Miracle-dz/UniFAR-FTUs huggingface dataset:
Lung tumour induction in mice after X-rays and neutrons.

Dose-response curves were determined for pulmonary adenomas and adenocarcinomas in mice after single acute doses of 200 kVp X-rays and cyclotron neutrons (E = 7.5 MeV). A serial-killing experiment established that the radiation induces the tumours and does not merely accelerate the appearance of spontanoeus cancers [corrected]. The dose versus incidence (I) of tumours in male and female mice for X-ray doses between 0.25 and 7.5 Gy is 'bell-shaped' and best fitted with a purely quadratic induction and exponential inactivation terms, i.e. I = A + BD2e-alpha D. In contrast, the tumour dose-response after 0.1-4.0 Gy of neutrons is best fitted by I = A + BDe-alpha D and is steeply linear less than or equal to 1 Gy, peaks between 1 and 3 Gy and sharply declines at 4.0 Gy. The data for the female mice less than or equal to 1 Gy neutrons are best fitted to the square root of the dose. A major objective of the experiments was to derive neutron RBE values. Because of the differences between the X-ray (quadratic) and neutron (linear) curves, the RBEn will vary inversely with decreasing X-ray dose. The RBE values at 1 Gy of X-rays derived from the B coefficients in the above equations are 7.4 +/- 3.2 (male and female); 8.6 +/- 3.6 (female) and 4.7 +/- 1.8 (male). These are high values and imply even higher values at the doses of interest to radiation protection. If, however, one restricts the analysis to the initial, induction side of the response (less than or equal to 1 Gy neutrons, less than or equal to 3 Gy X-rays) then good linear fits are obtainable for both radiations and indicate neutron RBE values of 7.4 +/- 2.3 for female mice and 4.5 +/- 1.8 for males, and these are independent of dose level.
Chromosome 17/17q gain and unaltered profiles in high resolution array‐CGH are prognostically informative in neuroblastoma

The prognostic relevance of chromosome 17 gain in neuroblastoma is still discussed. This investigation specifies the frequency, type, size, and transcriptional relevance in a large patient cohort. Primary tumor material of 202 patients was analyzed using high‐resolution oligonucleotide array‐based comparative genomic hybridization (aCGH) and correlated with clinical and survival data. A subset (n = 145) was correlated for differentially expressed genes (DEG) by microarray analysis. Chromosome 17 aCGH analysis showed numerical gain in 94/202 patients (47%), partial gain in 93/202 patients (46%), and no gain in 15/202 patients (7%). The frequency of partial gain was higher in stage 4 neuroblastoma (stage 1 15%; stage 2 12%; stage 3 16%; stage 4S 7%; and stage 4 50%). Overall survival (OS) was superior in patients with numerical gain compared with patients with partial gain or no gain (5‐y‐OS: 0.95 ± 0.02 vs. 0.63 ± 0.05 vs. 0.60 ± 0.13; P < 0.001). Gene expression analysis demonstrated 95/130 DEGs between tumors with numerical or partial chromosome/no gain. Only one DEG (CCKBR) was detected comparing tumors with partial gain and those with no gain. In patients with partial gain, the distribution of breakpoints did not correlate with stage and 11q status, but with MYCN amplification and 1p status. The “best” breakpoints in cases with partial 17q gain were at 42.5 Mb for event‐free and 26.6 Mb for OS. Numerical gain of chromosome 17 is associated with a better prognosis than partial and no gain. The group of tumors with partial gain was similar to the group without gain with respect to stage distribution, outcome, and gene expression profile. © 2014 Wiley Periodicals, Inc.
Inactivation of the p15 gene in children with acute lymphoblastic leukemia.

