessments that phylogenetic tress become established. Here, we review the advantages, disadvantages and use of different clonality markers. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Restrictions on phonemes in affixes: A crosslinguistic test of a popular hypothesis

Abstract The hypothesis that inflectional affixes use a restricted set of phonemes and that these are the less marked phonemes of the language is discussed and tested on the verbal affixes in a sample of twenty-three maximally unrelated languages. The results show that the tendency for languages to use only a smaller subset of their phonemes in verbal inflection than would be predicted by chance is only a weak trend and not by any means a universal of language. In addition, the tendency to use less marked or less complex segments in affixes is also only a trend and not a universal. However, some generalizations can be made about languages that have patterned exclusions from affixes. It is argued that no one explanation covers all the facts and that multiple diachronic trends, such as phonological reduction in grammaticization and the re-use of old affixes in creating new grammaticized affixes, produce the weak tendency evidenced by the data.
Effects of megagametophyte removal on DNA yield and early seedling growth in coastal Douglas-fir

Stratified seeds of coastal Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco var. menziesii) were germinated, sown in soil, and seed coats and megagametophytes were removed at various stages of early seedling development. Yield and quality of DNA extracted from the megagametophytes were related to several morphological traits of the seedlings after 2 months of growth in a controlled environment chamber. Regression and analysis of variance demonstrated nonlinear associations between stage of megagametophyte removal and seedling size traits, DNA yield and quality, and RNA presence. Megagametophyte removal when cotyledons had extended one-quarter of their length (about 4 mm) outside the seed coat (our stage 4) resulted in sufficient DNA for construction of saturated PCR- (polymerase chain reaction) based genome maps and had little effect on seedling development.
Pathophysiology of Acute Lymphoblastic Leukemia

The Acute lymphoblastic leukemia (ALL), it produced as a result of a process of malignant transformation of a progenitor lymphocytic cell in the B and T lineages. In ALL, the majority of the cases, the transformation affects the B lineage cells. Leukemia and other cancers share biological characteristics, as clonality. The molecular alterations that are required for the de‐ velopment of a malignant disease is a rare phenomenon when one considers the large number of target cells susceptible to this condition, in other words, a single genetic change rarely be sufficient for developing a malignant tumor. This means that a small percentage of people (1%) who develop malignant hematological disease, probably only 1 cell mutated in a critical gene for the proliferation, differentiation and survival of progenitor cells. There is evidence sup‐ porting a sequential multistep process, of alterations in several oncogenes in tumor suppressor genes or microRNA genes in cancerigen cells.
Considerations on energy absorption of HVDC circuit breakers

This article deals with possible solutions for energy absorption in HVDC transmission systems. Depending on the converter topology high current slopes can appear in case of DC short circuits. Besides the handling of high currents itself, HVDC Circuits Breakers have to decrease the energy stored in line inductances in order to interrupt. Although different breaker concepts have been proposed, energy absorption is yet generally based on high voltage surge arresters. Isolation and over-voltage protection level have to be well adapted to expected surges and metal oxide surge arresters fit this problem. However, validating the maximum switching action count of those breakers, lifetime considerations of ZnO varistors have to be studied critically. In this paper a comparison on dimensioning needs and voltage stresses regarding an HVDC environment shall be carried out for existing solutions and furthermore a new proposal using resistors in addition to freewheeling diodes shall be made. This is verified by simulations with MATLAB Simulink.
Apoptosis in cells of bronchoalveolar lavage: A cellular reaction in patients who die with sepsis and respiratory failure

