Miracle-dz/UniFAR-FTUs huggingface dataset:
Epigenetic Characteristics and Development of Embryos Cloned from Donor Cells Treated by Trichostatin A or 5-aza-2′-deoxycytidine1

Abstract Development to blastocyst following nuclear transfer is dependent on the donor cell's ability to reprogram its genome to that of a zygote. This reprogramming step is inefficient and may be dependent on a number of factors, including chromatin organization. Trichostatin A (TSA; 0–5 μM), a histone deacetylase inhibitor, was used to increase histone acetylation and 5-aza-2′-deoxycytidine (5-aza-dC; 0–5 μM), a DNA methyl-transferase inhibitor, was used to decrease methylation of chromatin in donor cells in an attempt to improve their reprogrammability. Adult fibroblast cells treated with 1.25 or 5 μM TSA had elevated histone H3 acetylation compared to untreated controls. Cells treated with 0.3 μM 5-aza-dC had decreased methylation compared to untreated controls. Both drugs at 0.08 μM caused morphological changes of the donor cells. Development to blastocysts by embryos cloned from donor cells after 0.08 or 0.3 μM 5-aza-dC treatments was lower than in embryos cloned from untreated control cells (9.7% and 4.2%, respectively, vs. 25.1%), whereas 0.08 μM TSA treatment of donor cells increased blastocyst development compared to controls (35.1% vs. 25.1%). These results indicate that partial erasure of preexisting epigenetic marks of donor cells improves subsequent in vitro development of cloned embryos.
Meta-analysis of non-statistically significant unreported effects

Published studies in Medicine (and virtually any other discipline) sometimes report that a difference or correlation did not reach statistical significance but do not report its effect size or any statistic from which the latter may be derived. Unfortunately, meta-analysts should not exclude these studies because their exclusion would bias the meta-analytic outcome, but also they cannot be included as null effect sizes because this strategy is also associated to bias. To overcome this problem, we have developed MetaNSUE, a novel method based on multiple imputations of the censored information. We also provide an R package and an easy-to-use Graphical User Interface for non-R meta-analysts.
Protein phosphorylation and kinome profiling reveal altered regulation of multiple signaling pathways in B lymphocytes from patients with systemic lupus erythematosus.

OBJECTIVE The cause of B lymphocyte hyperactivity and autoantibody production in systemic lupus erythematosus (SLE) remains unclear. Previously, we identified abnormalities in the level and translocation of signaling molecules in B cells in SLE patients. The present study was undertaken to examine the extent of signaling abnormalities that relate to altered B cell responses in SLE. METHODS B lymphocytes from 88 SLE patients and 72 healthy controls were isolated from blood by negative selection. Protein tyrosine phosphorylation and cellular kinase levels were analyzed by Western blotting, flow cytometry, and a kinome array protocol. Changes in protein phosphorylation were determined in ex vivo B cells and following B cell receptor engagement. RESULTS Differences in tyrosine phosphorylation in B cells from patients with SLE, compared with matched controls, were demonstrated. Further, the kinome array analysis identified changes in the activation of key kinases, i.e., the activity of phosphatidylinositol 3-kinase, which regulates survival and differentiation, was up-regulated and the activity of Rac and Rho kinases, which regulate the cytoskeleton and migration, was increased. In contrast, the activity of ATR, which regulates the cell cycle, was down-regulated in SLE patients compared with controls. Differences in signaling pathways were seen in all SLE B lymphocyte subsets that manifested phenotypic features of immature, mature, and memory cells. CONCLUSION This study revealed dysregulation in multiple signaling pathways that control key responses in B cells of SLE patients. Data generated in this study provide a molecular basis for further analysis of the altered B lymphocyte responses in SLE.
Cost-Sensitive Feature Selection by Optimizing F-Measures