CONTEXT Tumor suppressor genes act on the control of cell cycle progression. In pediatric neoplasias, some of these genes may be considered to be markers for diagnosis or relapse, thus probably representing prognostic indicators. OBJECTIVE To study the inactivation of the p15 gene in children with acute lymphoblastic leukemia. TYPE OF STUDY Retrospective study. SETTING Laboratory of Molecular Biology, Department of Pediatrics, Faculdade de Medicina de Ribeiráo Preto, Universidade de São Paulo. PARTICIPANTS Eighty-three children and adolescents with acute lymphoblastic leukemia were studied, with the examination of 83 bone marrow samples obtained at diagnosis, four obtained also during relapse, and two cerebrospinal fluid samples obtained from two cases of isolated relapse in the central nervous system. MAIN MEASUREMENTS Homologous deletion of the p15 gene by multiplex polymerase chain reaction, and screening for point mutations by polymerase chain reaction/single-strand conformational polymorphism. RESULTS Deletion of exon 2 of the p15 gene was observed in 15 children, including one case in which deletion was only verified during isolated central nervous system relapse. No case of exon 1 deletion, or that was suggestive of point mutations, was observed and no association between p15 gene inactivation and classic risk factors was established. CONCLUSION According to the literature, inactivation of the p15 gene by deletion of exon 2 in acute lymphoblastic leukemia found in the population studied would be considered to be a molecular marker for diagnosis or relapse. However, no correlation between p15 gene deletion and clinical prognostic indicators was observed.
Osteopontin Expression in Cardiomyocytes Induces Dilated Cardiomyopathy

Background—Inflammatory processes play a critical role in myocarditis, dilated cardiomyopathy, and heart failure. The expression of the inflammatory chemokine osteopontin (OPN) is dramatically increased in cardiomyocytes and inflammatory cells during myocarditis and heart failure in human and animals. However, its role in the development of heart diseases is not known. Methods and Results—To understand whether OPN is involved in cardiomyopathies, we generated a transgenic mouse (MHC-OPN) that specifically overexpresses OPN in cardiomyocytes with cardiac-specific promoter-directed OPN expression. Young MHC-OPN mice were phenotypically indistinguishable from their control littermates, but most of them died prematurely with a half-life of 12 weeks of age. Electrocardiography revealed conduction defects. Echocardiography showed left ventricular dilation and systolic dysfunction. Histological analysis revealed cardiomyocyte loss, severe fibrosis, and inflammatory cell infiltration. Most of these inflammatory cells were activated T cells with Th1 polarization and cytotoxic activity. Autoantibodies against OPN, cardiac myosin, or troponin I, were not found in the serum of MHC-OPN mice. Conclusions—These data show that OPN expression in the heart induces in vivo T-cell recruitment and activation leading to chronic myocarditis, the consequence of which is myocyte destruction and hence, dilated cardiomyopathy. Thus, OPN might therefore constitute a potential therapeutic target to limit heart failure.
Mammalian oocyte maturation.

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Mammalian oocyte maturation C. Thibault, D. Szöllösi, Micheline Gérard
Human Rhinovirus 2 Induces the Autophagic Pathway and Replicates More Efficiently in Autophagic Cells

ABSTRACT Picornaviruses rearrange cellular membranes to form cytosolic replication sites. In the case of poliovirus and several other picornaviruses, these membranes are derived from subversion of the cellular autophagy pathway. We also reported observation of autophagosome-like structures during infection by two human rhinoviruses (HRVs), HRV-2 and HRV-14 (W. T. Jackson et al., PLoS Biol. 3:e156, 2005). Another group reported that HRV-2 does not induce autophagosomes or respond to changes in cellular autophagy (M. Brabec-Zaruba, U. Berka, D. Blaas, and R. Fuchs, J. Virol. 81:10815-10817, 2007). In this study, we tested HRV-2-infected cells for activation of autophagic signaling and changes in virus growth in response to changes in autophagy levels. Our data indicate that HRV-2 induces and subverts the autophagic machinery to promote its own replication.
Bringing Computational Models of Word Naming Down to the Item Level