Objective Apoptosis represents a physiologic clearance mechanism in human tissues. The role of apoptosis has not been examined in lung cell populations, such as alveolar macrophages of septic patients, an organ frequently insulted in these patients. This study was designed to examine the effect of sepsis on the apoptosis of alveolar macrophages. Design Prospective study. Setting Intensive care unit and surgical intensive care and trauma unit of a large university hospital in Athens, Greece. Patients Bronchoalveolar lavage was obtained from 20 consecutive patients who met the criteria for sepsis, admitted to two intensive care units. Bronchoalveolar lavage was obtained from nine volunteers without lung disease who served as controls. Interventions None. Measurements and Main Results The specimens were analyzed by using annexin V binding, terminal deoxynucleotidyl transfer-mediated deoxyuridine 5-triphosphate nick end labeling (TUNEL), DNA laddering, light microscopy, and immunohistochemistry. Spontaneous apoptosis of bronchoalveolar lavage cells and particularly of alveolar macrophages was significantly decreased in septic patients compared with nonseptic controls. This finding was confirmed by using morphologic criteria and the TUNEL method. Furthermore, gel electrophoresis of DNA obtained from bronchoalveolar cells revealed that DNA fragmentation was not necessarily associated with apoptotic cell death. The bcl-2 gene was minimally expressed in the control group. An inverse correlation was found between the percentage of apoptotic alveolar macrophages and the severity of sepsis. Conclusions The prolonged survival of lung cells in septic patients and especially of alveolar macrophages may be attributable to the inhibition of apoptosis. This seems to represent an initial attempt of the host to increase the defense capacity to kill the invading microorganism, resulting in an unbalanced tissue load of cells and an uncontrolled release of toxic metabolites. Furthermore, the inhibition of apoptosis in septic patients may explain why lung function is impaired, leading to sepsis-induced acute respiratory distress syndrome and death.
Consumer Adoption - Risk Factor of Mobile Banking Services

Mobile banking services present a unique growth opportunity for mobile operators in emerging markets, and have already made good progress in bringing financial services to the previously unbanked populations of many developing countries. The potential is amazing, but what about the risks? In the complex process of establishing a mobile banking business model, many kinds of risks and factors need to be monitored and well-managed. Risk identification is the first stage of risk management. Correct risk identification ensures risk management effectiveness. Keeping the risks low makes it possible to use the full potential of mobile banking and carry out the planned business strategy. The focus should be on adoption of consumers which is the main risk factor of mobile banking services. Keywords—Consumer Adoption, Mobile Banking, Risk
Investigating the Use of Code Analysis and NLP to Promote a Consistent Usage of Identifiers

Meaningless identifiers as well as inconsistent use of identifiers in the source code might hinder code readability and result in increased software maintenance efforts. Over the past years, effort has been devoted to promoting a consistent usage of identifiers across different parts of a system through approaches exploiting static code analysis and Natural Language Processing (NLP). These techniques have been evaluated in small-scale studies, but it is unclear how they compare to each other and how they complement each other. Furthermore, a full-fledged larger empirical evaluation is still missing. ,,We aim at bridging this gap. We asked developers of five projects to assess the meaningfulness of the recommendations generated by three techniques, two already existing in the literature (one exploiting static analysis, one using NLP) and a novel one we propose. With a total of 922 rename refactorings evaluated, this is, to the best of our knowledge, the largest empirical study conducted to assess and compare rename refactoring tools promoting a consistent use of identifiers. Our study sheds light on the current state-of-the-art in rename refactoring recommenders, and indicates directions for future work.
Glutathione peroxidase 4 protects cortical neurons from oxidative injury and amyloid toxicity

Polyunsaturated fatty acids (PUFA) in membrane lipids are prone to attack by reactive oxygen species (ROS), and the resulting lipid peroxidation can cause injury and death of cells. Glutathione peroxidase 4 (Gpx4) is an antioxidant defense enzyme that can directly detoxify lipid hydroperoxides generated by ROS. Overexpression of Gpx4 has been shown to be protective against oxidative damage in several cell lines. We examined in this study the stress response of neurons with increased expression of Gpx4, because neurons are especially vulnerable to oxidative injury as a result of their high content of PUFA. Our results show that primary culture cortical neurons derived from Gpx4 transgenic mice, which had increased expression of Gpx4, had increased cell survival and reduced level of apoptosis after exposure to t‐butyl hydroperoxide and hydrogen peroxide. We also studied the protective role of Gpx4 against β‐amyloid toxicity, because β‐amyloid‐induced neural toxicity is believed to be mediated through lipid peroxidation. Primary culture cortical neurons from Gpx4 transgenic mice had significantly less cell toxicity than their wild‐type counterparts after exposure to Aβ25–35 and Aβ1–40 peptides, and apoptosis induced by Aβ25–35 was attenuated in neurons from Gpx4 transgenic mice. Our data demonstrate that overexpression of Gpx4 protects neurons against oxidative injury and β‐amyloid‐induced cytotoxicity. © 2006 Wiley‐Liss, Inc.
Periodontitis decreases the antiatherogenic potency of high density lipoprotein Published, JLR Papers in Press, September 16, 2003. DOI 10.1194/jlr.M300250-JLR200

