Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterisation of a GC-Rich Telomeric Satellite DNA in Eumeces schneideri Daudin (Reptilia, Scincidae)

A hitherto undescribed satellite DNA family (AvaII satDNA) has been isolated and characterised in Eumeces schneideri, a squamate reptile belonging to the family Scincidae. AvaII satDNA is characterised by a monomer length of 208 bp, a GC content of 59% and exhibits a certain degree of CpG methylation. FISH experiments with AvaII satDNA probe produced bright signals (i) at the end of the short arms of all subtelocentric chromosomes except for pair 14, in which the signal was at the end of the long arms, (ii) at the ends of both arms of the small metacentric chromosomes 12, and (iii) in a terminal position on the acrocentric chromosomes 11 and 13. AvaII satDNA repeats were not found in the metacentric pair 3, whereas only a weak interstitial signal occurred in the metacentric pairs 1 and 2. C-banding showed that this satellite represents most of the constitutive heterochromatin in the genome of this skink, and chromomycin A3 staining produced a clear signal overlapping with the satellite, except for NOR-associated heterochromatin. In addition, quantitative dot blot analysis showed that these repetitive sequences constitute about 3% of the genomic DNA of this lizard. AvaII satDNA sequence analysis revealed the occurrence of short guanine residue stretches for which a function in structural stability of these sequences and a role in recombination with telomeric sequences can be hypothesised. Fibre FISH experiments showed that on some chromatin fibres telomeric sequences and AvaII satellite DNA repeats are intermingled or overlapping.
Actual information storage with a recording density of 4 Tbit∕in. in a ferroelectric recording medium.

A new method to achieve real information recording with a density above 1 Tbit∕in. (2) in ferroelectric data storage systems is proposed. In this system, data bits were written in the form of the polarization direction, and the data were read by scanning nonlinear dielectric microscopy technique. The domain-switching characteristics of the virgin and inversely prepolarized media were compared, and the conditions of the pulse voltage for writing were optimized. As a result, actual data containing 64×64 bits were recorded at an areal density of 4 Tbit∕in. (2). The bit error rate was evaluated to be 1.2×10(-2).
Domain Organization of the ATP-sensitive Potassium Channel Complex Examined by Fluorescence Resonance Energy Transfer*

Background: We examined FRET between Kir6.2 and SUR1 domains of KATP channels, in various combinations. Results: FRET was detected within and between Kir6.2 subunits and between Kir6.2 and split SUR1 N-terminal constructs. Conclusion: Kir6.2 C termini are centrally located. SUR1 domains can self-associate and are close to Kir6.2 termini in the full complex. Significance: The results indicate domain architecture of this unique channel complex. KATP channels link cell metabolism to excitability in many cells. They are formed as tetramers of Kir6.2 subunits, each associated with a SUR1 subunit. We used mutant GFP-based FRET to assess domain organization in channel complexes. Full-length Kir6.2 subunits were linked to YFP or cyan fluorescent protein (CFP) at N or C termini, and all such constructs, including double-tagged YFP-Kir6.2-CFP (Y6.2C), formed functional KATP channels. In intact COSm6 cells, background emission of YFP excited by 430-nm light was ∼6%, but the Y6.2C construct expressed alone exhibited an apparent FRET efficiency of ∼25%, confirmed by trypsin digestion, with or without SUR1 co-expression. Similar FRET efficiency was detected in mixtures of CFP- and YFP-tagged full-length Kir6.2 subunits and transmembrane domain only constructs, when tagged at the C termini but not at the N termini. The FRET-reported Kir6.2 tetramer domain organization was qualitatively consistent with Kir channel crystal structures: C termini and M2 domains are centrally located relative to N termini and M1 domains, respectively. Additional FRET analyses were performed on cells in which tagged full-length Kir6.2 and tagged SUR1 constructs were co-expressed. These analyses further revealed that 1) NBD1 of SUR1 is closer to the C terminus of Kir6.2 than to the N terminus; 2) the Kir6.2 cytoplasmic domain is not essential for complexation with SUR1; and 3) the N-terminal half of SUR1 can complex with itself in the absence of either the C-terminal half or Kir6.2.
Identification and Characterization of Polyadenylation Signal (PAS) Variants in Human Genomic Sequences Based on Modified EST Clustering

