Miracle-dz/UniFAR-FTUs huggingface dataset:
Dnmt3b Prefers Germ Line Genes and Centromeric Regions: Lessons from the ICF Syndrome and Cancer and Implications for Diseases

The correct establishment and maintenance of DNA methylation patterns are critical for mammalian development and the control of normal cell growth and differentiation. DNA methylation has profound effects on the mammalian genome, including transcriptional repression, modulation of chromatin structure, X chromosome inactivation, genomic imprinting, and the suppression of the detrimental effects of repetitive and parasitic DNA sequences on genome integrity. Consistent with its essential role in normal cells and predominance at repetitive genomic regions, aberrant changes of DNA methylation patterns are a common feature of diseases with chromosomal and genomic instabilities. In this context, the functions of DNA methyltransferases (DNMTs) can be affected by mutations or alterations of their expression. DNMT3B, which is involved in de novo methylation, is of particular interest not only because of its important role in development, but also because of its dysfunction in human diseases. Expression of catalytically inactive isoforms has been associated with cancer risk and germ line hypomorphic mutations with the ICF syndrome (Immunodeficiency Centromeric instability Facial anomalies). In these diseases, global genomic hypomethylation affects repeated sequences around centromeric regions, which make up large blocks of heterochromatin, and is associated with chromosome instability, impaired chromosome segregation and perturbed nuclear architecture. The review will focus on recent data about the function of DNMT3B, and the consequences of its deregulated activity on pathological DNA hypomethylation, including the illicit activation of germ line-specific genes and accumulation of transcripts originating from repeated satellite sequences, which may represent novel physiopathological biomarkers for human diseases. Notably, we focus on cancer and the ICF syndrome, pathological contexts in which hypomethylation has been extensively characterized. We also discuss the potential contribution of these deregulated protein-coding and non-coding transcription programs to the perturbation of cellular phenotypes.
An "ageing" operator and its use in the highly constrained topological optimization of HVAC system design

The synthesis of novel heating, ventilating, and air-conditioning (HVAC), system configurations is a mixed-integer, non-linear, highly constrained, multi-modal, optimization problem, with many of the constraints being subject to time-varying boundary conditions on the system operation. It was observed that the highly constrained nature of the problem resulted in the dominance of the search by a single topology. This paper, introduces an new evolutionary algorithm operator that prevents topology dominance by penalizing solutions that have a dominant topology.The operator results in a range of dynamic behavior for the rates of growth in topology dominance. Similarly, the application of the ageing penalty can result in the attenuation of topology dominance, or more severely, the complete removal of a topology from the search. It was also observed that following the penalization of a dominant topology, the search was dynamically re-seeded with both new and previously evaluated topologies. It is concluded that the operator prevents topology dominance and increases the exploratory power of the algorithm.The application of an evolutionary algorithm with ageing to the synthesis of HVAC system configurations resulted in a novel design solution having a 15% lower energy use than the best of conventional system designs.
PRODUCTION AND CHARACTERIZATION OF SPONGE‐DOUGH BREAD USING SCALDED RYE

ABSTRACT In this work, flatbed scanning, instrumental texture analysis, spectrophotometric color determination (L*, a*, b*), moisture and specific volume measurements were used to evaluate the effects of the addition of rye flour or rye flakes, yeast and boiling water in different amounts in sponge-dough rye bread production. The treatments changed significantly (P < 0.05) the crumb cell area (mm2), cell diameter (mm), cell perimeter (mm), texture parameters and light reflectance (L*, a*, b*). Scalding process could be used to produce new textures and color of baked products. PRACTICAL APPLICATIONS Fermented foods contribute to about one-third of the diet worldwide. Fermentation causes changes in texture, flavor, appearance, nutrition and safety of food. Many cereal products start with heat treatment to change protein and starch properties, removal of antinutrients, natural toxicants and mycotoxins, before fermentation. The study of microstructure can be used to increase understanding of the changes that occur during processing of food and the role of different ingredients, allowing a better control of the structure and regulation of texture. Designing texturally appealing foods presents a new challenge to companies.
Draft Draft Draft Draft Draft Draft Draft Four-phase Patterns in Forced Oscillatory Systems Ii the Periodically Forced Belousov-zhabotinsky Reaction

