Miracle-dz/UniFAR-FTUs huggingface dataset:
The epidemiology of anaphylaxis in Europe: a systematic review

Anaphylaxis is an acute, potentially fatal, multi‐organ system, allergic reaction caused by the release of chemical mediators from mast cells and basophils. Uncertainty exists around epidemiological measures of incidence and prevalence, risk factors, risk of recurrence, and death due to anaphylaxis. This systematic review aimed to (1) understand and describe the epidemiology of anaphylaxis and (2) describe how these characteristics vary by person, place, and time.
A Multinomial Hidden Markov Model and its training by a combined iterative procedure

The paper proposes a new extension of Hidden Markov Models HMM for communication systems by allowing the Markovian transitions between the channel's states to be influenced by some external “catalyzers” e.g. environmental or experimental conditions. The stochastic influence of the catalyzers is expressed by multinomial link functions. We introduce a combined iterative training procedure, with the Baum--Welch algorithm as a framework, including some nested algorithms such as the Newton--Raphson and the Expectation--Maximization EM algorithms. The monotony of the log-likelihood function associated with our procedure is proven. A simulation study is provided in order to prove the good performances of the proposed combined iterative training procedure. We consider that the Multinomial HMM will be an important and useful extension of HMM in bioinformatics and biostatistics, due to the possible applications in modeling the “hidden” ion channels whose states could be influenced by external factors.
Nasal and exhaled nitric oxide is reduced in adult patients with cystic fibrosis and does not correlate with cystic fibrosis genotype.

STUDY OBJECTIVES Inducible nitric oxide synthase (iNOS) is upregulated in a number of inflammatory lung conditions, and exhaled nitric oxide (NO) concentration is increased. However, previous studies in children with cystic fibrosis (CF) have shown that exhaled NO is reduced. The purpose of this investigation was to study exhaled NO concentration in adults with CF, and to investigate the effect of CF genotype and respiratory tract infection on this measurement. DESIGN Exhaled and nasal NO levels were measured in 54 adult CF subjects and 37 healthy nonsmoking age-matched subjects using a chemiluminesence analyzer. Spirometry (FEV(1) and FVC), CF genotype, and bacterial colonization were also recorded. SETTING This study was conducted at a national CF center. RESULTS The mean age of patients was 26.9 years, and the mean FEV(1) was 50.5% predicted (range, 17 to 104%). Nasal NO in the CF patients (mean, 520 parts per billion [ppb]; confidence interval [CI], 452 to 588) was significantly lower (p < 0.001) than in control subjects (987 ppb; CI, 959 to 1,015). Exhaled NO was significantly lower (p < 0. 001) in CF patients (5.0 ppb; CI, 4.1 to 6.1) than in control subjects (7.3 ppb; CI, 6.8 to 7.8). FEV(1) did not correlate with nasal or exhaled NO. No association was observed between genotype and NO values or colonization with Pseudomonas aeruginosa. CONCLUSIONS Despite the airway inflammation that is characteristic of CF, both nasal and exhaled NO were reduced. There was no association with genotype or infection status. As NO has bacteriostatic effects and may augment mucociliary clearance, this observation may be of clinical importance.
Optimizing Motion Estimation for H.264 Encoding

Around 90% of the total encoding time of raw video into H.264 is spent in block-matching, a stage of Motion Estimation. In this paper we combine two block-matching optimizations that yield significant performance improvements on Motion Estimation: 4:1 subsampling by macroblock and truncation of the two less significant bits per sample. When applied to the JM Reference Encoder, our strategy showed an average speedup of 2.64 times in total encoding time with a small loss of quality (less than 0.5 dB).
The Tomato FRUITFULL Homologs TDR4/FUL1 and MBP7/FUL2 Regulate Ethylene-Independent Aspects of Fruit Ripening[W]

