Miracle-dz/UniFAR-FTUs huggingface dataset:
Long-term results after surgical treatment of postinfarction ventricular septal rupture.

OBJECTIVES Postinfarction ventricular septal rupture is a serious complication associated with high hospital mortality rates. The present study aimed to identify predictors of early and late outcome in patients with postinfarction ventricular septal defect over a period of 30 years. METHODS We retrospectively analysed clinical and operative data, predictors of early mortality and long-term survival in a series of 52 consecutive patients (male, n = 26; mean age, 67 ± 10 years) with postinfarction ventricular septal rupture that was surgically repaired at our institution between September 1982 and December 2012. The overall logistic EuroSCORE was 41 ± 24% and the follow-up rate was 100%. RESULTS The 30-day mortality rate was 36% (n = 19), and these 19 survivors were followed up for a mean of 7.8 ± 7.7 (median, 6.0) years. The actuarial survival rates of these 19 patients at 1, 5 and 10 years were 91, 75 and 31%, respectively. Univariate predictors of 30-day mortality comprised renal insufficiency, shock at surgery, emergency surgery, logistic EuroSCORE, three-vessel disease, significant left circumflex coronary arterial stenosis, significant right coronary arterial stenosis, incomplete revascularization, surgical duration and cardiopulmonary bypass time and multivariate analysis selected only incomplete coronary revascularization as an independent risk factor of 30-day mortality. CONCLUSIONS Early mortality rates after surgical repair of postinfarction septal rupture remained poor in this series. Most patients who survived for <30 days had a preoperative shock status. Preoperative improvement in shock status and aggressive coronary revascularization are mandatory for patients with ventricular septal rupture.
Impacts of drought on tree mortality and growth in a mixed hardwood forest

The tree and shrub species on a 16-ha watershed in the Coweeta Basin were sampled in 1984 and again in 1991 to determine the effects of drought on tree species composition and basal area growth. Mortality and radial growth were determined for tree species within three community types that represent a moisture gradient from moist to dry: cove-hardwoods > mixed-oak > oak-pine. Tree mortality from 1984 to 1991 was 20% and 23% in the cove-hardwoods and mixed-oak communities, respectively, compared to only 12% in the oak-pine type. With the exception of Oxydendrum arboreum and Robinia pseudoacacia, the oaks had higher percentage mortality than any other genus; Quercus velutina had 29%, 37%, and 20% mortality in the cove-hardwoods, mixed-oak, and oak-pine types, respectively; Quercus prinus had 23% mortality in the mixed-oak type; Quercus coccinea had 36% mortality in the mixed-oak type; and Quercus marilandica had 27% mortality in the oak-pine type. Mortality occurred mostly in the small-size class individuals (< 10 cm in diameter) for all species, suggesting that thinning was still an important process contributing to mortality 29 yr after clearcutting. Although growth of Liriodendron tulipifera was much higher than growth of either Quercus prinus or Quercus coccinea, growth in Liriodendron was significantly reduced by the 1985–88 drought and no growth reduction was observed for these two dominant Quercus species during the same time period.
Metformin pharmacogenomics: a genome-wide association study to identify genetic and epigenetic biomarkers involved in metformin anticancer response using human lymphoblastoid cell lines.