A large-scale analysis of human polyadenylation signals was carried out in silico. The most canonical AAUAAA hexamer and its 11 single-nucleotide variants that are most frequent in human genes were used to search for polyadenylation signals in the terminal sequences. Out of 18,277 poly(A) sites that were identified from 26,414 human genes, 82.5% of the sites were found to contain at least one of these 12 hexamers as a polyadenylation signal within 40 nucleotides upstream of the poly(A) site. The rest (17.5%) did not contain any of these hexamers, which suggests the existence of yet unknown signals. A total of 20,347 terminal sequences in close proximity to 12 polyadenylation signals were collected using modified EST clustering technique to establish a large-scale database of polyadenylation signals. To characterize the 12 hexamers, the locations of polyadenylation signals that were identified as "authentic" and the uracil contents of the downstream region of the signal were examined. Based on this analysis, the 11 variants of the canonical AAUAAA were identified as possibly forming "functional" signals as AAUAAA. Moreover, the observed frequency of 41.9% for AAUAAA was significantly lower than those of other reports, suggesting that the non-canonical variants are more important in the polyadenylation process than frequently recognized. Since the poly(A) sites processed by those non-canonical variants have not been generally annotated in major gene databases, it is important to determine whether the variant hexamers could work as polyadenylation signals that may be responsible for generating heterogeneity of mRNAs by alternative polyadenylation.
Ultrastructural characteristics and lysozyme content in hypergranular and variant type of acute promyelocytic leukaemia

We investigated the electronmicroscopic (EM) features and cellular lysozyme (LZ) content in 16 cases of acute promyelocytic leukaemia (APL): 11 cases of the hypergranular form (M3) and five cases of the microgranular variant (M3‐V). The main EM features in all cases were: irregular, folded or bilobed nuclei, many cytoplasmic granules, distended rough endoplasmic reticulum (RER) cisternae which, in some cases, presented as stellate forms (more frequent in M3‐V), and bundles of cytoplasmic microfilaments. Many Auer rods were present in M3 cases and few in M3‐V; most of these disclosed parallel tubular arrays (PTA) with a varied periodicity ranging from 13 to 26 nm. There was a significant difference between M3 and M3‐V (P<0.0001) in both the number of granules per cell section (62.9 ± 34.5 v 38.0 ± 23.6) and in the granule section area (0.044±0.033 v 0.026±0.015 μm2). In some cases, mainly in M3‐V, we found cells with large granules containing PTA which probably represent poorly developed Auer rods. Intracellular LZ content assayed by a post‐embedding immunogold method, showed high granular LZ density (in the range of that found in M4 and M5) in M3 cells and very low granular LZ content in M3‐V. This study adds new objective parameters for the diagnosis of these two types of APL and provides new information on their LZ pattern of expression.
Decision Analysis of the Cost-Effectiveness of Repetitive Transcranial Magnetic Stimulation Versus Electroconvulsive Therapy for Treatment of Nonpsychotic Severe Depression

Abstract Background: Repetitive transcranial magnetic stimulation (rTMS) is a new treatment with promise for resistant depression. Objective: We tested the economic feasibility of this new method compared with electroconvulsive therapy (ECT). Method: An economic decision analysis was used to compare the costs of three different treatment strategies for nonpsychotic severe depression. The strategies were: ECT alone; rTMS alone; and rTMS followed by ECT for nonresponders (rTMS-to-ECT). We calculated 12-month costs and quality adjusted life years (QALYs) for the three treatment options for all nonpsychotic, severely depressed United States patients who would have otherwise undergone ECT. A sensitivity analysis was performed to test the degree of change in outcome with various parameter changes.
Higher-order wavefront aberrations induced by small ablation area and sub-clinical decentration in simulated corneal refractive surgery using a perturbed schematic eye model

The purpose was to investigate the effect of decentered ablation in myopic corneal refractive surgery by simulation. Wavefront aberrations in a small pupil area (radius: 2 mm) for photopic vision and in a large pupil area (radius: 3 mm) for mesopic vision with simulated refractive surgery were analyzed using Zernike polynomials. Radii of ablation were 3, 2.5 and 2 mm. Decentrations of ablation were 0 mm and 0.5 mm. Change of the surface shape by ablation was considered a perturbation, while Gullstrand’s schematic eye was used as un-perturbed optics. For photopic vision, wavefront aberrations were about the same as with unperturbed optics. For mesopic vision, the results were heavily dependent on the radius of ablation area. When the radius was 3 mm, wavefront aberrations did not increase very much compared to un-perturbed optics. When the radius was smaller than 3 mm, spherical aberration was induced by centered ablations, and coma was also induced by decentered ablations. In conclusion, small ablation areas or subclinical decentrations of ablations could cause serious amounts of wavefront aberrations to the optics of the eye in the simulations.
The ischemic heart--experimental models.