We investigate pattern formation in self-oscillating systems forced by an external periodic perturbation. Experimental observations and numerical studies of reaction-diffusion systems and an analysis of an amplitude equation are presented. The oscillations in each of these systems entrain to rational multiples of the perturbation frequency for certain values of the forcing frequency and amplitude. We focus on the subhar-monic resonant case where the system locks at one fourth the driving frequency, and four-phase rotating spiral patterns are observed at low forcing amplitudes. The spiral patterns are studied using an amplitude equation for periodically forced oscillating systems. The analysis predicts a bifurcation (with increasing forcing) from rotating four-phase spirals to standing two-phase patterns. This bifurcation is also found in periodically forced reaction-diffusion equations, the FitzHugh-Nagumo and Brusselator models, even far from the onset of oscillations where the amplitude equation analysis is not strictly valid. In a Belousov-Zhabotinsky chemical system periodically forced with light we also observe four-phase rotating spiral wave patterns. However, we have not observed the transition to standing two-phase patterns, possibly because with increasing light intensity the reaction kinetics become excitable rather than oscillatory. Spatially extended systems characterized by the coexistence of two or more stable states compose a broad class of nonequilibrium pattern forming systems. The most common multistable systems are those that exhibit bistability, (e.g. chemical systems [1, 2], vertically vibrated granular systems [3], and binary fluid convection [4]). Spatial patterns in these systems involve alternating domains of the two different stable states, which are separated from each other by interfaces or fronts. Bistable systems support a variety of patterns from spiral waves to splitting spots and labyrinths [5–9]. In some systems, such as the ferrocyanide-iodate-sulfite reaction [6, 10] and the oxidation of carbon monoxide on a platinum surface [11], the bistability arises from the nonlinear nature of the system. In other systems such as liquid crystals in a rotating magnetic field [12–14] and periodically forced os-cillators [15], the bistability arises from a broken symmetry. Periodically forced oscillatory systems are convenient systems for exploring multistability in pattern formation since the number of coexisting stable states can be controlled by changing the forcing frequency. Applying a periodic force of sufficient amplitude and at a frequency Ò Ñ ¼ , where ¼ is the oscillation frequency of the unforced system, entrains the system to the forcing frequency. The entrained system has Ò stable states each with the same oscillation …
Carbon monoxide pretreatment prevents respiratory derangement and ameliorates hyperacute endotoxic shock in pigs

Endotoxic shock, one of the most prominent causes of mortality in intensive care units, is characterized by pulmonary hypertension, systemic hypotension, heart failure, widespread endothelial activation/injury, and clotting culminating in disseminated intravascular coagulation and multi‐organ system failure. In the last few years, studies in rodents have shown that administration of low concentrations of carbon monoxide (CO) exerts potent therapeutic effects in a variety of diseases/disorders. In this study, we have administered CO (one our pretreatment at 250 ppm) in a clinically relevant, well‐characterized model of LPS‐induced acute lung injury in pigs. Pretreatment only with inhaled CO significantly ameliorated several of the acute pathological changes induced by endotoxic shock. In terms of lung physiology, CO pretreatment corrected the LPS‐induced changes in resistance and compliance and improved the derangement in pulmonary gas exchange. In terms of coagulation and inflammation, CO reduced the development of disseminated intravascular coagulation and completely suppressed serum levels of the proinflammatory IL‐1β in response to LPS, while augmenting the anti‐inflammatory cytokine IL‐10. Moreover, the effects of CO blunted the deterioration of kidney and liver function, suggesting a beneficial effect in terms of end organ damage associated with endotoxic shock. Lastly, CO pretreatment prevents LPS‐induced ICAM expression on lung endothelium and inhibits leukocyte marginalization on lung parenchyma.
Time-resolved spectroscopy based on white-light generation of short pulses in a photonic crystal fiber

