Miracle-dz/UniFAR-FTUs huggingface dataset:
The Mitochondrial Genome of Soybean Reveals Complex Genome Structures and Gene Evolution at Intercellular and Phylogenetic Levels

Determining mitochondrial genomes is important for elucidating vital activities of seed plants. Mitochondrial genomes are specific to each plant species because of their variable size, complex structures and patterns of gene losses and gains during evolution. This complexity has made research on the soybean mitochondrial genome difficult compared with its nuclear and chloroplast genomes. The present study helps to solve a 30-year mystery regarding the most complex mitochondrial genome structure, showing that pairwise rearrangements among the many large repeats may produce an enriched molecular pool of 760 circles in seed plants. The soybean mitochondrial genome harbors 58 genes of known function in addition to 52 predicted open reading frames of unknown function. The genome contains sequences of multiple identifiable origins, including 6.8 kb and 7.1 kb DNA fragments that have been transferred from the nuclear and chloroplast genomes, respectively, and some horizontal DNA transfers. The soybean mitochondrial genome has lost 16 genes, including nine protein-coding genes and seven tRNA genes; however, it has acquired five chloroplast-derived genes during evolution. Four tRNA genes, common among the three genomes, are derived from the chloroplast. Sizeable DNA transfers to the nucleus, with pericentromeric regions as hotspots, are observed, including DNA transfers of 125.0 kb and 151.6 kb identified unambiguously from the soybean mitochondrial and chloroplast genomes, respectively. The soybean nuclear genome has acquired five genes from its mitochondrial genome. These results provide biological insights into the mitochondrial genome of seed plants, and are especially helpful for deciphering vital activities in soybean.
Liver fat content and T2*: simultaneous measurement by using breath-hold multiecho MR imaging at 3.0 T--feasibility.

Research ethics committee approval was obtained for this study, and written informed consent was obtained from all participants. The purpose was to prospectively evaluate the feasibility of breath-hold multiecho in- and out-of-phase magnetic resonance (MR) imaging for simultaneous lipid quantification and T2* measurement. A spoiled gradient-echo sequence with seven echo times alternately in phase and out of phase was used at 3.0 T. Imaging was performed in a lipid phantom, in five healthy volunteers (all men; mean age, 37 years), and in five obese individuals with hyperlipidemia or diabetes (four men, one woman; mean age, 53 years). A biexponential curve-fitting model was used to derive the relative signal contributions from fat and water, and these results were compared with results of liver proton MR spectroscopy, the reference standard. There was a significant correlation between multiecho and spectroscopic measurements of hepatic lipid concentration (r(2) = 0.99, P < . 001). In vivo, the T2* of water was consistently longer than that of fat and reliably enabled the signal components to be correctly assigned. In the lipid phantom, the multiecho method could be used to determine the fat-to-water ratio and the T2* values of fat and water throughout the entire range of fat concentrations. Multiecho imaging shows promise as a method of simultaneous fat and T2* quantification.
Cysteine Scanning Mutagenesis of α4, a Putative Pore-Lining Helix of the Bacillus thuringiensis Insecticidal Toxin Cry1Aa

ABSTRACT Helix α4 of Bacillus thuringiensis Cry toxins is thought to line the lumen of the pores they form in the midgut epithelial cells of susceptible insect larvae. To define its functional role in pore formation, most of the α4 amino acid residues were replaced individually by a cysteine in the Cry1Aa toxin. The toxicities and pore-forming abilities of the mutated toxins were examined, respectively, by bioassays using neonate Manduca sexta larvae and by a light-scattering assay using midgut brush border membrane vesicles isolated from M. sexta. A majority of these mutants had considerably reduced toxicities and pore-forming abilities. Most mutations causing substantial or complete loss of activity map on the hydrophilic face of the helix, while most of those having little or only relatively minor effects map on its hydrophobic face. The properties of the pores formed by mutants that retain significant activity appear similar to those of the pores formed by the wild-type toxin, suggesting that mutations resulting in a loss of activity interfere mainly with pore formation.
Brain structure and verbal function across adulthood while controlling for cerebrovascular risks