Feature selection is beneficial for improving the performance of general machine learning tasks by extracting an informative subset from the high-dimensional features. Conventional feature selection methods usually ignore the class imbalance problem, thus the selected features will be biased towards the majority class. Considering that F-measure is a more reasonable performance measure than accuracy for imbalanced data, this paper presents an effective feature selection algorithm that explores the class imbalance issue by optimizing F-measures. Since F-measure optimization can be decomposed into a series of cost-sensitive classification problems, we investigate the cost-sensitive feature selection by generating and assigning different costs to each class with rigorous theory guidance. After solving a series of cost-sensitive feature selection problems, features corresponding to the best F-measure will be selected. In this way, the selected features will fully represent the properties of all classes. Experimental results on popular benchmarks and challenging real-world data sets demonstrate the significance of cost-sensitive feature selection for the imbalanced data setting and validate the effectiveness of the proposed method.
Local analysis of inverse problems: Hölder stability and iterative reconstruction

We consider a class of inverse problems defined by a nonlinear mapping from parameter or model functions to the data, where the inverse mapping is Hölder continuous with respect to appropriate Banach spaces. We analyze a nonlinear Landweber iteration and prove local convergence and convergence rates with respect to an appropriate distance measure. Opposed to the standard analysis of the nonlinear Landweber iteration, we do not assume source and nonlinearity conditions, but this analysis is based solely on the Hölder continuity of the inverse mapping.
The Relationship between Public Libraries and Google: Too much Information

This article explores the implications of a shift from public to private provision of information through focusing on the relationship between Google and public libraries. This relationship has sparked controversy, with concerns expressed about the integrity of search results, the Google Book project, and Google the company. In this paper, these concerns are treated as symptoms of a deeper divide, the fundamentally different conceptions of information that underpin the stated aim of Google and libraries to provide access to information. The paper concludes with some principles necessary for the survival of public libraries and their contribution to a robust democracy in a rapidly expanding Googleverse.
Field Demonstration of the Activated Iron Technology for Removing Heavy Metals from Flue-Gas-Desulfurization Wastewater

The Activated Iron Process (AIP) technology, which is renamed from the hybrid zero-valent-iron (hZVI) process, is a novel chemical treatment process that has shown great potential in previous laboratory and field bench-scale tests for removing selenium, mercury, and nutrients from the flue-gas-desulfurization wastewater. In this study, a pilot-scale demonstration was conducted to continuously treat 3.8-7.6 L/min (1-2 gpm) of the FGD wastewater at a coal-fired power plant for five months. Results show that the AIP process could simultaneously reduce selenate-Se from 1-3 mg/L to below 10 μg/L and mercury from over 100 μg/L to below 10 ng/L, in compliance with new stringent effluent discharge limits planned by the USEPA for Se and Hg. Moreover, the process efficiently removed a broad spectrum of heavy metals such as As(III), As(V), Cr(VI), Cd(II), Pb(II) and Cu(II) from ppm level to near or sub-ppb level. A 3-stage AIP reactor with a combined hydraulic retention time of 8-12 h was sufficient for Se treatment and a single stage for Hg and other heavy metals. The process had a competitive economics and consumed ~0.3 kg ZVI per 1 m FGD wastewater treated at a cost of about $0.6/m. Solid waste production and energy consumption were reasonably low. The AIP process is scalable. The successful pilot study demonstrates that the AIP technology can be a reliable, low-cost, high-performance treatment platform with numerous application potentials, particularly, for solving some of the toughest heavy metal water problems
Persistent Pelagic Habitats in the Baja California to Bering Sea (B2B) Ecoregion

The Baja California to Bering Sea (B2B) Marine Conservation Initiative seeks to establish a network of Marine Protected Areas within the Exclusive Economic Zones of the NAFTA countries- Canada, Mexico, and the United States. This network is designed to capture ecologically significant habitat for marine species of common conservation con- cern and pelagic regions of high productivity, with due consideration for the inter-annual sea surface temperature fluc- tuations of the El Nino Southern Oscillation (ENSO). Here, we present analytical methods that define pelagic habitat based upon the density of steep temperature gradients, or fronts, and we quantify their spatial and temporal persist- ence over a single ENSO cycle (1996-1999) to benefit marine conservation and marine management strategies. We find that less than 1% of the Northeast Pacific ocean exhibits a persistent ( > 8 mo/yr) concentration of tem- perature fronts (> .2km/km 2 ) within and between years. The Baja California Frontal System (BCFS) is the largest con- centration found within the multinational federal waters, between 0 and 300 km east of Baja California Sur. The BCFS appears more active under La Nina conditions, while the next largest persistent concentration, North Pacific Transition Zone, appears more active under El Nino conditions. We demonstrate habitat functions associated with the BCFS for blue whales (Balaenoptera musculus), swordfish (Xiphias gladius), and striped marlin (Tetrapturus audax). We recommend management and protection for this pelagic "hotspot" to the Mexican government and the tri-national Commission for Environmental Cooperation.
Knowledge of Meaning: An Introduction to Semantic Theory