We report on an instrument for time-resolved spectroscopy (TRS) based on white-light generation in a highly non-linear crystal fiber. TRS in the visible and near-infrared region at picosecond-to-nanosecond time scales has attracted increased interest in recent years owing to the possibility of spectroscopic analysis of turbid media, such as biological tissues. A self-mode-locked Ti:Sapphire oscillator pumped by an Ar:ion laser provides pulses 50 - 100 fs long, at 85 MHz repetition rate. The light is focused into a crystal fiber, which consists of a core surrounded by a mesh of air-filled holes. White light is generated by a combination of several non-linear effects in the fiber. We optimize the spectrum for measurements in the region 600 - 1000 nm. For detection, we use an imaging spectrometer coupled to a 16-channel photomultiplier tube, enabling simultaneous detection in 16 wavelength bands. We use time-correlated single-photon counting to record the signal, with a temporal resolution of ~160 ps. To demonstrate the system, we have performed measurements of the diffuse time-resolved reflectance of tissue phantoms made of epoxy resin with added scattering and absorbing materials. The data was evaluated using a light propagation model based on diffusion theory, to extract the scattering and absorption coefficients of the medium. The results corresponded very well with previous measurements on the phantoms performed using other TRS instruments.
Crystallization behavior and nucleation analysis of poly(l‐lactic acid) with a multiamide nucleating agent

To accelerate the crystallization of poly(L-lactic acid) (PLLA) and enhance its crystallization ability, a multiamide nucleator (TMC) was introduced into the PLLA matrix. The thermal characteristics, isothermal and nonisothermal crystallization behavior of pure PLLA and TMC-nucleated PLLA were investigated by differential scanning calorimetry. The determination of thermal characteristics shows that the addition of TMC can significantly decrease the onset temperature of cold crystallization and meanwhile elevate the total crystallinity of PLLA. For the isothermal crystallization process, it is found that the overall crystallization rate is much faster in TMC-nucleated PLLA than in pure PLLA and increases as the TMC content is increased, however, the crystal growth form and crystalline structure are not influenced much despite the presence of TMC. In the case of nonisothermal crystallization, the nucleation efficiency and nucleation activity were estimated and the results indicate that excellent nucleation-promoting effect could be achieved when the weight percentage of TMC is chosen between 0.25% and 0.5%. Polarized optical microscopy observation reveals that the nuclei number of PLLA increases and the spherulite size reduces greatly with the addition of TMC. POLYM. ENG. SCI., 2012. © 2011 Society of Plastics Engineers
Building and Refining General Purpose Computing Clusters in an Emerging HPCOriented Research Environment

The increasing uptake of HPC, and cluster computing in particular, has led many people to develop creative solutions to the technical challenges that they encounter in the establishment of useful HPC facilities. Proven solutions from our experiences in acquiring and building research clusters for general purpose scientific use are presented to a number of such issues, ranging from the performance evaluation of vendor bids to matters of user management. Examples of the latter being techniques for limiting manual SSHing to compute nodes and the use of group accounts that empower user groups to take ownership of their specialized software.
Toll-like receptors are critical for clearance of Brucella and play different roles in development of adaptive immunity following aerosol challenge in mice