Results obtained by experimental studies of the ischemic heart have been of tremendous importance for the understanding of physiology, biochemistry and lately also the molecular genetics of the heart. Experimental models in use for the study of the ischemic heart involve studies on the integrated organism, experiments with isolated hearts or multicellular preparation, and also studies of cells isolated from the heart. Regional ischemia in the anaesthetized animal has been a standard model. Knowledge about infarct size limitation as well as heart function in acute and chronic ischemia has been obtained based on experiments in a wide variety of species. The isolated perfused heart has been subjected to extensive use. As a result, the understanding of intracellular processes is constantly developing. Cell models and transgenic-mice models represent promising additions. Each model and each species has certain advantages and disadvantages. Variability in susceptibility towards ischemia and reperfusion is also present. The consequences of ischemia can be described as contractile dysfunction and stunning, arrhythmia and infarction each representing different endpoints of injury. The experimental model is also heavily dependent on the endpoint that is chosen for the study. Results obtained in one experimental model can, therefore, not be generalized into universal conclusions about the ischemic heart. With respect to the human and the disease caused by myocardial ischemia, fragments of knowledge put together from different types of experimental models create the background for successful design of potential treatment.
Fast Plasmonic Laser Nanowelding for a Cu‐Nanowire Percolation Network for Flexible Transparent Conductors and Stretchable Electronics

A facile fast laser nanoscale welding process uses the plasmonic effect at a nanowire (NW) junction to suppress oxidation and successfully fabricate a Cu-NW-based percolation-network conductor. The "nanowelding" process does not require an inert or vacuum environment. Due to the low-temperature and fast-process nature, plasmonic laser nanowelding may form Cu-nanowire networks on heat-sensitive, flexible or even stretchable substrates.
Astrocytic production of nerve growth factor in motor neuron apoptosis: implications for amyotrophic lateral sclerosis

Reactive astrocytes frequently surround degenerating motor neurons in patients and transgenic animal models of amyotrophic lateral sclerosis (ALS). We report here that reactive astrocytes in the ventral spinal cord of transgenic ALS‐mutant G93A superoxide dismutase (SOD) mice expressed nerve growth factor (NGF) in regions where degenerating motor neurons expressed p75 neurotrophin receptor (p75NTR) and were immunoreactive for nitrotyrosine. Cultured spinal cord astrocytes incubated with lipopolysaccharide (LPS) or peroxynitrite became reactive and accumulated NGF in the culture medium. Reactive astrocytes caused apoptosis of embryonic rat motor neurons plated on the top of the monolayer. Such motor neuron apoptosis could be prevented when either NGF or p75NTR was inhibited with blocking antibodies. In addition, nitric oxide synthase inhibitors were also protective. Exogenous NGF stimulated motor neuron apoptosis only in the presence of a low steady state concentration of nitric oxide. NGF induced apoptosis in motor neurons from p75NTR +/+ mouse embryos but had no effect in p75NTR –/– knockout embryos. Culture media from reactive astrocytes as well as spinal cord lysates from symptomatic G93A SOD mice‐stimulated motor neuron apoptosis, but only when incubated with exogenous nitric oxide. This effect was prevented by either NGF or p75NTR blocking‐antibodies suggesting that it might be mediated by NGF and/or its precursor forms. Our findings show that NGF secreted by reactive astrocytes induce the death of p75‐expressing motor neurons by a mechanism involving nitric oxide and peroxynitrite formation. Thus, reactive astrocytes might contribute to the progressive motor neuron degeneration characterizing ALS.
Mesoscale Deposition Technology for Electronics Applications