Early noncomputational models of word recognition have typically attempted to account for effects of categorical factors such as word frequency (high vs low) and spelling-to-sound regularity (regular vs irregular) More recent computational models that adhere to general connectionist principles hold the promise of being sensitive to underlying item differences that are only approximated by these categorical factors In contrast to earlier models, these connectionist models provide predictions of performance for individual items In the present study, we used the item-level estimates from two connectionist models (Plaut, McClelland, Seidenberg, & Patterson, 1996, Seidenberg & McClelland, 1989) to predict naming latencies on the individual items on which the models were trained The results indicate that the models capture, at best, slightly more variance than simple log frequency and substantially less than the combined predictive power of log frequency, neighborhood density, and orthographic length. The discussion focuses on the importance of examining the item-level performance of word-naming models and possible approaches that may improve the models' sensitivity to such item differences
Problems in using p-curve analysis and text-mining to detect rate of p-hacking and evidential value

Background. The p-curve is a plot of the distribution of p-values reported in a set of scientific studies. Comparisons between ranges of p-values have been used to evaluate fields of research in terms of the extent to which studies have genuine evidential value, and the extent to which they suffer from bias in the selection of variables and analyses for publication, p-hacking. Methods. p-hacking can take various forms. Here we used R code to simulate the use of ghost variables, where an experimenter gathers data on several dependent variables but reports only those with statistically significant effects. We also examined a text-mined dataset used by Head et al. (2015) and assessed its suitability for investigating p-hacking. Results. We show that when there is ghost p-hacking, the shape of the p-curve depends on whether dependent variables are intercorrelated. For uncorrelated variables, simulated p-hacked data do not give the “p-hacking bump” just below . 05 that is regarded as evidence of p-hacking, though there is a negative skew when simulated variables are inter-correlated. The way p-curves vary according to features of underlying data poses problems when automated text mining is used to detect p-values in heterogeneous sets of published papers. Conclusions. The absence of a bump in the p-curve is not indicative of lack of p-hacking. Furthermore, while studies with evidential value will usually generate a right-skewed p-curve, we cannot treat a right-skewed p-curve as an indicator of the extent of evidential value, unless we have a model specific to the type of p-values entered into the analysis. We conclude that it is not feasible to use the p-curve to estimate the extent of p-hacking and evidential value unless there is considerable control over the type of data entered into the analysis. In particular, p-hacking with ghost variables is likely to be missed.
EMF Profiles: A Lightweight Extension Approach for EMF Models

Domain-Specific Modeling Languages (DSMLs) are getting more and more attention as a key element of Model Driven Engineering. As any other software artifact, DSMLs should continuously evolve to adapt to the changing needs of the domain they represent. Unfortunately, right now evolution of DSMLs is a costly process that requires changing the DSML metamodel and re-creating the complete modeling environment. In this paper we advocate for the use of EMF Profiles, an adaptation of the UML Profile concept to DSMLs. Profiles have been a key enabler for the success of UML by providing a lightweight language-inherent extension mechanism which is expressive enough to cover an important subset of extension scenarios. We believe a similar concept for DSMLs would provide a valuable extension mechanism which has been so far neglected by current metamodeling tools. Apart from direct metamodel profiles, we also propose reusable profile definition mechanisms whereby profiles are defined independently of any DSML and, later on, coupled with all DSMLs that can benefit from these profiles. Our approach has been implemented in a prototype integrated in the EMF environment.
The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion

The amphipod crustacean Parhyale hawaiensis is a blossoming model system for studies of developmental mechanisms and more recently regeneration. We have sequenced the genome allowing annotation of all key signaling pathways, transcription factors, and non-coding RNAs that will enhance ongoing functional studies. Parhyale is a member of the Malacostraca clade, which includes crustacean food crop species. We analysed the immunity related genes of Parhyale as an important comparative system for these species, where immunity related aquaculture problems have increased as farming has intensified. We also find that Parhyale and other species within Multicrustacea contain the enzyme sets necessary to perform lignocellulose digestion (“wood eating”), suggesting this ability may predate the diversification of this lineage. Our data provide an essential resource for further development of Parhyale as an experimental model. The first malacostracan genome will underpin ongoing comparative work in food crop species and research investigating lignocellulose as an energy source.
Hypothyroidism and renal function in patients with systolic heart failure.