Brucella spp. cause undulant fever in humans and brucellosis in variety of other animals. Both innate and adaptive immunity have been shown to be important in controlling Brucella infection. Toll-like receptors (TLRs) represent a group of pattern recognition receptors (PRRs) that play critical roles in the host innate immune response, as well as development of adaptive immunity. In the current report, we investigated the role of TLR signaling in the clearance of Brucella and development of adaptive immunity in TLR2−/−, TLR4−/−, or MyD88−/− mice following aerosol exposure to B. melitensis 16 M. Consistent with previous reports, MyD88 is required for efficient clearance of Brucella from all three organs (lung, spleen, and liver). The results reveal Th2-skewed immune responses in TLR2−/− mice late in infection and support a TLR2 requirement for efficient clearance of Brucella from the lungs, but not from the spleen or liver. Similarly, TLR4 is required for efficient clearance of Brucella from the lung, but exhibits a minor contribution to clearance from the spleen and no demonstrable contribution to clearance from the liver. Lymphocyte proliferation assays suggest that the TLRs are not involved in the development of cell-mediated memory response to Brucella antigen. Antibody detection reveals that TLR2 and 4 are required to generate early antigen-specific IgG, but not during the late stages of infection. TLR2 and 4 are only transiently required for IgM production and not at all for IgA production. In contrast, MyD88 is essential for antigen specific IgG production late in infection, but is not required for IgM generation over the course of infection. Surprisingly, despite the prominent role for MyD88 in clearance from all tissues, MyD88-knockout mice express significantly higher levels of serum IgA. These results confirm the important role of MyD88 in controlling infection in the spleen while providing evidence of a prominent contribution to protection in other tissues. In addition, although TLR4 and TLR2 contribute little to control of spleen infection, a significant contribution to clearance of lung infection is described.
Application of FASTAR Code in Multimedia Broadcast Multicast Service

This paper evaluates the performance of FASTAR code in Multimedia Broadcast Multicast Service (MBMS) System. It is demonstrated that FASTAR code, which is optimised for erasure channel through its overhead minimising degree distribution, can improve the system performance compared to the conventional systematic Raptor code. The system is simulated under the Evolved UMTS Terrestrial Radio Access (E-UTRA) network environment according to 3GPP LTE-A specifications. The extent of the improvement and its relation to the system parameters are also studied.
Bilingual Welsh–English children's acquisition of vocabulary and reading: implications for bilingual education

Previous studies have highlighted early differences in bilinguals' rate of language acquisition in comparison with monolinguals. However, these differences seem to disappear with increasing age and exposure to the language, and do so quicker in dominant community languages than in minority status languages. This study aimed to replicate these findings in relation to literacy development. Three groups of Welsh–English bilinguals (L1 Welsh, simultaneous bilinguals and L1 English) were given receptive vocabulary tasks and reading tasks in Welsh and in English. An additional group of monolingual English-speaking controls was given the English tasks. Results revealed differential performance among the bilinguals in relation to the English tasks, with the L1 English bilinguals and monolinguals performing closer to age norms than L1 Welsh and simultaneous bilinguals by the end of primary school education. No differences were found between the L1 English bilinguals and the monolinguals on either task. On the Welsh measures, performance mirrored those of previous studies, on both tasks, demonstrating higher levels of performance relative to increasing amounts of exposure to Welsh. The implications of these findings for bilingual education strategies, particularly in relation to the development of bilingual language competence in minority language situations, are discussed.
Acquired color vision and visual field defects in patients with ocular hypertension and early glaucoma

Purpose: To study acquired color vision and visual field defects in patients with ocular hypertension (OH) and early glaucoma. Methods: In a prospective study we evaluated 99 eyes of 56 patients with OH without visual field defects and no hereditary color deficiencies, followed up for 4 to 6 years (mean = 4.7 ± 0.6 years). Color vision defects were studied using a special computer program for Farnsworth–Munsell 100 hue test and visual field tests were performed with Humphrey analyzer using program 30–2. Both tests were repeated every six months. Results: In fifty-six eyes, glaucomatous defects were observed during the follow-up period. There was a statistically significant difference in total error score (TES) between eyes that eventually developed glaucoma (157.89 ± 31.79) and OH eyes (75.51 ± 31.57) at the first examination (t value 12.816, p < 0.001). At the same time visual field indices were within normal limits in both groups. In the glaucomatous eyes the earliest statistical significant change in TES was identified at the first year of follow-up and was −20.62 ± 2.75 (t value 9.08, p < 0.001) while in OH eyes was −2.11 ± 4.36 (t value 1.1, p = 0.276). Pearson’s coefficient was high in all examinations and showed a direct correlation between TES and mean deviation and corrected pattern standard deviation in both groups. Conclusion: Quantitative analysis of color vision defects provides the possibility of follow-up and can prove a useful means for detecting early glaucomatous changes in patients with normal visual fields.
Serum Uric Acid Is Independently Associated with Metabolic Syndrome in Subjects with and without a Low Estimated Glomerular Filtration Rate

