Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystal structure of an archaeal Sm protein from Sulfolobus solfataricus

Introduction. Members of the Sm protein family share a common bipartite sequence motif called Sm domain, which consists of the Sm1 and Sm2 motifs separated by a loop of variable length. The Sm domain contains an N-terminal -helix and five strongly bent antiparallel -strands. Multiple sequence alignment of Sm1and Sm2-type proteins reveals the most conserved and highly conserved residues among the family (Fig. 1). In eukaryotes, Sm and Sm-like (Lsm) proteins associate with RNA to form the core domain of small nuclear ribonucleoprotein particles (snRNPs), which are involved in various RNA-processing events such as messenger RNA (mRNA) decapping and degradation, pre-mRNA splicing, and telomere replication. In snRNPs that are involved in pre-mRNA splicing, Sm proteins bind to the so-called Sm site, a U-rich, single-stranded region containing the consensus sequence PAU4–6GP, where P is any purine. Through database searches, Sm-related proteins were also identified in archaea and eubacteria. The function of Sm proteins in archaea is currently not clear. However, Archaeoglobus fulgidus Sm1and Sm2-type proteins (AF-Sm1 and AFSm2) have been shown to interact with ribonuclease (RNase) P RNA in vivo, which seems consistent with the earlier immunoprecipitation results of the yeast Lsm2–7 complex with pre-RNase P RNA. These findings suggest that archaeal Sm proteins may have a function in transfer RNA (tRNA) processing. Archaeal Sm proteins also exhibit similar oligomerization and RNA binding properties as their eukaryotic counterparts. Archaeal genomes encode at most three Sm-related proteins forming homoheptameric or hexameric complexes. Sm3-type proteins contain an additional C-terminal domain, which is highly conserved in the Sm3 subfamily. The crystal structure of AF-Sm1 complexed with oligo U5 represents the first high-resolution picture of binding of RNA to the archaeal Sm core. Here we report the X-ray structure of the Sulfolobus solfataricus Sm1-type protein (SS-Sm1) at 1.68 Å resolution. The SS-Sm1 structure forms a heptameric ring 68 Å in diameter with a central cavity of 14 Å. Both the monomer fold and the heptameric ring structure of SS-Sm1 are similar to that of other archaeal Sm proteins. The heptameric structure is maintained through interactions between 4and 5-strands of adjacent monomers. Band shift experiments indicate that SS-Sm1 binds to short oligo U stretches in vitro (data not shown). The SS-Sm1 heptamer shows a different charge distribution on the RNA binding side of the ring compared to the AF-Sm1 and Pyrococcus abyssi Sm1 (PA-Sm1) proteins.
Lossless compression of ECG signals

In this paper the authors study the compression techniques for electrocardiogram (ECG) signals based on Block Sorting Techniques. They introduce a new and faster block transformation than the Burrows and Wheeler Transformation (BWT), and later compare them for ECG data compression. They show that their algorithm yields better compression gain than the Burrows and Wheeler's algorithm (BWA), Gzip and the Shorten waveform coder for lossless ECG data compression.
Effect of Ionic Composition of Suspending Solution on Virus Adsorption by a Soil Column

The effect of various electrolytes on the adsorption of poliovirus was measured in 250-cm-long soil columns with ceramic samplers at different depths. Viruses suspended in deionized water moved much farther through the soil than those suspended in tap water, whereas movement in sewage water was intermediate. The salt content of the tap water and sewage water promoted virus adsorption, but evidently the organic compounds in sewage retarded adsorption. When viruses were suspended in chloride solutions of K+, Na+, Ca+, and Mg2+, virus adsorption increased as the cation concentration and valence increased. The depth of virus penetration was related to the ionic strength of the solutions. Virus penetration data for NO3−, SO42−, and H2PO4− salts of K+, Na+, and Ca2+ indicated that other anions were more effective than Cl− in promoting virus adsorption. Also, NH4+ was more effective than other cations in limiting the penetration depth of viruses. It seems that ions composed of radicals are more effective than ions composed of single atoms in promoting virus adsorption. Al3+ was the most effective ion in limiting virus penetration, probably owing to flocculation of the viruses. Adding AlCl3 concentrations to secondary sewage effluent to provide an Al3+ concentration of 0.1 mM reduced the virus penetration depth to 40 cm. These studies show that the ionic composition of the suspending solutions must be considered in predicting virus penetration depths, and it may be practical to add low concentrations of a flocculating agent such as AlCl3 to sewage water to limit virus movement through very porous soils.
Profitability and Capital Structure: An Empirical Study of French and Hungarian Wine Producers in 2004-2013