Metformin is currently considered as a promising anticancer agent in addition to its anti-diabetic effect. To better individualize metformin therapy and explore novel molecular mechanisms in cancer treatment, we conducted a pharmacogenomic study using 266 lymphoblastoid cell lines (LCLs). Metformin cytotoxicity assay was performed using the MTS assay. Genome-wide association (GWA) analyses were performed in LCLs using 1.3 million SNPs, 485k DNA methylation probes, 54k mRNA expression probe sets, and metformin cytotoxicity (IC50s). Top candidate genes were functionally validated using siRNA screening, followed by MTS assay in breast cancer cell lines. Further study of one top candidate, STUB1, was performed to elucidate the mechanisms by which STUB1 might contribute to metformin action. GWA analyses in LCLs identified 198 mRNA expression probe sets, 12 SNP loci, and 5 DNA methylation loci associated with metformin IC50 with P-values <10−4 or <10−5. Integrated SNP/methylation loci-expression-IC50 analyses found 3 SNP loci or 5 DNA methylation loci associated with metformin IC50 through trans-regulation of expression of 11 or 26 genes with P-value <10−4. Functional validation of top 61 candidate genes in 4 IPA networks indicated down regulation of 14 genes significantly altered metformin sensitivity in two breast cancer cell lines. Mechanistic studies revealed that the E3 ubiquitin ligase, STUB1, could influence metformin response by facilitating proteasome-mediated degradation of cyclin A. GWAS using a genomic data-enriched LCL model system, together with functional and mechanistic studies using cancer cell lines, help us to identify novel genetic and epigenetic biomarkers involved in metformin anticancer response.
Utilisation of evidence-based practices by ASD early intervention service providers

A number of autism intervention practices have been demonstrated to be effective. However, the use of unsupported practices persists in community early intervention settings. Recent research has suggested that personal, professional and workplace factors may influence intervention choices. The aim of this research was to investigate knowledge and use of strategies, organisational culture, individual attitudes, sources of information and considerations informing intervention choices by early intervention providers. An online survey was completed by 72 early intervention providers from four organisations across Australia. Providers reported high levels of trust and access of information from internal professional development, therapists and external professional development. A range of considerations including child factors, family values and research were rated as important in informing intervention choices. Participants reported greater knowledge and use of evidence-based and emerging practices than unsupported. Levels of use were linked to levels of knowledge, as well as some organisational and attitudinal factors. Areas for future research and implications are discussed.
Comparative analysis of the transcriptome of injured nerve segments reveals spatiotemporal responses to neural damage in mice

Nerves are particularly vulnerable to damage due to their unique structure with meter‐long axons. In the peripheral nervous system neurons and Schwann cells can activate the injury‐response program that directs axons to either regenerate or degenerate after traumatic nerve injury. However, the differences between the genetic programs driving nerve regeneration and degeneration have not yet been described extensively. To understand these differences, in this study we have compared the injury‐induced transcriptomic changes between the regenerating proximal segment and the degenerating distal segment of a transected nerve, at different post‐injury time points. We analyzed the spatiotemporal dynamics of the mouse transcriptome using a sciatic nerve‐injury model by means of RNA sequencing. The results of the differentially regulated genes (DEGs) analysis show that some DEG groups are similarly regulated in both proximal and distal segments, and primarily display a positive correlation. However, some DEG groups are exclusively regulated in either the proximal or the distal segment, suggesting that these DEG groups constitute a genetic network for distinguishing the regenerative and degenerative responses. In addition, our gene ontology analysis revealed an enrichment of particular biological processes in different phases and locations. Thus, our data provide a spatiotemporal profile of the transcriptomes that are differentially regulated in either regenerating or degenerating nerves, in vivo. The specific biological processes enriched in the DEG groups might delineate the injury‐responsive program that induces contrasting regenerative and degenerative responses in different nerve segments.
Degrees of Freedom of the Three-User Rank-Deficient MIMO Interference Channel

We provide the degrees of freedom (DoF) characterization for the three-user M<sub>T</sub> × M<sub>R</sub> multiple-input-multipleoutput (MIMO) interference channel (IC) with rank-deficient channel matrices, where each transmitter is equipped with M<sub>T</sub> antennas and each receiver with M<sub>R</sub> antennas, and the interfering channel matrices from each transmitter to the other two receivers are of ranks D<sub>1</sub> and D<sub>2</sub>, respectively. One important intermediate step for both the converse and achievability arguments is to convert the fully-connected rank-deficient channel into an equivalent partially-connected full-rank MIMO-IC by invertible linear transformations. As such, existing techniques developed for full-rank MIMO-IC can be incorporated to derive the DoF outer and inner bounds for the rank-deficient case. Our result shows that when the interfering links are weak in terms of the channel ranks, i.e., D<sub>1</sub> + D<sub>2</sub> ≤ min(M<sub>T</sub>, M<sub>R</sub>), zero forcing is sufficient to achieve the optimal DoF. On the other hand, when D<sub>1</sub> + D<sub>2</sub> > min(M<sub>T</sub> , M<sub>R</sub>), a combination of zero forcing and interference alignment is in general required for DoF optimality. The DoF characterization obtained in this paper unifies several existing results in the literature.
Robust Generation of Quiescent Porcine Valvular Interstitial Cell Cultures