The development and decline of brain structure and function throughout adulthood is a complex issue, with cognitive aging trajectories influenced by a host of factors including cerebrovascular risk. Neuroimaging studies of age‐related cognitive decline typically reveal a linear decrease in gray matter (GM) volume/density in frontal regions across adulthood. However, white matter (WM) tracts mature later than GM, particularly in regions necessary for executive functions and memory. Therefore, it was predicted that a middle‐aged group (MC: 35–45 years) would perform best on a verbal working memory task and reveal greater regional WM integrity, compared with both young (YC: 18–25 years) and elder groups (EC: 60+ years). Diffusion tensor imaging (DTI) and magnetoencephalography (MEG) were obtained from 80 healthy participants. Objective measures of cerebrovascular risk and cognition were also obtained. As predicted, MC revealed best verbal working memory accuracy overall indicating some maturation of brain function between YC and MC. However, contrary to the prediction fractional anisotropy values (FA), a measure of WM integrity, were not greater in MC (i.e., there were no significant differences in FA between YC and MC but both groups showed greater FA than EC). An overall multivariate model for MEG ROIs showed greater peak amplitudes for MC and YC, compared with EC. Subclinical cerebrovascular risk factors (systolic blood pressure and blood glucose) were negatively associated with FA in frontal callosal, limbic, and thalamic radiation regions which correlated with executive dysfunction and slower processing speed, suggesting their contribution to age‐related cognitive decline. Hum Brain Mapp 38:3472–3490, 2017. © 2017 Wiley Periodicals, Inc.
Quantization of inductively shunted superconducting circuits

We present a method for calculating the energy levels of superconducting circuits that contain highly anharmonic, inductively-shunted modes with arbitrarily strong coupling. Our method starts by calculating the normal modes of the linearized circuit and proceeds with numerical diagonalization in this basis. As an example, we analyze the Hamiltonian of a fluxonium qubit inductively coupled to a readout resonator. While elementary, this simple example is nontrivial because it cannot be efficiently treated by the method known as "black-box quantization," numerical diagonalization in the bare harmonic oscillator basis, or perturbation theory. Calculated spectra are compared to measured spectroscopy data, demonstrating excellent quantitative agreement between theory and experiment.
Prospective Community-Based Study of Stroke in Northern Portugal: Incidence and Case Fatality in Rural and Urban Populations

Background and Purpose— Mortality statistics indicate that Portugal has the highest stroke mortality in Western Europe. Data on stroke incidence in Northern Portugal, the region with the highest mortality, are lacking. This study was designed to determine stroke incidence and case fatality in rural and urban populations in Northern Portugal. Methods— All suspected first-ever-in-a-lifetime strokes occurring between October 1998 and September 2000 in 37 290 residents in rural municipalities and 86 023 living in the city of Porto were entered in a population-based registry. Standard definitions and comprehensive sources of information were used for identification of patients who were followed-up at 3 and 12 months after onset of symptoms. Results— During a 24-month period, 688 patients with a first-ever stroke were registered, 226 in rural and 462 in urban areas. The crude annual incidence was 3.05 (95% CI, 2.65 to 3.44) and 2.69 per 1000 (95% CI, 2.44 to 2.93) for rural and urban populations, respectively; the corresponding rates adjusted to the European standard population were 2.02 (95% CI, 1.69 to 2.34) and 1.73 (95% CI, 1.53 to 1.92). Age-specific incidence followed different patterns in rural and urban populations, reaching major discrepancy for those 75 to 84 years old, 20.2 (95% CI, 16.1 to 25.0) and 10.9 (95% CI, 9.0 to 12.8), respectively. Case fatality at 28 days was 14.6% (95% CI, 10.2 to 19.3) in rural and 16.9% (95% CI, 13.7 to 20.6) in urban areas. Conclusions— Stroke incidence in rural and urban Northern Portugal is high compared to that reported in other Western Europe regions. The high official mortality in our country, which could be explained by a relatively high incidence, was not because of a high case fatality rate.
Some Studies in Machine Learning Using the Game of Checkers