Current textbooks in formal semantics are all versions of, or introductions to, the same paradigm in semantic theory: Montague Grammar. Knowledge of Meaning is based on different assumptions and a different history. It provides the only introduction to truth- theoretic semantics for natural languages, fully integrating semantic theory into the modern Chomskyan program in linguistic theory and connecting linguistic semantics to research elsewhere in cognitive psychology and philosophy. As such, it better fits into a modern graduate or undergraduate program in linguistics, cognitive science, or philosophy. Furthermore, since the technical tools it employs are much simpler to teach and to master, Knowledge of Meaning can be taught by someone who is not primarily a semanticist. Linguistic semantics cannot be studied as a stand-alone subject but only as part of cognitive psychology, the authors assert. It is the study of a particular human cognitive competence governing the meanings of words and phrases. Larson and Segal argue that speakers have unconscious knowledge of the semantic rules of their language, and they present concrete, empirically motivated proposals about a formal theory of this competence based on the work of Alfred Tarski and Donald Davidson. The theory is extended to a wide range of constructions occurring in natural language, including predicates, proper nouns, pronouns and demonstratives, quantifiers, definite descriptions, anaphoric expressions, clausal complements, and adverbs. Knowledge of Meaning gives equal weight to philosophical, empirical, and formal discussions. It addresses not only the empirical issues of linguistic semantics but also its fundamental conceptual questions, including the relation of truth to meaning and the methodology of semantic theorizing. Numerous exercises are included in the book.
Comparative analysis of MPPT techniques for a photovoltaic system in cundinamarca

The simulation and discussion of five MPPT techniques for a PV system under various conditions of uniform and partial shading conditions (PSC) is presented. The techniques considered are hill climbing (HC), fuzzy logic control (FLC), perturbed extremum seeking control (PESC), firefly algorithm (FA), and cuckoo search algorithm (CS). Based on models previously stated in the literature, and inspired in a photovoltaic (PV) system in Cundinamarca, a comparative analysis is done based on the efficiency which measures performance in steady state, and the integral absolute error (IAE), which facilitate the analysis in both transient and steady state. Under uniform shading conditions fuzzy logic performs better than the other techniques under both mentioned criteria, followed by CS which shows a high efficiency but a slower convergence time. Also, PESC has shown a good performance, while being less complex than FLC. Under partial shading conditions cuckoo search demonstrates better performance in efficiency and convergence time than the firefly algorithm.
Physiological responses to high-speed, open-wheel racecar driving.

UNLABELLED High-speed auto racing has been demonstrated to produce accelerated heart rate (HR) during competition. However, it has not been determined whether the increase in HR was due to physical work efforts or a result of emotional stress. PURPOSE The purpose of this investigation was to examine the physiological responses associated with open-wheel automobile driving at competitive speeds. METHODS Oxygen consumption and HR were assessed in seven professional automobile racing drivers during two incrementally paced driving sessions. A portable metabolic analyzer and EKG were directly attached to the subjects as they participated in driving tests on an oval speedway and a roadway course. Maximal physiological responses of the subjects were also determined during a graded treadmill test. RESULTS During treadmill testing, maximal oxygen consumption (VO2max) ranged from of 42.0 to 59.7 mL x kg(-1) x min(-1) (mean +/- SD = 47.6+/-8.1). The road course and oval speedway testing at competitive speeds elicited mean VO2 values of 38.5 and 21.9 mL x kg(-1) x min(-1), respectively, which correspond to 79% and 45% of VO2max. Road course driving produced mean HR values of 152 beats x min(-1) with 142 beats x min(-1) recorded when driving at competitive speed on the speedway course. CONCLUSIONS Professional open-wheel race drivers possess cardiorespiratory capacity similar to athletes participating in sports such as basketball, football, and baseball. The VO2 and HR responses to road course driving were similar to those previously reported in traditional sports settings. The findings of this study suggest that professional open-wheel racing drivers should be regarded as athletes that encounter significant physiological stresses. (2)
Predictors for a positive blood culture in African children with pneumonia.