Abstract Background: Profitability of the Hungarian wine industry has been a focus of numerous research studies due to the centuries-old history and the recent changes. Objectives: The aim of the study is to analyse the capital structure of the Hungarian and the French wine industries and demonstrate the benefits of the usage of an international company database. Methods/Approach: First, the database and the applied methods are described and then the descriptive statistical analysis of the industry is presented. The two set hypotheses are aimed at testing the main contradiction between the pecking order and the trade-off theory, which is related to profitability and the usage of external funds. Results: The analysis examines the differences between the funding policies applied in the two countries. This was carried out by means of a discriminant analysis, which indicates the financing characteristics of French and Hungarian wine producers. In order to confirm the results of the discriminant analysis we conducted a cluster analysis on the same sample where 3 out of 4 variables proved to be significant in classifying the two groups. Conclusions: The main conclusion of the study is that the behaviour of the factors explaining the development of the capital structure differs significantly in the two examined countries.
Interobserver Reliability of a “Standardized Psychiatric Examination” (SPE) for Case Ascertainment (DSM‐III)

The authors describe the Standardized Psychiatric Examination (SPE), a new method for conducting psychiatric examinations in both clinical and research settings that preserves the clinical method. The SPE provides a consistent replicable format for eliciting and recording psychiatric history, signs, and symptoms without perturbing the patient-clinician interaction. By means of the SPE, the clinician can formulate diagnoses using DSM-III or ICD-9 criteria and yet generate CATEGO profiles derived from the Present State Examination, 9th edition. Psychiatrists using the SPE demonstrated high interrater reliability in ascertaining individual psychopathological symptoms (Kappa range, 0.55 to 1.0) and in making DSM-III diagnoses (Kappa range, 0.79 to 1.0) among a sample of study subjects (N = 43) drawn from both a psychiatric inpatient population and a large community sample of nonpatients from the Epidemiological Catchment Area (ECA) study. The implications of the SPE for clinical practice and for research are discussed.
Pediatric non-alcoholic steatohepatitis: the first report on the ultrastructure of hepatocyte mitochondria.

AIM To investigate the ultrastructure of abnormal hepatocyte mitochondria, including their cellular and hepatic zonal distribution, in bioptates in pediatric non-alcoholic steatohepatitis (NASH). METHODS Ultrastructural investigations were conducted on biopsy liver specimens obtained from 10 children (6 boys and 4 girls) aged 2-14 years with previously clinicopathologically diagnosed NASH. The disease was diagnosed if liver biopsy revealed steatosis, inflammation, ballooned hepatocytes, Mallory hyaline, or focal necrosis, varying degrees of fibrosis in the absence of clinical, serological, or histological findings of infectious liver diseases, autoimmune hepatitis, metabolic liver diseases, or celiac disease. For ultrastructural analysis, fresh small liver blocks (1 mm(3) volume) were fixed in a solution containing 2% paraformaldehyde and 2.5% glutaraldehyde in 0.1 mol/L cacodylate buffer. The specimens were postfixed in osmium tetroxide, subsequently dehydrated through a graded series of ethanols and propylene oxide, and embedded in Epon 812. The material was sectioned on a Reichert ultramicrotome to obtain semithin sections, which were stained with methylene blue in sodium borate. Ultrathin sections were contrasted with uranyl acetate and lead citrate, and examined using an Opton EM 900 transmission electron microscope. RESULTS Ultrastructural analysis of bioptates obtained from children with non-alcoholic steatohepatitis revealed characteristic repetitive mitochondrial abnormalities within hepatocytes; mainly mitochondrial polymorphisms such as megamitochondria, loss of mitochondrial cristae, and the presence of linear crystalline inclusions within the mitochondrial matrix of an increased electron density. The crystalline inclusions were particularly evident within megamitochondria (MMC), which seemed to be distributed randomly both within the hepatic parenchymal cell and the zones of hepatic lobule, without special variations in abundance. The inclusions appeared as bundles viewed longitudinally, or as an evenly spaced matrix in cross section, and frequently caused mitochondrial deformation. The average diameter of these linear structures was 10 nm and the average space between them 20 nm. Sometimes enlarged intramitochondrial granules were seen in their vicinity. Foamy cytoplasm of hepatocytes was found, resulting from the proliferation of smooth endoplasmic reticulum and glycogen accumulation. The perivascular space of Disse was frequently dilated, and contained transitional hepatic stellate cells, as well as mature and/or newly forming collagen fiber bundles. CONCLUSION Marked ultrastructural abnormalities observed in hepatocyte mitochondria, especially their polymorphism in the form of MMC and loss of mitochondrial cristae, accompanied by foamy cytoplasm, clearly indicate a major role of these organelles in the morphogenesis of pediatric NASH. Our findings seem to prove the high effectiveness of electron microscopy in the diagnosis of the disease.
Herpes zoster in Hodgkin's disease. Clinical, histologic, and immunologic correlations