Background Valvular interstitial cells (VICs) in the healthy aortic valve leaflet exhibit a quiescent phenotype, with <5% of VICs exhibiting an activated phenotype. Yet, in vitro culture of VICs on tissue culture polystyrene surfaces in standard growth medium results in rapid transformation to an activated phenotype in >90% of cells. The inability to preserve a healthy VIC phenotype during in vitro studies has hampered the elucidation of mechanisms involved in calcific aortic valve disease. This study describes the generation of quiescent populations of porcine VICs in 2‐dimensional in vitro culture and their utility in studying valve pathobiology. Methods and Results Within 4 days of isolation from fresh porcine hearts, VICs cultured in standard growth conditions were predominantly myofibroblastic (activated VICs). This myofibroblastic phenotype was partially reversed within 4 days, and fully reversed within 9 days, following application of a combination of a fibroblast media formulation with culture on collagen coatings. Specifically, culture in this combination significantly reduced several markers of VIC activation, including proliferation, apoptosis, α‐smooth muscle actin expression, and matrix production, relative to standard growth conditions. Moreover, VICs raised in a fibroblast media formulation with culture on collagen coatings exhibited dramatically increased sensitivity to treatment with transforming growth factor β1, a known pathological stimulus, compared with VICs raised in either standard culture or medium with a fibroblast media formulation. Conclusions The approach using a fibroblast media formulation with culture on collagen coatings generates quiescent VICs that more accurately mimic a healthy VIC population and thus has the potential to transform the study of the mechanisms of VIC activation and dysfunction involved in the early stages of calcific aortic valve disease.
Next-Generation Annotation of Prokaryotic Genomes with EuGene-P: Application to Sinorhizobium meliloti 2011

The availability of next-generation sequences of transcripts from prokaryotic organisms offers the opportunity to design a new generation of automated genome annotation tools not yet available for prokaryotes. In this work, we designed EuGene-P, the first integrative prokaryotic gene finder tool which combines a variety of high-throughput data, including oriented RNA-Seq data, directly into the prediction process. This enables the automated prediction of coding sequences (CDSs), untranslated regions, transcription start sites (TSSs) and non-coding RNA (ncRNA, sense and antisense) genes. EuGene-P was used to comprehensively and accurately annotate the genome of the nitrogen-fixing bacterium Sinorhizobium meliloti strain 2011, leading to the prediction of 6308 CDSs as well as 1876 ncRNAs. Among them, 1280 appeared as antisense to a CDS, which supports recent findings that antisense transcription activity is widespread in bacteria. Moreover, 4077 TSSs upstream of protein-coding or non-coding genes were precisely mapped providing valuable data for the study of promoter regions. By looking for RpoE2-binding sites upstream of annotated TSSs, we were able to extend the S. meliloti RpoE2 regulon by ∼3-fold. Altogether, these observations demonstrate the power of EuGene-P to produce a reliable and high-resolution automatic annotation of prokaryotic genomes.
Common bean varieties demonstrate differential physiological and metabolic responses to the pathogenic fungus Sclerotinia sclerotiorum.