BACKGROUND Blood culture isolation rates for children with pneumonia are generally low. Therefore it would be helpful if epidemiologic studies could identify children who have a higher than average chance of yielding a positive culture. METHODS Simple clinical and laboratory predictors of a positive blood culture were investigated in 1222 children younger than 5 years of age with pneumonia who presented at rural dispensaries in The Gambia, West Africa. RESULTS A high temperature (chi square for linear trend, 24.1; P < 0.0001), a rapid respiratory rate (chi square for linear trend, 6.33; P = 0.010), dehydration (odds ratio, 2.33; P < 0.001), nasal flaring (odds ratio, 2.06; P = 0.001), grunting (odds ratio, 4.01; P < 0.001), dullness to percussion (odds ratio, 2.31; P < 0.001), bronchial breathing (odds ratio, 2.61; P < 0.001) and diminished breath sounds (odds ratio, 2.07; P < 0.001) were positive predictors for a positive blood culture. Wheezing (odds ratio, 0.16; P < 0.001) and malaria parasitemia (odds ratio, 0.26; P = 0.008) were negative predictors. A combination of these findings were used to assess how the number of cultures taken might be reduced without substantially reducing the yield of positive cultures. For example it was found that exclusion of children with a temperature of < 38.0 degrees C and/or a respiratory rate of < 50/min and/or wheezing would have reduced the number of cultures taken by 55.6% but would have led to a loss of only 31.3% of positive cultures. CONCLUSION Careful selection of children investigated by blood culture could help to reduce the work required during the preparations for and conduct of pneumococcal vaccine trials.
Oral mucosal lesions and temporomandibular joint impairment of elderly people in the South East Local Government Area of Ibadan.

OBJECTIVE To determine the prevalence of oral mucosal lesions, temporomandibular joint (TMJ) impairment and oral health-related habits in the elderly people in South East Local Government Area (SELGA) in Ibadan. BACKGROUND DATA SELGA is one of the largest local government areas in Oyo State, Nigeria and has a population of 225,800. DESIGN A cross-sectional survey. METHODOLOGY A randomly selected sample of 690 elderly people from 23 wards in SELGA were examined by two trained and calibrated examiners using mirror, probe and natural light. RESULTS One hundred and fifty-five (22.46%) of the elderly examined had one or more oral pathology lesions, representing infection-related swelling, non-infection-related swelling, pre-malignant lesions, denture stomatitis, non-denture based ulcers, angular cheilitis, geographic tongue, scrotal tongue, lichen planus, hyper-pigmentation and TMJ impairment. Fifty-five (35.5%) of these pathologies were infection-related swellings. Six (3.9%) of the pathologies were denture-related stomatitis, 14(9.03%) were pre-malignant lesions, 14(9.03%) were non-infection-related swelling, while 27 (17.4%) were TMJ impairment. The rest of the lesions constituted the remaining 25.1%. Only 15.9% of the participants had tobacco-related habits, 10.7% drank alcohol, whilst 41.6% chewed kola nuts. CONCLUSION Oral pathoses prevalence (22.46%) was similar to findings in developed countries (29.9%) but with a reversal of causal factors, infection-related swellings were more common, whereas pre-malignant lesions were less common. The infections were mostly complications from periodontal disease, which culminated in abscess formation. Tobacco-related habits were not highly prevalent among the elderly people in SELGA. However, oral pathoses resulting from nutritional deficiencies were the third most frequent lesions observed.
NOTCH1 Mutations in T-Cell Acute Lymphoblastic Leukemia: Prognostic Significance and Implication in Multifactorial Leukemogenesis