Ripening of the tomato fruit is accompanied by an increase in ethylene production and involves color changes, altered sugar metabolism, tissue softening, and the synthesis of aroma volatiles. This study shows that the MADS domain transcription factors FUL1 and FUL2 play a role in the regulation of these ripening processes, but in an ethylene-independent manner. Tomato (Solanum lycopersicum) contains two close homologs of the Arabidopsis thaliana MADS domain transcription factor FRUITFULL (FUL), FUL1 (previously called TDR4) and FUL2 (previously MBP7). Both proteins interact with the ripening regulator RIPENING INHIBITOR (RIN) and are expressed during fruit ripening. To elucidate their function in tomato, we characterized single and double FUL1 and FUL2 knockdown lines. Whereas the single lines only showed very mild alterations in fruit pigmentation, the double silenced lines exhibited an orange-ripe fruit phenotype due to highly reduced lycopene levels, suggesting that FUL1 and FUL2 have a redundant function in fruit ripening. More detailed analyses of the phenotype, transcriptome, and metabolome of the fruits silenced for both FUL1 and FUL2 suggest that the genes are involved in cell wall modification, the production of cuticle components and volatiles, and glutamic acid (Glu) accumulation. Glu is responsible for the characteristic umami taste of the present-day cultivated tomato fruit. In contrast with previously identified ripening regulators, FUL1 and FUL2 do not regulate ethylene biosynthesis but influence ripening in an ethylene-independent manner. Our data combined with those of others suggest that FUL1/2 and TOMATO AGAMOUS-LIKE1 regulate different subsets of the known RIN targets, probably in a protein complex with the latter.
Factors Associated with Multiple Biomarkers of Systemic Inflammation

Background: While much is known about correlates of C-reactive protein (CRP), little is known about correlates of other inflammation biomarkers. As these measures are increasingly being used in epidemiologic studies, it is important to determine what factors affect inflammation biomarker concentrations. Methods: Using age, sex, and body mass index (BMI) adjusted linear regression, we examined 38 exposures (demographic and anthropometric measures, chronic disease history, NSAIDs, dietary factors, and supplement use) of 8 inflammation biomarkers [CRP, IL1β, IL6, IL8, TNFα, and soluble TNF receptors (sTNFR) in plasma; and prostaglandin E2 metabolite (PGE-M) in urine] in 217 adults, ages 50 to 76 years. Results: Increasing age was associated with higher concentrations of all biomarkers except IL1β. BMI was positively associated with CRP and sTNFR I and II. Saturated fat intake was associated with increased CRP, sTNFRII, TNFα, and IL1β, whereas eicosapentaenoic acid + docosahexaenoic acid (EPA+DHA) intake (diet or total) was associated with decreased CRP, TNFα, and IL1β. Results for sex were varied: CRP and IL6 were lower among men, whereas PGE-M and sTNFRI were higher. Higher CRP was also associated with smoking, hormone replacement therapy use, and γ-tocopherol intake; lower CRP with physical activity, and intakes of dietary vitamin C and total fiber. Conclusions: Although the associations varied by biomarker, the factors having the greatest number of significant associations (P ≤ 0.05) with the inflammation biomarkers were age, BMI, dietary saturated fat, and EPA+DHA omega-3 fatty acids. Impact: Our results suggest that potential confounders in epidemiologic studies assessing associations with inflammation biomarkers vary across specific biomarkers. Cancer Epidemiol Biomarkers Prev; 25(3); 521–31. ©2016 AACR.
Measuring the exposome: A powerful basis for evaluating environmental exposures and cancer risk

Advances in laboratory sciences offer much in the challenge to unravel the complex etiology of cancer and to therefore provide an evidence‐base for prevention. One area where improved measurements are particularly important to epidemiology is exposure assessment; this requirement has been highlighted through the concept of the exposome. In addition, the ability to observe genetic and epigenetic alterations in individuals exposed to putative risk factors also affords an opportunity to elucidate underlying mechanisms of carcinogenesis, which in turn may allow earlier detection and more refined molecular classification of disease. In this context the application of omics technologies to large population‐based studies and their associated biobanks raise exciting new avenues of research. This review considers the areas of genomics, transcriptomics, epigenomics and metabolomics and the evidence to date that people exposed to well‐defined factors (for example, tobacco, diet, occupational exposures, environmental pollutants) have specific omics profiles. Although in their early stages of development these approaches show promising evidence of distinct exposure‐derived biological effects and indicate molecular pathways that may be particularly relevant to the carcinogenic process subsequent to environmental and lifestyle exposures. Such an interdisciplinary approach is vital if the full benefits of advances in laboratory sciences and investments in large‐scale prospective cohort studies are to be realized in relation to cancer prevention. Environ. Mol. Mutagen. 54:480‐499, 2013. © 2013 Wiley Periodicals, Inc.
miR-29a modulates SCD expression and is regulated in response to a saturated fatty acid diet in juvenile genetically improved farmed tilapia (Oreochromis niloticus)