Plant physiology and metabolism are important components of a plant response to microbial pathogens. Physiological resistance of common bean (Phaseolus vulgaris L.) to the fungal pathogen Sclerotinia sclerotiorum has been established, but the mechanisms of resistance are largely unknown. Here, the physiological and metabolic responses of bean varieties that differ in physiological resistance to S. sclerotiorum are investigated. Upon infection, the resistant bean variety A195 had a unique physiological response that included reduced photosynthesis and maintaining a higher leaf surface pH during infection. Leaf metabolomics was performed on healthy tissue adjacent to the necrotic lesion at 16, 24, and 48 hr post inoculation, and 144 metabolites were detected that varied between A195 and Sacramento following infection. The metabolites that varied in leaves included amines/amino acids, organic acids, phytoalexins, and ureides. The metabolic pathways associated with resistance included amine metabolism, uriede-based nitrogen remobilization, antioxidant production, and bean-specific phytoalexin production. A second experiment was conducted in stems of 13 bean genotypes with varying resistance. Stem resistance was associated with phytoalexin production, but unlike leaf metabolism, lipid changes were associated with susceptibility. Taken together, the data supports a multifaceted, physiometabolic response of common bean to S. sclerotiorum that mediates resistance.
Topological Interference Management for K-User Downlink Massive MIMO Relay Network Channel

In this paper, we study the emergence of topological interference alignment and the characterizing features of a multi-user broadcast interference relay channel. We propose an alternative transmission strategy named the relay space-time interference alignment (R-STIA) technique, in which a K -user multiple-input-multiple-output (MIMO) interference channel has massive antennas at the transmitter and relay. Severe interference from unknown transmitters affects the downlink relay network channel and degrades the system performance. An additional (unintended) receiver is introduced in the proposed R-STIA technique to overcome the above problem, since it has the ability to decode the desired signals for the intended receiver by considering cooperation between the receivers. The additional receiver also helps in recovering and reconstructing the interference signals with limited channel state information at the relay (CSIR). The Alamouti space-time transmission technique and minimum mean square error (MMSE) linear precoder are also used in the proposed scheme to detect the presence of interference signals. Numerical results show that the proposed R-STIA technique achieves a better performance in terms of the bit error rate (BER) and sum-rate compared to the existing broadcast channel schemes.
Emergent cellular self-organization and mechanosensation initiate follicle pattern in the avian skin

Mechanics of follicle patterning in skin Studies of skin organogenesis have presupposed that a periodic molecular prepattern is responsible for the initiation of a periodic pattern of hair or feathers. To date, however, these initiating molecules have remained elusive. Using chicken skin as a model system, Shyer et al. found that the periodic spacing of feathers is triggered by mechanical rather than molecular events (see the Perspective by Grill). Furthermore, these mechanical events shape both the structure of prefeathers and their molecular identity. Science, this issue p. 811; see also p. 750 In developing chick skin, mechanical force establishes skin follicle patterning. The spacing of hair in mammals and feathers in birds is one of the most apparent morphological features of the skin. This pattern arises when uniform fields of progenitor cells diversify their molecular fate while adopting higher-order structure. Using the nascent skin of the developing chicken embryo as a model system, we find that morphological and molecular symmetries are simultaneously broken by an emergent process of cellular self-organization. The key initiators of heterogeneity are dermal progenitors, which spontaneously aggregate through contractility-driven cellular pulling. Concurrently, this dermal cell aggregation triggers the mechanosensitive activation of β-catenin in adjacent epidermal cells, initiating the follicle gene expression program. Taken together, this mechanism provides a means of integrating mechanical and molecular perspectives of organ formation.
Ureaplasma diversum Genome Provides New Insights about the Interaction of the Surface Molecules of This Bacterium with the Host