In 163 consecutively irradiated patients with Hodgkin's disease, Stage I–III, herpes zoster subsequently occurred in 31 (19%). The incidence of zoster was increased in patients with mixed cellularity histology, Stage III disease, and in those patients with early stages treated with extensive irradiation. The majority of patients developed shingles within 6 months of primary treatment, a result suggestive of immunosuppression by lymphoma and/or irradiation, and was not associated with a high incidence of relapse. In those whose zoster occurred later than 6 months following primary therapy, a high incidence of lymphomatous recurrence (10/13) was noted, making herpes zoster an important prognosticator only in these selected individuals.
Infinite-Dimensional Dynamical Systems: An Introduction to Dissipative Parabolic PDEs and the Theory of Global Attractors

Part I. Functional Analysis: 1. Banach and Hilbert spaces 2. Ordinary differential equations 3. Linear operators 4. Dual spaces 5. Sobolev spaces Part II. Existence and Uniqueness Theory: 6. The Laplacian 7. Weak solutions of linear parabolic equations 8. Nonlinear reaction-diffusion equations 9. The Navier-Stokes equations existence and uniqueness Part II. Finite-Dimensional Global Attractors: 10. The global attractor existence and general properties 11. The global attractor for reaction-diffusion equations 12. The global attractor for the Navier-Stokes equations 13. Finite-dimensional attractors: theory and examples Part III. Finite-Dimensional Dynamics: 14. Finite-dimensional dynamics I, the squeezing property: determining modes 15. Finite-dimensional dynamics II, The stong squeezing property: inertial manifolds 16. Finite-dimensional dynamics III, a direct approach 17. The Kuramoto-Sivashinsky equation Appendix A. Sobolev spaces of periodic functions Appendix B. Bounding the fractal dimension using the decay of volume elements.
Implementing a diabetes prevention program in a rural African-American church.

OBJECTIVES The purpose of this study was to determine the feasibility of implementing a diabetes prevention program (DPP) in a rural African-American church. METHODS A six-session DPP, modeled after the successful National Institutes of Health (NIH) DPP, was implemented in a rural African-American church. Adult members of the church identified as high risk for diabetes, based on results of a risk questionnaire, were screened with a fasting glucose. Persons with prediabetes, a fasting glucose of 100-125 mg/dL, participated in the six-session, Lifestyle Balance Church DPP. The primary outcomes were attendance rates and changes in fasting glucose, weight and body mass index measured at baseline, six- and 12-month follow-up. RESULTS Ninety-nine adult church members were screened for diabetes risk. Eleven had impaired fasting glucose. Ten of 11 participated in the six-session intervention, for an attendance rate of 78%. After the intervention and 12-month follow-up, there was a mean weight loss of 7.9 lbs and 10.6 lbs, respectively. CONCLUSIONS This pilot project suggests that a modified six-session DPP can be translated to a group format and successfully implemented in a church setting. Further randomized studies are needed to determine the effectiveness of such an intervention.
Maintenance of normal length improves protein balance and energy status in isolated rat skeletal muscles.