ABSTRACT MicroRNAs (miRNAs) are small non-coding RNAs that regulate target gene expression by binding to the 3′ untranslated region (3′ UTR) of the target mRNA. MiRNAs regulate a large variety of genes, including those involved in liver biology and disease. Here, we report for the first time that miR-29a post-transcriptionally regulates stearoyl-CoA desaturase (SCD) by binding to its 3′ UTR in genetically improved farmed tilapia (GIFT), Oreochromis niloticus, as shown by a 3′ UTR luciferase reporter assay. miR-29a antagomir treatment in vivo resulted in significant upregulation of SCD expression. We found that miR-29a expression was negatively correlated with SCD expression in GIFT liver. Inhibition of miR-29a led to a significant increase in SCD expression on day 60 induced by a saturated fatty acid diet, thereby increasing conversion of 16:0 and 18:0 to 16:1 and 18:1, respectively, and activating serum insulin, which would favor glucose and lipid uptake by the liver. These results indicate that miR-29a regulates SCD levels by binding to its 3′ UTR, and this interaction affects saturated fatty acid stress induction and insulin and lipid accumulation in serum. Our results suggest that miR-29a is critical in regulating lipid metabolism homeostasis in GIFT liver, and this might provide a basis for understanding the biological processes and therapeutic intervention encountered in fatty liver. Summary: miR-29a targets SCD 3′ UTR directly. Inhibition of miR-29a could mediate conversion of C16:0 and C18:0 to C16:1 and C18:1, respectively, and activate serum insulin and glucose uptake in GIFT by increasing SCD.
Lightweight Technologies for Knowledge Based Collaborative Applications

The paper describes ways to use collaborative technologies to support activities in knowledge based processes. It stresses the importance of matching the technology to the activity. It also defines that activities change to the process and the technology must coevolve with the processes by providing services that change as the process evolves. The paper defines the technologies needed at the different activities together with a platform to support these services and ways for the services to coevolve with the process. A prototype based on workspace technology showing such evolution is described.
A shared random effect parameter approach for longitudinal dementia data with non‐ignorable missing data

A significant source of missing data in longitudinal epidemiologic studies on elderly individuals is death. It is generally believed that these missing data by death are non‐ignorable to likelihood based inference. Inference based on data only from surviving participants in the study may lead to biased results. In this paper we model both the probability of disease and the probability of death using shared random effect parameters. We also propose to use the Laplace approximation for obtaining an approximate likelihood function so that high dimensional integration over the distributions of the random effect parameters is not necessary. Parameter estimates can be obtained by maximizing the approximate log‐likelihood function. Data from a longitudinal dementia study will be used to illustrate the approach. A small simulation is conducted to compare parameter estimates from the proposed method to the ‘naive’ method where missing data is considered at random. Copyright © 2004 John Wiley & Sons, Ltd.
Enterochromaffin Cell Hyperplasia in Irritable Pouch Syndrome

BACKGROUND:Irritable pouch syndrome (IPS) is a functional disease in patients with ileal pouch-anal anastomosis following colectomy for ulcerative colitis (UC). The pathophysiology of IPS is characterized by the presence of visceral hypersensitivity, similar to that seen in irritable bowel syndrome. However, the exact etiology and pathogenesis of IPS are not known. We hypothesized that serotonin-containing enteroendocrine cells or enterochromaffin (EC) cell hyperplasia and alterations in the mucosal immune cells may contribute to the patients' symptoms. The aim of the study was to assess EC cell hyperplasia and alterations in the mucosal immune cells in IPS.METHODS:The Pouchitis Disease Activity Index (PDAI) was used to quantify symptoms and mucosal inflammation in 36 patients with IPS and 25 patients with normal pouches. The histology and immunohistochemistry of pouch mucosal biopsies were assessed by a blinded gastrointestinal pathologist for intraepithelial lymphocytes (IEL), CD3+ T cells, CD25- (interleukin [IL]-2 receptor), tryptase- (mast cells), and serotonin-expressing cells. The numbers of IEL and immune-stained cells were compared between the two groups.RESULTS:Both groups were compatible demographically in terms of age, gender, duration of UC, stage, indication, and duration of the pouch surgery. There were no differences in the number of IEL, CD3+ T cells, CD25+ cells, and mast cells between the IPS and normal control groups. However, there were a significantly larger number of EC cells in the IPS group than that in the control group (54.8 ± 24.9 vs 36.7 ± 17.5 per 4 200× epithelial cells, P < 0.005). The number of EC cells appeared to be correlated with the symptom score (r = 0.276, P = 0.032). There were no significant correlations between the PDAI endoscopy and histology scores and the number of EC cells or between the PDAI scores and the number of IEL or other immune-stained cells.CONCLUSIONS:A greater number of EC cells were found in the IPS group than the normal pouch group, and the number of EC cells appeared to be correlated with the clinical symptoms of IPS. EC cell hyperplasia may be a contributing mechanism of visceral hypersensitivity and symptoms in IPS.
Colloquium: Physics of optical lattice clocks