The continual drive for smaller, more powerful and economic electronic systems, has led to the development of a new manufacturing technology, Maskless Mesoscale Materials Deposition (M3D). Without masks or resists, features down to 10 microns can be directly written in a wide variety of materials, including metals, ceramics, polymers and adhesives, on virtually any surface material - silicon, glass, polymers, metals and ceramics. For polymer substrates with a low temperature tolerance, M3D locally processes the deposition through a laser scanning process. The end result is a high-quality thin film with excellent edge definition and near-bulk electronic properties. As a CAD driven, additive manufacturing process, M3D provides significant environmental benefits and reduced processing requirements, eliminating the waste associated with traditional subtractive (e.g. mask and etch) processes. M3D can also precisely deposit materials on non-planar substrates. With no physical contact with the substrate by any portion of the tool other than the deposition stream, conformal writing is easily achieved. Other benefits include: • Time Compression and Increased Manufacturing Agility, • Lower Costs and • Better Product Designs. This paper will detail the benefits of M3D technology in creating mesoscale features for electronics assembly and semiconductor packaging applications. It will outline some of the current application areas including polymer deposition for electronics.
Investigation of Gain Dependent Relative Intensity Noise in Fiber Brillouin Amplification

Fiber Brillouin amplifier intensity noise is investigated experimentally for a distributed feedback and external cavity diode laser. Since relative intensity noise is a serious performance limitation in Brillouin amplification applications, a detailed investigation is carried out with measurements of integrated overall noise and noise spectrum for different pump and signal powers. Fundamental conclusions on pump and gain depletion for different laser linewidths are drawn. High spectral resolution measurements performed within the Brillouin gain spectrum demonstrate that signal-to-noise ratio increases as the seed signal power increases. In addition, a computational model using the finite-difference time domain method is presented showing excellent agreement with the experimental results.
Plasma HHV‐8 viral load in HHV‐8‐related lymphoproliferative disorders associated with HIV infection

This is a mono‐institutional analysis of the clinical features, immunological and virological findings, and prognostic factors of patients with HIV infection and HHV‐8‐lymphoproliferative disorders. Patients with Multicentric Castleman Disease and HHV‐8‐related lymphoma diagnosed and treated from April 1987 to June 2004 were included in the study. HHV‐8 and HIV plasma viral load, CD4+ count, hematologic parameters, and general wellbeing (performance status) were assessed at the onset of the diseases and analyzed in order to identify possible prognostic factors. Nine patients with Multicentric Castleman disease, and 16 with HHV‐8‐related lymphomas (13 primary effusion lymphomas and 3 solid lymphomas), were diagnosed and treated out of 327 HIV‐related non‐Hodgkin's lymphomas. Four patients with Multicentric Castleman disease received only antiretroviral drugs; 5 HAART plus oral etoposide. Nine patients with primary effusion lymphoma were treated with a CHOP‐like regimen (Cyclophosphamide, Prednisone anthracyclines, Vinca alkaloids, Bleomycin, Etoposide) and HAART; 1 with etoposide and HAART, 1 with HAART alone. The patients with solid lymphoma underwent CHOP‐like chemotherapy. Patients with Multicentric Castleman disease showed lower median values of HHV‐8 viral load and longer overall survival compared with HHV‐8‐related lymphomas. Patients with viral load of HHV‐8, >40,000 cp/ml had a significant shorter overall survival. In the univariate analysis, HHV‐8‐related lymphoma, HHV‐8 viral load >40,000 cp/ml and performance status >2 were associated with an increased risk of death. Multivariate analysis confirmed the diagnosis of lymphoma as an independent predictor of shorter survival. J. Med. Virol. 81:888–896, 2009. © 2009 Wiley‐Liss, Inc.
Toward exoskeleton control based on steady state visual evoked potentials

Brain-machine interfaces (BMIs) are systems that establish a direct connection between the human brain and a machine. These systems are applicable to neuro-rehabilitation. In this study, we propose a method of finding optimal threshold of canonical correlation analysis (CCA) based steady state visual evoked potentials (SSVEPs) classification for detecting resting state and reducing misclassification. As a result, we successfully found optimal threshold for the best performance. This result shows the possibility of SSVEP based exoskeleton online control with a proposed method.
Does the six-minute walk test measure walking performance or physical fitness in persons with multiple sclerosis?