To clarify how muscle length or tension influences protein balance, we examined rates of protein synthesis and degradation in rat muscles incubated at different lengths. In soleus and extensor digitorum longus, protein degradation was lowest at resting length in situ (Lo), where the muscles are under slight tension. Muscles that were unrestrained shortened spontaneously and showed 25-45% greater net protein breakdown than muscles fixed at Lo. Protein synthesis did not differ in the two groups initially, but by 4 or 6 h was 25% greater in muscles at Lo. Maintenance of Lo improved overall protein balance largely through the reduction in proteolysis. In addition, muscles at Lo maintained high levels of ATP and phosphocreatine for 6 h, whereas the unrestrained muscles lost about half their energy stores. The acceleration of proteolysis in the shortened muscle appears independent of prostaglandin E2. However, the acceleration of protein breakdown in the unrestrained muscles could be prevented with inhibitors of thiol proteases (e.g., Ep-475 or leupeptin) or by incubation in Ca2+-free medium or with dantrolene (an inhibitor of Ca2+ release from sarcoplasmic reticulum). These treatments did not reduce the low level of proteolysis in muscles at Lo. Thus, if muscles are allowed to shorten in vitro, proteolysis is activated by a Ca2+-dependent mechanism, involving thiol proteases.
Redacted Disclosure

In this paper we investigate a firm's decision to redact proprietary information from its material contract filings. Information redaction results when the Security and Exchange Commission (SEC) grants a firm's request to withhold information from investors in its material contract filings, presumably because the information is proprietary. We hypothesize that when firms redact information, measures of adverse selection deteriorate. That is, the redaction of proprietary information from material contracts should be associated with: a larger adverse selection component of the bid-ask spread; reductions in market depth; and lower market turnover. In addition, we conjecture that the decision to redact depends on whether the firm plans on raising capital, the competitiveness of the firm's industry, and the performance of the firm. Overall the results of our analysis generally support our predictions. We find that when firms redact information, contemporaneous measures of the adverse selection component of the bid-ask spread rise, and market depth and share turnover deteriorate; this suggests an increase in adverse selection. We also find firms are less likely to redact when they issue long term debt, and are more likely to redact when they are in a competitive industry or experience losses.
Lacustrine systems of Clearwater Mesa (James Ross Island, north-eastern Antarctic Peninsula): geomorphological setting and limnological characterization

Abstract Lentic freshwater habitats are important centres of biodiversity within the infrequent ice-free oases across Antarctica. Given imminent climate changes, it is crucial to catalogue these habitats in order to provide baseline data for future monitoring and biological surveys. The lacustrine systems of Clearwater Mesa, a previously unexplored part of James Ross Island, north-eastern Antarctic Peninsula, are described here. We conducted basic geomorphological and limnological surveys over three Antarctic summers (2009–16) to characterize landscape evolution, infer the origin of lake basins and assess the variability in their water chemistry. Stable shallow lakes, formed in depressions between lava tumuli following the last deglaciation, were found to dominate the volcanic mesa, although several peripheral lakes in ice-proximal settings appear to have formed recently as a result of post-Neoglacial ice recession. We found large heterogeneity in conductivity (~10–7000 μS cm−1), despite the lithologically uniform substrate. This variability was shown to be related to lake type, basin type (open vs closed), meltwater source and proximity to the coast. Inter-annual differences were attributed to changes in sea spray influx and snow accumulation driven by variable weather conditions. Overall, the ion composition of lakes suggested that sea spray was the dominant source of ions, followed by the weathering of bedrock.
Gene-gene and gene - clinical factors interaction in acute myocardial infarction: a new detailed risk chart.