Recently invented and demonstrated optical lattice clocks hold great promise for improving the precision of modern time keeping. These clocks aim at the 10{sup -18} fractional accuracy, which translates into a clock that would neither lose nor gain a fraction of a second over an estimated age of the Universe. In these clocks, millions of atoms are trapped and interrogated simultaneously, dramatically improving clock stability. Here the principles of operation of these clocks are discussed and, in particular, a novel concept of magic trapping of atoms in optical lattices. Recently proposed microwave lattice clocks are also highlights and several applications that employ the optical lattice clocks as a platform for precision measurements and quantum information processing.
Effect of repeated methylphenidate administration on presynaptic dopamine and behaviour in young adult rats

Methylphenidate, a dopamine reuptake inhibitor, is the most common treatment for attention-deficit hyperactivity disorder and may be prescribed for years, despite little evidence of any long-term benefit, nor knowledge of potential chronic side-effects. Therefore, this study examined the acute and longer-term behavioural effects and assessed striatal dopamine function following subchronic methylphenidate administration to adolescent rats. Male hooded Lister rats received methylphenidate (4 mg/kg i.p. twice daily for 4 days) or saline (1 ml/kg) and the acute locomotor and stereotype behaviour was monitored on days 1 and 4, novel object exploration on day 2 and, following 12 days drug withdrawal, the long-term effect examined on social interaction on day 16. Ex-vivo K+ (20 mM)- and methylphenidate (0.1 mM)-induced [3H]dopamine release from striatal slices and striatal monoamine content were measured on day 18. Compared with saline, methylphenidate induced mild hyperactivity without stereotypy but did not alter novel object exploration and, following withdrawal, had no long-term effect on social interaction. In striatal slices from controls, both K+ and methylphenidate elevated [3H]dopamine release (p < 0.01) while only combined treatment elevated release in methylphenidate pretreated rats, although striatal monoamine content was unaltered compared with control rats. In summary, a repeated dose of methylphenidate that had acute behavioural effects produced no long-term alteration in social interaction but attenuated presynaptic striatal dopamine function.
Sn-Equivariant Symmetry-Breaking bifurcations

I analyze generic symmetry-breaking bifurcations of SN-equivariant vector fields (where genericity is in the restricted space of SN-equivariant systems). The normal form for the Liapunov–Schmidt reduced bifurcation problem is derived, and its codimension 1 symmetry-breaking bifurcations are investigated. Branch equations are given along with the conditions for stability, and the parameter space is partitioned accordingly. Applications in complex systems theory are suggested in which the dynamics of SN-equivariant systems are used to model the emergent behavior of systems of multiple interacting agents.
Novel mutation in TP63 associated with ectrodactyly ectodermal dysplasia and clefting syndrome and T cell lymphopenia