BACKGROUND There is psychometric evidence that supports the six-minute walk (6MW) as a measure of walking performance, whereas other psychometric data support it as a submaximal measure of physical fitness in persons with MS. OBJECTIVE The current cross-sectional study compared measures of walking performance and physical fitness as head-to-head predictors of 6MW distance in a sample of persons with MS across the disability spectrum. METHODS All participants completed the 6MW test, as well as other measures of walking performance (i.e., timed-25 foot walk, gait velocity captured by a GaitRite electronic walkway) and physical fitness (i.e., peak aerobic capacity, lower limb muscular strength). RESULTS 6MW distance was strongly associated with measures of walking performance and physical fitness, though the correlations were significantly stronger for measures of walking performance than physical fitness (z > 4.04, p < 0.01). Walking performance explained a large portion of variance in 6MW distance (R2 > 0.85), and measures of physical fitness explained minimal variance in 6MW distance over-and-above that of measures of walking performance (ΔR2 < 0.06). CONCLUSIONS The current results suggest that 6MW distance is primarily a measure of walking performance rather than aerobic and muscular fitness in MS.
Towards performance-oriented perfective evolution of BPMN models

Simulation techniques are successfully applied to analyze and validate the performance of a business process (BP) since the early phases of its lifecycle, when the BP representation is commonly specified in BPMN. The BP simulation model is first to be built from the BPMN model, then implemented and finally executed to yield the performance indices of interest.
Psychological stress impairs short-term muscular recovery from resistance exercise.

PURPOSE The primary aim of this study was to determine whether chronic mental stress moderates recovery of muscular function, perceived energy, fatigue, and soreness in the first hour after a bout of strenuous resistance exercise. METHODS Thirty-one undergraduate resistance training students (age = 20.26 ± 1.34 yr) completed the Perceived Stress Scale and Undergraduate Stress Questionnaire (USQ; a measure of life event stress) and completed fitness testing. After 5 to 14 d of recovery, they performed an acute heavy-resistance exercise protocol (10-repetition maximum (RM) leg press test plus six sets: 80%-100% of 10 RM). Maximal isometric force (MIF) was assessed before exercise, after exercise, and at 20, 40, and 60 min postexercise. Participants also reported their levels of perceived energy, fatigue, and soreness. Recovery data were analyzed with hierarchical linear modeling growth curve analysis. RESULTS Life event stress significantly moderated linear (P = 0.013) and squared (P = 0.05) recovery of MIF. This relationship held even when the model was adjusted for fitness, workload, and training experience. Likewise, perceived stress moderated linear recovery of MIF (P = 0.023). Neither USQ nor Perceived Stress Scale significantly moderated changes in energy, fatigue, or soreness. CONCLUSION Life event stress and perceived stress both moderated the recovery of muscular function, but not psychological responses, in the first hour after strenuous resistance exercise.
Comparison between Three Methods of Fetal Weight Estimation during the Active Stage of Labor Performed by Residents: A Prospective Cohort Study

Objective: To compare the accuracy of ultrasonographic, calculated, and clinical methods for the estimation of fetal weight (EFW) performed during active labor by residents. Methods: Parturients in active labor underwent prospectively EFW by 3 methods: ultrasonographic, clinical, and calculated (extrapolating EFW from a previous scan). Three different blinded residents evaluated each woman. Background variables were examined for their effect on the accuracy of each method. Comparison of the methods for the detection of macrosomia and small for gestational age (SGA) was also performed. Results: Among the 405 women recruited, the rates of accuracy of ultrasonographic, clinical, and calculated EFW (within ±10%) was 72.5, 74.3, and 71.1%, respectively. The correlation coefficient between the methods and actual birth weight (ABW) were 0.702-0.611 (using 7 Hadlock formulas), 0.649, and 0.622, respectively (all p < 0.001). By logistic regression, epidural analgesia was associated with higher and second stage of labor with lower accuracy of ultrasonographic EFW. For the detection of macrosomia, clinical (p < 0.001) and calculated EFWs (p = 0.035) were superior to ultrasonographic EFW. For the detection of SGA, ultrasonographic EFW was superior to calculated (p < 0.001) and clinical (p < 0.001) EFWs. Conclusion: All 3 methods performed by residents during labor correlated well with ABW. Clinical and calculated EFWs were superior for macrosomia detection, whereas ultrasonographic EFW was superior for SGA detection.