Objective. The relationship among serum uric acid (SUA), metabolic syndrome, and chronic kidney disease (CKD) is unclear. We examined whether SUA level is an independent risk factor for chronic kidney disease and whether the association between SUA and metabolic syndrome is affected by kidney function. Methods. We analyzed 28,745 subjects (17,478 men, 11,267 women, age 20–49 yrs) who underwent health examinations at this hospital between 2000 and 2007. Hyperuricemia was defined as SUA level > 7.7 mg/dl in men or > 6.6 mg/dl in women. Kidney function was assessed by estimated glomerular filtration rate (eGFR) using the Modification of Diet in Renal Disease Study equation modified for Chinese subjects. Impaired renal function with low GFR was defined as eGFR < 90 ml/min/1.73 m2. The UA-low GFR groups were defined according to the observed combination of hyperuricemia and low GFR: Group A (absence of both hyperuricemia and low GFR); Group B (presence of low GFR but no hyperuricemia); Group C (presence of hyperuricemia but not low GFR); and Group D (presence of both hyperuricemia and low GFR). Results. The prevalence of hyperuricemia, metabolic syndrome, and impaired kidney function with low GFR was 20.3% (27.6% in men, 8.9% in women), 7.6% (10.6% in men, 3.0% in women), and 9.9% (11.6% in men, 7.1% in women), respectively. The Pearson correlation between SUA and eGFR was only −0.26 (−0.21 in men, −0.22 in women; p < 0.001). In men, the age-adjusted odds ratio (OR) of metabolic syndrome was 1.41 (Group B), 2.45 (Group C), and 2.58 (Group D) in comparison with Group A. In women, the age-adjusted OR of metabolic syndrome was 0.83 (Group B), 5.47 (Group C), and 3.31 (Group D) in comparison with Group A. Conclusion. Hyperuricemia is prevalent in the Taiwan population. Hyperuricemia is only weakly associated with renal function, but is strongly associated with metabolic syndrome with or without a low eGFR.
Risk Factors for Smartphone Addiction in Korean Adolescents: Smartphone Use Patterns

With widespread use of the smartphone, clinical evidence for smartphone addiction remains unclear. Against this background, we analyzed the effect of smartphone use patterns on smartphone addiction in Korean adolescents. A total of 370 middle school students participated. The severity of smartphone addiction was measured through clinical interviews and the Korean Smartphone Addiction Proneness Scale. As a result, 50 (13.5%) were in the smartphone addiction group and 320 (86.5%) were in the healthy group. To investigate the effect of smartphone use patterns on smartphone addiction, we performed self-report questionnaires that assessed the following items: smartphone functions mostly used, purpose of use, problematic use, and parental attitude regarding smartphone use. For smartphone functions mostly used, the addiction group showed significantly higher scores in “Online chat. ” For the purpose of use, the addiction group showed significantly higher “habitual use,” “pleasure,” “communication,” “games,” “stress relief,” “ubiquitous trait,” and “not to be left out. ” For problematic use, the addiction group showed significantly higher scores on “preoccupation,” “tolerance,” “lack of control,” “withdrawal,” “mood modification,” “conflict,” “lies,” “excessive use,” and “loss of interest. ” For parental attitude regarding children's smartphone use, the addiction group showed significantly higher scores in “parental punishment. ” Binary logistic regression analysis indicated that “female,” “use for learning,” “use for ubiquitous trait,” “preoccupation,” and “conflict” were significantly correlated with smartphone addiction. This study demonstrated that the risk factors for smartphone addiction were being female, preoccupation, conflict, and use for ubiquitous trait; the protective factor was use for learning. Future studies will be required to reveal the additional clinical evidence of the disease entity for smartphone addiction.