A male child with clinical features consistent with EEC/EECUT plus syndrome (ectrodactyly, ectodermal dysplasia, clefting, urinary tract abnormalities, and thymic abnormalities) including mild ectodermal abnormalities, ectrodactyly of hands and feet, cleft palate, bilateral hydronephrosis, and T cell lymphopenia is reported. He was noted to have T cell receptor excision circle (TREC) analysis below the cutoff for normal on newborn screening and T cell lymphopenia on further immunologic evaluation. A novel, presumably pathogenic de novo 3 bp deletion in exon 7 of TP63 (c.970_972delATT; NCBI Reference Sequence NM_003722.4) was identified. This observation provides supporting evidence for the association between TP63 mutations and EECUT plus syndrome. Clinicians caring for infants presenting with EEC spectrum disorders in the newborn period should also consider the possibility of T cell lymphopenia. © 2013 Wiley Periodicals, Inc.
Comparison of the MB/BacT and BACTEC 460 TB Systems

We have read the recent report by Brunello et al. (1) about a comparative study between the MB/BacT and the BACTEC 460 TB systems for recovery of mycobacteria. We have carried out a similar study with 500 clinical specimens (89% respiratory and 24.3% nonrespiratory), and we would like to make some comments. First, like Brunello et al., we did not find any statistically significant differences between the two systems, but the rates of recovery of Mycobacterium tuberculosis we obtained were lower than those of Brunello et al. (81.6% versus 99.1% for MB/BacT and 84.4% versus 100% for BACTEC 460 TB) (1). Rohner et al. (2) have reported recovery rates of 89 and 93%, respectively, for the MB/BacT and BACTEC 460 TB systems. With regard to the time to detection, Brunello et al. found an average of 13.2 days for MB/BacT and 9.9 days for BACTEC 460 TB. These results are quite different from our own findings (17.9 days for MB/BacT and 14.5 for BACTEC 460 TB), which are in complete agreement with those of Rohner et al. (2). The three studies are coincident in the time lags for detection by the MB/BacT system versus the BACTEC 460 TB system (3 days on average). Brunello et al. (1) suggest that the better performance of the two systems in their study could be explained by the higher number of smear-positive specimens they tested: 84% versus 64.2% in the study of Rohner et al. (2). (The number of smear-positive specimens in our study was 59%.) However, there must be another reason because they also obtained excellent results for smear-negative specimens (98.1% for MB/BacT and 100% for BACTEC 460 TB), in contrast to our own results (65.3% for both systems). We did not find any explanation for this great difference.
Learners' participation in informal Japanese-English internet chat

It has been widely claimed that computer mediated communication offers unique opportunities for language learners, including the ability to take on the roles of ‘writer’ and ‘reader’, ‘teacher’ and ‘learner’. Hence, it is important for teachers and learners to be aware of not only the linguistic and interactional characteristics of especially bilingual chat, but also how participants in an intercultural setting may switch between roles. Learning about one’s second language from a peer, and in turn, teaching that peer about one’s native language may allow both participants opportunities to develop as language experts. This article utilises naturalistic bilingual chat data and follow-up interviews to examine the implications of these findings for learners, teachers and researchers.
Evolutionary analysis of the influenza A virus M gene with comparison of the M1 and M2 proteins

Phylogenetic analysis of 42 membrane protein (M) genes of influenza A viruses from a variety of hosts and geographic locations showed that these genes have evolved into at least four major host-related lineages: (i) A/Equine/prague/56, which has the most divergent M gene; (ii) a lineage containing only H13 gull viruses; (iii) a lineage containing both human and classical swine viruses; and (iv) an avian lineage subdivided into North American avian viruses (including recent equine viruses) and Old World avian viruses (including avianlike swine strains). The M gene evolutionary tree differs from those published for other influenza virus genes (e.g., PB1, PB2, PA, and NP) but shows the most similarity to the NP gene phylogeny. Separate analyses of the M1 and M2 genes and their products revealed very different patterns of evolution. Compared with other influenza virus genes (e.g., PB2 and NP), the M1 and M2 genes are evolving relatively slowly, especially the M1 gene. The M1 and M2 gene products, which are encoded in different but partially overlapping reading frames, revealed that the M1 protein is evolving very slowly in all lineages, whereas the M2 protein shows significant evolution in human and swine lineages but virtually none in avian lineages. The evolutionary rates of the M1 proteins were much lower than those of M2 proteins and other internal proteins of influenza viruses (e.g., PB2 and NP), while M2 proteins showed less rapid evolution compared with other surface proteins (e.g., H3HA). Our results also indicate that for influenza A viruses, the evolution of one protein of a bicistronic gene can affect the evolution of the other protein. (ABSTRACT TRUNCATED AT 400 WORDS)