The extent to which hypothyroidism affects renal function in patients with heart failure remains incompletely explored, despite the known adverse prognostic implications of renal dysfunction in these patients.In a pilot retrospective study, we evaluated 75 patients (age, >or=18 yr) with left ventricular ejection fractions <0.40. Forty-five patients had normal thyroid function (thyroid-stimulating hormone [TSH], 0.35-5.5 micro IU/mL) and 30 had hypothyroidism. The group with hypothyroidism was subdivided into 17 patients who had controlled hypothyroidism (TSH, 0.35-5.5 micro IU/mL) and 13 who had uncontrolled hypothyroidism (TSH, >5.5 micro IU/mL). Renal function, measured in terms of glomerular filtration rate, was analyzed once in each patient, and the populations were statistically compared, with P <0.05 conferring statistical significance.Baseline characteristics in all groups were similar. Mean glomerular filtration rate was better in patients with normal thyroid function than those with hypothyroidism (75.45 +/- 31.48 vs 63.95 +/- 21.43 mL/min/1.73 m2; P=0.032). There was no significant difference between patients with controlled hypothyroidism (66.89 +/- 24.18 mL/min/1.73 m2) and those with normal thyroid function (P=0.131). In patients with uncontrolled hypothyroidism, mean glomerular filtration rate (60.2 +/- 17.4 mL/min/1.73 m2) was significantly worse than in patients with normal thyroid function (P=0.015). We found that heart-failure patients with insufficiently treated hypothyroidism have worse renal function than do patients whose thyroid function is normal or whose hypothyroidism is effectively treated. Larger studies will be needed in order to evaluate this conclusion further. We recommend that hypothyroidism in heart-failure patients be strictly controlled, lest it affect prognosis adversely.
Detecting activities of daily living in first-person camera views

We present a novel dataset and novel algorithms for the problem of detecting activities of daily living (ADL) in firstperson camera views. We have collected a dataset of 1 million frames of dozens of people performing unscripted, everyday activities. The dataset is annotated with activities, object tracks, hand positions, and interaction events. ADLs differ from typical actions in that they can involve long-scale temporal structure (making tea can take a few minutes) and complex object interactions (a fridge looks different when its door is open). We develop novel representations including (1) temporal pyramids, which generalize the well-known spatial pyramid to approximate temporal correspondence when scoring a model and (2) composite object models that exploit the fact that objects look different when being interacted with. We perform an extensive empirical evaluation and demonstrate that our novel representations produce a two-fold improvement over traditional approaches. Our analysis suggests that real-world ADL recognition is “all about the objects,” and in particular, “all about the objects being interacted with. ”
Evaluation of Intracellular Labeling with Micron-Sized Particles of Iron Oxide (MPIOs) as a General Tool for In Vitro and in Vivo Tracking of Human Stem and Progenitor Cells

Magnetic resonance imaging (MRI)-based tracking is increasingly attracting attention as a means of better understanding stem cell dynamics in vivo. Intracellular labeling with micrometer-sized particles of iron oxide (MPIOs) provides a practical MRI-based approach due to superior detectability relative to smaller iron oxide particles. However, insufficient information is available about the general utility across cell types and the effects on cell vitality of MPIO labeling of human stem cells. We labeled six human cell types from different sources: mesenchymal stem cells derived from bone marrow (MSCs), mesenchymal stem cells derived from adipose tissue (ASCs), presumptive adult neural stem cells (ad-NSCs), fetal neural progenitor cells (f-NPCs), a glioma cell line (U87), and glioblastoma tumor stem cells (GSCs), with two different sizes of MPIOs (0.9 and 2.84 μm). Labeling and uptake efficiencies were highly variable among cell types. Several parameters of general cell function were tested in vitro. Only minor differences were found between labeled and unlabeled cells with respect to proliferation rate, mitotic duration, random motility, and capacity for differentiation to specific phenotypes. In vivo behavior was tested in chicken embryos and severe combined immunodeficient (SCID) mice. Postmortem histology showed that labeled cells survived and could integrate into various tissues. MRI-based tracking over several weeks in the SCID mice showed that labeled GSCs and f-NPCs injected into the brain exhibited translocations similar to those seen for unlabeled cells and as expected from migratory behavior described in previous studies. The results support MPIO-based cell tracking as a generally useful tool for studies of human stem cell dynamics in vivo.
Opportunities&Challenges In Automatic Speech Recognition