Whole genome sequencing and analyses of Ureaplasma diversum ATCC 49782 was undertaken as a step towards understanding U. diversum biology and pathogenicity. The complete genome showed 973,501 bp in a single circular chromosome, with 28.2% of G+C content. A total of 782 coding DNA sequences (CDSs), and 6 rRNA and 32 tRNA genes were predicted and annotated. The metabolic pathways are identical to other human ureaplasmas, including the production of ATP via hydrolysis of the urea. Genes related to pathogenicity, such as urease, phospholipase, hemolysin, and a Mycoplasma Ig binding protein (MIB)—Mycoplasma Ig protease (MIP) system were identified. More interestingly, a large number of genes (n = 40) encoding surface molecules were annotated in the genome (lipoproteins, multiple-banded antigen like protein, membrane nuclease lipoprotein and variable surface antigens lipoprotein). In addition, a gene encoding glycosyltransferase was also found. This enzyme has been associated with the production of capsule in mycoplasmas and ureaplasma. We then sought to detect the presence of a capsule in this organism. A polysaccharide capsule from 11 to 17 nm of U. diversum was observed trough electron microscopy and using specific dyes. This structure contained arabinose, xylose, mannose, galactose and glucose. In order to understand the inflammatory response against these surface molecules, we evaluated the response of murine macrophages J774 against viable and non-viable U. diversum. As with viable bacteria, non-viable bacteria were capable of promoting a significant inflammatory response by activation of Toll like receptor 2 (TLR2), indicating that surface molecules are important for the activation of inflammatory response. Furthermore, a cascade of genes related to the inflammasome pathway of macrophages was also up-regulated during infection with viable organisms when compared to non-infected cells. In conclusion, U. diversum has a typical ureaplasma genome and metabolism, and its surface molecules, including the identified capsular material, represent major components of the organism immunopathogenesis.
Credit risk assessment and the information content of financial ratios : a multi-country perspective

This paper revisits the problem of building a multicriteria additive value model for credit risk assessment, with a particular focus on quantitative criteria. The analysis deals with the information content of financial ratios collected from the European BACH-ESD database, covering aggregate firm data for seven countries – Austria, Belgium, France, Germany, Italy, Portugal and Spain – fifteen sectors and three size classes. A cross-sectional study is conducted employing non-parametric testing in order to look for similarities in the data, according to the multiple dimensions of the sample. Profitability, liquidity and leverage ratios exhibit different patterns of variation across countries, sectors and sizes, but the profitability indicators seem to have the greatest discriminating power, implying more specific benchmarks for credit risk assessment. It is also found that size and sector breakdowns are mostly relevant, while the country factor is somewhat less, for performance benchmarking. Moreover, the fact that the financial indicators show negligible differences across firms in many cases conveys a compelling argument for the accrued value, and central role, of qualitative information –market and management – in the decision making process, notably using a MCDA model.
EmotionLines: An Emotion Corpus of Multi-Party Conversations

Feeling emotion is a critical characteristic to distinguish people from machines. Among all the multi-modal resources for emotion detection, textual datasets are those containing the least additional information in addition to semantics, and hence are adopted widely for testing the developed systems. However, most of the textual emotional datasets consist of emotion labels of only individual words, sentences or documents, which makes it challenging to discuss the contextual flow of emotions. In this paper, we introduce EmotionLines, the first dataset with emotions labeling on all utterances in each dialogue only based on their textual content. Dialogues in EmotionLines are collected from Friends TV scripts and private Facebook messenger dialogues. Then one of seven emotions, six Ekman's basic emotions plus the neutral emotion, is labeled on each utterance by 5 Amazon MTurkers. A total of 29,245 utterances from 2,000 dialogues are labeled in EmotionLines. We also provide several strong baselines for emotion detection models on EmotionLines in this paper.
A New Calibration Method for Commercial RGB-D Sensors

Commercial RGB-D sensors such as Kinect and Structure Sensors have been widely used in the game industry, where geometric fidelity is not of utmost importance. For applications in which high quality 3D is required, i.e., 3D building models of centimeter-level accuracy, accurate and reliable calibrations of these sensors are required. This paper presents a new model for calibrating the depth measurements of RGB-D sensors based on the structured light concept. Additionally, a new automatic method is proposed for the calibration of all RGB-D parameters, including internal calibration parameters for all cameras, the baseline between the infrared and RGB cameras, and the depth error model. When compared with traditional calibration methods, this new model shows a significant improvement in depth precision for both near and far ranges.