AIMS The complex pathogenesis of acute myocardial infarction (AMI) implicates phenotypic and genetic heterogeneity. In this pilot case-control study single nucleotide polymorphism (SNP) in several inflammatory genes, such as interleukin (IL)-1beta, IL-6, IL-10, alpha-1-antichymotrypsin (ACT), tumor necrosis factor alpha (TNF)-alpha and interferon gamma (IFN)-gamma genes along with SNPs of genes regulating vascular functions (vascular endothelial growth factor; VEGF) and cholesterol synthesis (hydroxy-methyl-glutaryl CoA reductase; HMGCR) were investigated. METHODS Patients were genotyped with RT-PCR technique and data were analyzed with a new mathematical algorithm named Auto Contractive Map. RESULTS The Auto Contractive Map (AutoCM), was applied in AMI patients with the aim to detect and evaluate the relationships among genetic factors, clinical variables and classical risk factors. Genes were selected because their strong regulatory effect on inflammation and SNP in these gene were located in the promoter region. In the connectivity map generated by AutoCM a group of variables was directly linked with the AMI status; these were: gender (male), early age at onset (50-65 years), HMGCR gene (CC wild type genotype), IL-1betaCT, IL-6 GG and VEGF CC genotypes. This direct link suggested a possible pathogenetic association with AMI. Other genetic, clinical and phenotypic variables were associated to the disease under a statistically defined hierarchy showed in the new connectivity map generated by AutoCM. CONCLUSION These analyses suggested that genotypes of few inflammatory genes, a SNP in HMGCR gene, middle age, gender, low HDL and diabetes were very informative variables to predict the risk of AMI.
Relationships between the histological grade of cutaneous mast cell tumours in dogs, their survival and the efficacy of surgical resection

The histological grade of 340 cutaneous mast cell tumours derived from 280 dogs was determined by an established histological grading system; 87 of the tumours (26 per cent) were well differentiated, 199 (59 per cent) were intermediately differentiated and 54 (16 per cent) were poorly differentiated. The one-year survival rates for the dogs with tumours of these three grades were significantly different (P=0-0001), being 100 per cent, 92 per cent and 46 per cent, respectively. The median survival time for the dogs with poorly differentiated tumours was 278 days, significantly shorter than that for the dogs with either intermediately or well-differentiated tumours, which were both over 1300 days. Regrowth of the tumours was identified in 10 (19 per cent) of the dogs with poorly differentiated tumours, 12 (6 per cent) of the dogs with intermediately differentiated tumours and one of the dogs with well-differentiated tumours; only three of the tumours which regrew had initially had complete margins. The results suggest that wide surgical margins are not a prerequisite for a successful long-term outcome in dogs with well-differentiated cutaneous mast cell tumours.
Effects of environmental factors on the population genetic diversity in the Chinese endangered and endemic medicinal plant Notopterygium incisum

Correlation between environmental factors and genetic diversity of 23 populations throughout the distribution range of Notopterygium incisum was examined using nuclear internal transcribed spacer gene fragment (ITS) and chloroplast DNA (cpDNA) rpl20-rps12 intergenic spacer. A total of 635 nucleotides of ITS were sequenced from 343 individuals. 26 haplotypes were defined by 26 variable sites. A total of 772 nucleotides of rpl20-rps12were sequenced from 253 individuals. 30 haplotypes were defined by 26 variable sites. Based on cpDNA rpl20-rps12 region, the correlations between the haplotype diversity, nucleotide diversity and environmental factors were all non-significant. However, based on ITS sequences, a significant positive relationship was observed between haplotype diversity and ammonium nitrogen, annual average rainfall and elevation, as well as between nucleotide diversity and ammonium nitrogen and annual average rainfall. Synchronously, significant negative relationships were observed between haplotype diversity and latitude and variation coefficient of rainfall, as well as between nucleotide diversity and latitude. Latitude, elevation, annual average rainfall, variation coefficient of rainfall and ammonium nitrogen were the dominant factors that influenced the genetic diversity of N. incisum. The genetic diversity of N. incisum tended to increase in the environment with lower latitude, more rainfall, more ammonium nitrogen, higher elevation and a more stable climate.
Attitudes and Experiences With Older Adults: A Case for Service Learning for Undergraduates

The current study examined whether relationship quality with older adults currently and in childhood, as well as experience with older adults, was associated with biases toward older adults and interest in working with older adults as a possible career area. The authors sampled undergraduate students (N = 753, M = 18.97 years, SD = 2.11 years) from a Northern California university. In hierarchical regression analyses, higher perceived quality of relationships with older adult family members, higher perceived social support, and lower perceived conflict from relationships with older adults was significantly associated with positive attitudes toward older adults. Interest in working with older adults was significantly associated with taking courses in aging, providing care to an older adult, and volunteering with older adults. These results suggest that positive relationships with older adults are useful in reducing biases, though student interactions with older adults are key in helping to promote interest in working with older adults.