Abstract A new signature-table technique is described together with an improved book-learning procedure which is thought to be much superior to the linear polynomial method. Full use is made of the so-called “alpha-beta” pruning and several forms of forward pruning to restrict the spread of the move tree and to permit the program to look ahead to a much greater depth than it otherwise could do. While still unable to outplay checker masters, the program's playing ability has been greatly improved.tplay checker masters, the
Worsening of Left Ventricular End‐Systolic Volume and Mitral Regurgitation without Increase in Left Ventricular Dyssynchrony on Acute Interruption of Cardiac Resynchronization Therapy

Background: Responders to cardiac resynchronization therapy (CRT) have greater left ventricular (LV) dyssynchrony than nonresponders prior to CRT. Aim: We conducted this study to see whether the long term responders have more worsening of LV dyssynchrony and LV function on acute interruption of CRT. Materials and Methods: We identified 22 responders and 13 nonresponders who received CRT as per standard criteria for 23.73 ± 7.9 months (median 24.5 months). We assessed the acute change in LV function, mitral regurgitation (MR) and compared LV dyssynchrony in CRT on and off modes. Results: On turning off CRT, there was no significant worsening of LV dyssynchrony in both responders and nonresponders. The dyssynchrony measurements by SPWMD, TDI and 3D echocardiography did not correlate significantly. LVESV increased (p = 0.02) and MR (p = 0.01) worsened in CRT‐off mode in responders only without significant change in LVEF or LV dimensions. Discussion and Conclusion: In long‐term responders to CRT, there is alteration in the function of remodeled LV with acute interruption of CRT, without significant worsening of LV dyssynchrony. The role of different echocardiographic parameters in the assessment of LV dyssynchrony remains controversial. Even after long‐term CRT reversely remodels the LV, the therapy needs to be continued uninterrupted for sustained benefits.
A Unified Traffic Model for MPEG-4 and H.264 Video Traces

This paper presents a frame-level hybrid framework for modeling MPEG-4 and H.264 multi-layer variable bit rate (VBR) video traffic. To accurately capture long-range-dependent and short-range-dependent properties of VBR sequences, we use wavelets to model the distribution of I-frame sizes and a simple time-domain model for P/B frame sizes. However, unlike previous studies, we analyze and successfully model both inter-GOP (group of pictures) and intra-GOP correlation in VBR video and build an enhancement-layer model using cross-layer correlation. Simulation results demonstrate that our model effectively preserves the temporal burstiness and captures important statistical features (e.g., the autocorrelation function and the frame-size distribution) of original traffic. We also show that our model possesses lower complexity and has better performance than the previous methods in both single- and multi-layer sequences.
NLPR at Multilingual Opinion Analysis Task in NTCIR7

This paper presents our work in the simplified Chinese opinion analysis task in NTCIR7. For identifying the subjective sentences, the domain adaptation technique was applied in our method, so that the data in NTCIR6 can be used for training subjective classifier. The evaluation results proves that the method proposed in this paper is effective. In extracting the opinion holder, we used the CRF model, which was combined with manual designed heuristics rules. For CRF model we not only extracted part-of-speech features, semantic class features, contextual features, but also some dependency features through parsing analysis. The evaluation results prove that the proposed method is effective for extracting opinion holders.
Lessons learned from real DSL experiments

Over the years, our group, led by Bob Baker, designed and implemented three domain-specific languages for use by outside people in real situations. The first language described the communication format of messages used by NATO to specify command-and-control messages between people and equipment; the processor we generated checked these messages for consistency. The second language was in part graphical, part textual, and was used to demonstrate how naval ship formations were constituted and the constrained movements they could undergo. The last language was a mixture of graphics, text, and declarative information specified using three different COTS products. It was used to describe census survey "instruments," used to collect census data in the field. The code generated was to be installed in the survey takers' laptops. Each of these was actually a prototype for what would have taken more time to engineer and polish before putting into practice. Although each effort was essentially successful, none of the languages was ever followed up with the subsequent engineering efforts that we expected or at least hoped for. The first two were demonstrated and reviewed informally. The last effort was more seriously reviewed, in that training sessions and a formal review process were undertaken to evaluate the potential effectiveness of the product. Herein I elaborate where these language efforts succeeded and where they failed, gleaning lessons for others who take the somewhat risky step of committing to develop a DSL for a particular user community.
REDUCED CHLOROPLAST COVERAGE genes from Arabidopsis thaliana help to establish the size of the chloroplast compartment