Periodontitis, a consequence of persistent bacterial infection and chronic inflammation, has been suggested to predict coronary heart disease (CHD). The aim of this study was to investigate the impact of periodontitis on HDL structure and antiatherogenic function in cholesterol efflux in vitro. HDL was isolated from 30 patients (age 43.6 ± 6.1 years, mean ± SD) with periodontitis before and after (3.2 ± 1.4 months) periodontal treatment. The capacity of HDL for cholesterol efflux from macrophages (RAW 264.7), HDL composition, and key proteins of HDL metabolism were determined. After periodontal treatment, phospholipid transfer protein (PLTP) activity was 6.2% (P < 0.05) lower, and serum HDL cholesterol concentration, PLTP mass, and cholesteryl ester transfer protein activity were 10.7% (P < 0.001), 7.1% (P = 0.078), and 19.4% (P < 0.001) higher, respectively. The mean HDL2/HDL3 ratio increased from 2.16 ± 0.87 to 3.56 ± 0.48 (P < 0.05). HDL total phospholipid mass and sphingomyelin-phosphatidylcholine ratio were 7.4% (P < 0.05) and 36.8% (P < 0.001) higher, respectively. The HDL-mediated cholesterol efflux tended to be higher after periodontal treatment; interestingly, this increase was significant (P < 0.05) among patients whose C-reactive protein decreased (53.7% reduction, P = 0.015) and who were positive by PCR for Actinobacillus actinomycetemcomitans. These results suggest that periodontitis causes similar, but milder, changes in HDL metabolism than those that occur during the acute-phase response and that periodontitis may diminish the antiatherogenic potency of HDL, thus increasing the risk for CHD.
Extending shooting-and-bouncing rays method with uniform theory of diffraction for installed antennas

The shooting-and-bouncing rays (SBR) method for solving large-scale radiation and scattering problems uses geometrical optics (GO) ray tracing to extend physical optics (PO) to multi-bounce geometries. In this paper, we explain how the accuracy of SBR for installed antenna geometries can be improved with the addition of uniform theory of diffraction (UTD) rays. The UTD rays provide ray coverage and paint surface currents in shadow regions, augmenting the radiation from surface currents painted by the GO rays. A realistic installed antenna application is presented as an example.
Framework for educational robotics: a multiphase approach to enhance user learning in a competitive arena

Educational robotics involves using robots as an educational tool to provide a long term, and progressive learning activity, to cater to different age group. The current concern is that, using robots in education should not be an instance of a one-off project for the sole purpose of participating in a competitive event. Instead, it should be a sustainable long-term progression spanning the primary school to pre-university level. This article presents a framework for robotics using a multiphase approach to enhance user learning in a competitive arena.
Conservation de la nature et développement : l'intégration impossible ?

La conservation de la nature est aujourd'hui placee a un tournant. Les politiques de protection de la nature cherchent depuis trente ans a integrer des objectifs de developpement, mais cette integration s'avere plus difficile que prevue. L'histoire de la conservation est deja longue. Apres les premieres tentatives de gestion integree aux XVIIIe et XIXe siecles, apres les politiques etatiques centralisees des parcs nationaux et des reserves naturelles au XXe siecle, elle connait actuellement un troisieme souffle qui lui permet de se placer comme un exemple concret de developpement durable. Mais la conservation peine a definir de nouveaux modeles qui puissent repondre a la fois aux besoins de gestion durable des ecosystemes et aux exigences des acteurs concernes. Comment amenager l'espace de maniere a assurer a la fois l'exploitation et la preservation de la nature ? Comment articuler la diversite biologique avec la diversite des pratiques de gestion des milieux ? Comment developper une valorisation des ressources naturelles qui puisse profiter aux plus defavorises ? Comment, finalement, faire en sorte que la conservation puisse deboucher sur des regulations emancipatrices, davantage que sur des politiques repressives et conservatrices ? De maniere inedite en France, cet ouvrage fait le point sur differentes experiences de «conservation integree» dans une perspective critique et en les replacant dans l'histoire de la protection de la nature. Des exemples concrets sont associes a des analyses plus generales du modele dominant de conservation integree. Pour celui-ci, la marchandisation de la nature et la participation locale sont les fers de lance de l'integration entre conservation et developpement. Mais les differentes contributions de l'ouvrage montrent que cette double focalisation est a la fois vecteur et frein d'une reelle reappropriation sociale. Une nouvelle forme d'integration apparait des lors necessaire, qui puisse articuler le local, le national et le transnational, et donner a la conservation les outils mondiaux de regulations dont elle a besoin pour sortir de sa «reserve». (Resume d'auteur)