Purpose: NOTCH signaling pathway is essential in T-cell development and NOTCH1 mutations are frequently present in T-cell acute lymphoblastic leukemia (T-ALL). To gain insight into its clinical significance, NOTCH1 mutation was investigated in 77 patients with T-ALL. Experimental Design: Detection of NOTCH1 mutation was done using reverse transcription-PCR amplification and direct sequencing, and thereby compared according to the clinical/biological data of the patients. Results: Thirty-two mutations were identified in 29 patients (with dual mutations in 3 cases), involving not only the heterodimerization and proline/glutamic acid/serine/threonine domains as previously reported but also the transcription activation and ankyrin repeat domains revealed for the first time. These mutations were significantly associated with elevated WBC count at diagnosis and independently linked to short survival time. Interestingly, the statistically significant difference of survival according to NOTCH1 mutations was only observed in adult patients (>18 years) but not in pediatric patients (≤18 years), possibly due to the relatively good overall response of childhood T-ALL to the current chemotherapy. NOTCH1 mutations could coexist with HOX11, HOX11L2, or SIL-TAL1 expression. The negative effect of NOTCH1 mutation on prognosis was potentiated by HOX11L2 but was attenuated by HOX11. Conclusion:NOTCH1 mutation is an important prognostic marker in T-ALL and its predictive value could be even further increased if coevaluated with other T-cell-related regulatory genes. NOTCH pathway thus acts combinatorially with oncogenic transcriptional factors on T-ALL pathogenesis.
Probabilistic causation, preemption and counterfactuals

Counterfactual theories of Causation have had problems with cases of probabilistic causation and preemption. I put forward a counterfactual theory that seems to deal with these problematic cases and also has the virtue of providing an account of the alleged asymmetry between hasteners and delayers: the former usually being counted as causes, the latter not. I go on to consider a new type of problem case that has not received so much attention in the literature, those I dub catalysts and anti-catalysts, and show how my account needs to be adjusted to deliver the right verdicts in these cases. The net result is a particular conception of a cause that I try to spell out in the closing section of the paper. In that section, I also briefly discuss causal asymmetry and the purpose behind providing a counterfactual theory of causation.
Évaluation et rééducation de la mémoire de travail après chirurgie éveillée de gliomes infiltrants

Les gliomes de bas grade et les differentes therapeutiques qu’impose leur traitement sont source de troubles cognitifs divers, que seules des investigations orthophoniques et neuropsychologiques poussees permettent d’objectiver. La memoire de travail, notamment, est une fonction dont le deficit est souvent decrit chez les patients operes en eveille de gliomes infiltrants. Partant du constat que les pratiques d’evaluation et de reeducation sont tres heterogenes, nous avons decide de tester des epreuves d’evaluation de la memoire de travail et un materiel de reeducation cognitive specifique. Les outils d’evaluation choisis, en reference au modele de Baddeley, ont ete testes sur 10 patients dont les resultats ont ete compares a une population appariee de 19 sujets-controles. L’efficacite de ce type de reeducation pour cette population a fait l’objet d’une etude preliminaire de petit groupe (6 patients) en methodologie a deux bras en simple aveugle. Les resultats indiquent que les outils d’evaluation objectivent bien des troubles de la memoire de travail, et que certaines epreuves sont sensibles a cette population. Le protocole de reeducation revele son efficacite.
Supporting Agent-Oriented Modelling with UML

Software engineering relies on the possibility of describing a system at different levels of abstraction. Agent-oriented software engineering introduces a new level of abstraction, that we called agent level, to allow the architect modelling a system in terms of interacting agents. This level of abstraction is not supported by an accepted set of tools and notations yet, even if a number of proposals are available. This paper introduces: (i) An UML-based notation capable of modelling a system at the agent level and (ii) A development framework, called ParADE, exploiting such a notation. The notation we propose is formalized in terms of a UML profile and it supports the realisation of artefacts modelling two basic concepts of the agent level, i.e., the architecture of the multi-agent system and the ontology followed by agents. The choice of formalising our notation in terms of a UML profile allows using it with any off-the-shelf CASE tool. The ParADE framework takes advantage of this choice by providing a code generator capable of producing skeletons of FIPA-compliant agents from XMI files of agent-oriented models. The developer is requested to complete the generated skeletons exploiting the services that ParADE and the underlying agent platform provide.