Significance Mechanisms that determine the cellular volume allocated to organelles are largely unknown. We demonstrate that in the plant Arabidopsis thaliana, a small gene family that encodes proteins of unknown function contributes to a mechanism that establishes the proportion of cellular volume devoted to chloroplasts. We show that this mechanism resides outside of the chloroplast by demonstrating that the protein that makes the greatest contribution to this mechanism resides in the cytoplasm and nucleus and that the trafficking of this protein between the cytoplasm and nucleus may regulate this mechanism. A deeper understanding of this mechanism may lead to the rational manipulation of chloroplast compartment size, which may lead to more efficient photosynthesis and increased yields from important crop plants. Eukaryotic cells require mechanisms to establish the proportion of cellular volume devoted to particular organelles. These mechanisms are poorly understood. From a screen for plastid-to-nucleus signaling mutants in Arabidopsis thaliana, we cloned a mutant allele of a gene that encodes a protein of unknown function that is homologous to two other Arabidopsis genes of unknown function and to FRIENDLY, which was previously shown to promote the normal distribution of mitochondria in Arabidopsis. In contrast to FRIENDLY, these three homologs of FRIENDLY are found only in photosynthetic organisms. Based on these data, we proposed that FRIENDLY expanded into a small gene family to help regulate the energy metabolism of cells that contain both mitochondria and chloroplasts. Indeed, we found that knocking out these genes caused a number of chloroplast phenotypes, including a reduction in the proportion of cellular volume devoted to chloroplasts to 50% of wild type. Thus, we refer to these genes as REDUCED CHLOROPLAST COVERAGE (REC). The size of the chloroplast compartment was reduced most in rec1 mutants. The REC1 protein accumulated in the cytosol and the nucleus. REC1 was excluded from the nucleus when plants were treated with amitrole, which inhibits cell expansion and chloroplast function. We conclude that REC1 is an extraplastidic protein that helps to establish the size of the chloroplast compartment, and that signals derived from cell expansion or chloroplasts may regulate REC1.
Cellular and organismal ageing: Role of the p53 tumor suppressor protein in the induction of transient and terminal senescence

In recent years, an impact of the p53 tumor suppressor protein in the processes of cellular and organismal ageing became evident. First hints were found in model organisms like Saccharomyces cerevisiae, Caenorhabditis elegans, and Drosophila melanogaster where a clear connection between ageing phenotypes and pathways that are regulated by p53, were found. Interestingly, pathways that are central to the ageing process are usually also involved in energy metabolism and are highly conserved throughout evolution. This also supports the long known empiric finding that caloric restriction has a positive impact on the life span of a wide variety of organisms. Within the last years, on the molecular level, an involvement of the insulin‐like growth factor and of the histone deacetylase SRIT1 could be shown. Insight on the impact of p53 on ageing at the organismal level came from mice expressing aberrant forms of the p53 protein. Obviously, the balance of the full length p53 protein and of the shorter p44/ΔNp53 isomer bear a strong impact on ageing. The shorter isoform regulates full length p53 and in cases where there is too much of the longer isoform, this leads to elevated apoptosis resulting in decreased tumor incidence but also in premature ageing due to exhaustion of the renewal potential. Therefore, modulating the expression of the truncated p53 isoform accordingly, might lead to increased health‐span and elevated life‐span. J. Cell. Biochem. 101: 1355–1369, 2007. © 2007 Wiley‐Liss, Inc.
Allergic contact dermatitis to some medicaments

Over the years, changes have had to be made in the list of topical drags most frequently responsible for allergic contact dermatitis. The 4 most common sensitizers in Italy in the past have been penicillin. Sulfonamide, promethazine and neomycin. Now the list is headed by neomycin, benzoeaine and ethylenediamine. Antihislumines and parabens are less frequently observed as sensilizers. The increasing topical use of new drujis and additives, as well as older sensitizers, produces reactions 10 other substances, such as non‐steroidal anti‐inflammatory agents, some antimycotic drugs, propylene glycol and benzoyl peroxide.
Towards a computationally intelligent lesson adaptation for a distance learning course