Automatic speech recognition enables a wide range of current and emerging applications such as automatic transcription, multimedia content analysis, and natural human-computer interfaces. This paper provides a glimpse of the opportunities and challenges that parallelism provides for automatic speech recognition and related application research from the point of view of speech researchers. The increasing parallelism in computing platforms opens three major possibilities for speech recognition systems: improving recognition accuracy in non-ideal, everyday noisy environments; increasing recognition throughput in batch processing of speech data; and reducing recognition latency in realtime usage scenarios. This paper describes technical challenges, approaches taken, and possible directions for future research to guide the design of efficient parallel software and hardware infrastructures.
Molecular cloning and functional analysis of the geneencoding geranylgeranyl diphosphate synthase fromJatropha curcas

Geranylgeranyl diphosphate (GGPP) synthase (GGPPS, EC: 2.5.1.29) catalyzes the condensation of isopentenyl diphosphate (IPP) with allylic diphosphates to yield (all-E)-GGPP. GGPP is one of the key precursors in the biosynthesis of biologically significant isoprenoid compounds. Here we report for the first time the cloning of a full-length cDNA encoding GGPPS (Jc-GGPPS) from Jatropha curcas L. The full-length cDNA was 1414 base pair (bp), with an 1110-bp open reading frame (ORF) encoding a 370- amino-acids polypeptide. Bioinformatic analysis revealed that Jc-GGPPS is a member of the polyprenyltransferases with two highly conserved aspartate-rich motifs, and showed high homology to other plant GGPPSs. Phylogenetic tree analysis indicated that plant GGPPSs could be classified into two groups, angiosperm and gymnosperm, while Jc-GGPPS had closer relationship with angiosperm plant GGPPSs. Functional analysis of Jc-GGPPS in GGPPS-deficient mutant plasmid pAC-BETA (³ crtE) demonstrated that Jc-GGPPS mediated the biosynthesis of carotenoid and provided the general precursor for diterpenes biosynthesis
Tumor vascularity and hematogenous metastasis in experimental murine intraocular melanoma.

PURPOSE The purpose of this study is to test the hypothesis that primary tumor vascularity in a murine model of intraocular melanoma positively correlates with the development and hematogenous spread of metastasis. METHODS Forty 12-week-old C57BL6 mice were inoculated in either the anterior chamber (AC) or posterior compartment (PC) of 1 eye with 5 x 10(5) cells/microL of Queens tissue culture melanoma cells. The inoculated eye was enucleated at 2 weeks; the mice were sacrificed at 4 weeks postinoculation, and necropsies were performed. The enucleated eyes were examined for histologic and ultrastructural features, including relationship of tumor cells to tumor vascular channels, vascular pattern, and mean vascular density. RESULTS Melanoma grew and was confined to the eye in 12 of 20 AC eyes and 10 of 20 PC eyes. Histologic and electron microscopic examination showed tumor invasion into vascular channels. Five of 12 AC tumors (42%) and 8 of 10 PC tumors (80%) metastasized. All of the AC tumors, but none of the PC tumors, that distantly metastasized also metastasized to ipsilateral cervical lymph nodes (P = .00535). There was no statistically significant difference of vascular pattern between the melanomas that did and did not metastasize to lungs in the PC group (P = .24), although there was a significant difference in the AC group (P = .02). Tumors with high-grade vascular patterns were more likely to metastasize than tumors with low-grade vascular patterns in the AC group. The mean vascular density positively correlated with the presence and number of metastases in both groups (P = .0000 and P < .001, respectively). There was no statistically significant difference of vascular pattern and mean vascular density for AC versus PC melanoma (P = .97). CONCLUSIONS The rate of metastasis in this murine intraocular melanoma model positively correlates with primary tumor vascularity. The melanoma metastasizes via invasion of tumor vascular channels. AC melanoma also metastasizes through regional lymphatics.