A neuro-fuzzy approach is introduced to implement lesson adaptation in a Web-based course. Several key points that affect the effectiveness of an adaptive learning environment are investigated the development of the educational material, the structure of the domain knowledge, the instructional design and the evaluation of the learner knowledge under uncertainty. The proposed approach allows the generation of the content of a hypermedia page from pieces of educational material based on goal-oriented teaching and making use of the background knowledge of the learner.
VI. Genome Structure and Cognitive Map of Williams Syndrome

Williams syndrome (WMS) is a most compelling model of human cognition, of human genome organization, and of evolution. Due to a deletion in chromosome band 7q11.23, subjects have cardiovascular, connective tissue, and neurodevelopmental deficits. Given the striking peaks and valleys in neurocognition including deficits in visual-spatial and global processing, preserved language and face processing, hypersociability, and heightened affect, the goal of this work has been to identify the genes that are responsible, the cause of the deletion, and its origin in primate evolution. To do this, we have generated an integrated physical, genetic, and transcriptional map of the WMS and flanking regions using multicolor metaphase and interphase fluorescence in situ hybridization (FISH) of bacterial artificial chromosomes (BACs) and P1 artificial chromosomes (PACs), BAC end sequencing, PCR gene marker and microsatellite, large-scale sequencing, cDNA library, and database analyses. The results indicate the genomic organization of the WMS region as two nested duplicated regions flanking a largely single-copy region. There are at least two common deletion breakpoints, one in the centromeric and at least two in the telomeric repeated regions. Clones anchoring the unique to the repeated regions are defined along with three new pseudogene families. Primate studies indicate an evolutionary hot spot for chromosomal inversion in the WMS region. A cognitive phenotypic map of WMS is presented, which combines previous data with five further WMS subjects and three atypical WMS subjects with deletions; two larger (deleted for D7S489L) and one smaller, deleted for genes telomeric to FZD9, through LIMK1, but not WSCR1 or telomeric. The results establish regions and consequent gene candidates for WMS features including mental retardation, hypersociability, and facial features. The approach provides the basis for defining pathways linking genetic underpinnings with the neuroanatomical, functional, and behavioral consequences that result in human cognition.
Identification of a Pro-Angiogenic Potential and Cellular Uptake Mechanism of a LMW Highly Sulfated Fraction of Fucoidan from Ascophyllum nodosum

Herein we investigate the structure/function relationships of fucoidans from Ascophyllum nodosum to analyze their pro-angiogenic effect and cellular uptake in native and glycosaminoglycan-free (GAG-free) human endothelial cells (HUVECs). Fucoidans are marine sulfated polysaccharides, which act as glycosaminoglycans mimetics. We hypothesized that the size and sulfation rate of fucoidans influence their ability to induce pro-angiogenic processes independently of GAGs. We collected two fractions of fucoidans, Low and Medium Molecular Weight Fucoidan (LMWF and MMWF, respectively) by size exclusion chromatography and characterized their composition (sulfate, fucose and uronic acid) by colorimetric measurement and Raman and FT-IR spectroscopy. The high affinities of fractionated fucoidans to heparin binding proteins were confirmed by Surface Plasmon Resonance. We evidenced that LMWF has a higher pro-angiogenic (2D-angiogenesis on Matrigel) and pro-migratory (Boyden chamber) potential on HUVECs, compared to MMWF. Interestingly, in a GAG-free HUVECs model, LMWF kept a pro-angiogenic potential. Finally, to evaluate the association of LMWF-induced biological effects and its cellular uptake, we analyzed by confocal microscopy the GAGs involvement in the internalization of a fluorescent LMWF. The fluorescent LMWF was mainly internalized through HUVEC clathrin-dependent endocytosis in which GAGs were partially involved. In conclusion, a better characterization of the relationships between the fucoidan structure and its pro-angiogenic potential in GAG-free endothelial cells was required to identify an adapted fucoidan to enhance vascular repair in ischemia.