Miracle-dz/UniFAR-FTUs huggingface dataset:
Numerical Models of Pore Pressure and Stress Changes Along Basement Faults Due to Wastewater Injection: Applications to the 2014 Milan, Kansas Earthquake

We have developed groundwater flow models to explore the possible relationship between wastewater injection and the 12 November 2014 Mw 4.8 Milan, Kansas earthquake. We calculate pore pressure increases in the uppermost crust using a suite of models in which hydraulic properties of the Arbuckle Formation and the Milan earthquake fault zone, the Milan earthquake hypocenter depth, and fault zone geometry are varied. Given pre‐earthquake injection volumes and reasonable hydrogeologic properties, significantly increasing pore pressure at the Milan hypocenter requires that most flow occur through a conductive channel (i.e., the lower Arbuckle and the fault zone) rather than a conductive 3‐D volume. For a range of reasonable lower Arbuckle and fault zone hydraulic parameters, the modeled pore pressure increase at the Milan hypocenter exceeds a minimum triggering threshold of 0.01 MPa at the time of the earthquake. Critical factors include injection into the base of the Arbuckle Formation and proximity of the injection point to a narrow fault damage zone or conductive fracture in the pre‐Cambrian basement with a hydraulic diffusivity of about 3–30 m2/s. The maximum pore pressure increase we obtain at the Milan hypocenter before the earthquake is 0.06 MPa. This suggests that the Milan earthquake occurred on a fault segment that was critically stressed prior to significant wastewater injection in the area. Given continued wastewater injection into the upper Arbuckle in the Milan region, assessment of the middle Arbuckle as a hydraulic barrier remains an important research priority.
International Journal of Molecular Sciences the Fungal Mycobiome and Its Interaction with Gut Bacteria in the Host

The advent of sequencing technology has endowed us with the capacity to study microbes constituting the human commensal community that were previously non-culturable. Much of the initial works have concentrated on the bacterial flora constituting the gut microbiome, since specimens are readily accessible in health and disease. Less, however, is understood of the " silent population " —the fungal species, also known as the mycobiome. Living in symbiosis with bacteria as commensals in our body, it is perceivable that the mycobiome exerts an inadvertent influence on the microbiome. We review here the recent knowledge gained from study of the interaction between the mycobiome and microbiome in health and disease susceptibility, immunity, and consequences from antimicrobial treatment.
Dual Regulation of a Chimeric Plant Serine/Threonine Kinase by Calcium and Calcium/Calmodulin (*)

A chimeric Ca/calmodulin-dependent protein kinase (CCaMK) gene characterized by a catalytic domain, a calmodulin-binding domain, and a neural visinin-like Ca-binding domain was recently cloned from plants (Patil, S., Takezawa, D., and Poovaiah, B. W.(1995) Proc. Natl. Acad. Sci. U. S. A. 92, 4797-4801). The Escherichia coli-expressed CCaMK phosphorylates various protein and peptide substrates in a Ca/calmodulin-dependent manner. The calmodulin-binding region of CCaMK has similarity to the calmodulin-binding region of the α-subunit of multifunctional Ca/calmodulin-dependent protein kinase (CaMKII). CCaMK exhibits basal autophosphorylation at the threonine residue(s) (0.098 mol of P/mol) that is stimulated 3.4-fold by Ca (0.339 mol of P/mol), while calmodulin inhibits Ca-stimulated autophosphorylation to the basal level. A deletion mutant lacking the visinin-like domain did not show Ca-stimulated autophosphorylation activity but retained Ca/calmodulin-dependent protein kinase activity at a reduced level. Ca-dependent mobility shift assays using E. coli-expressed protein from residues 358-520 revealed that Ca binds to the visinin-like domain. Studies with site-directed mutants of the visinin-like domain indicated that EF-hands II and III are crucial for Ca-induced conformational changes in the visinin-like domain. Autophosphorylation of CCaMK increases Ca/calmodulin-dependent protein kinase activity by about 5-fold, whereas it did not affect its Ca-independent activity. This report provides evidence for the existence of a protein kinase in plants that is modulated by Ca and Ca/calmodulin. The presence of a visinin-like Ca-binding domain in CCaMK adds an additional Ca-sensing mechanism not previously known to exist in the Ca/calmodulin-mediated signaling cascade in plants.
In STI interventions, size matters

The investigator must juggle sample size and effect size to produce a study with a priori credibility and ex post facto utility Sample size and effect size are interrelated parameters that have been given insufficient consideration in analyses of two major outcome measures in the field of sexually transmitted infections (STI) prevention—STI incidence and condom use. Their inter-relation highlights two critical features of interventions—statistical significance and epidemiological importance. Though there are a myriad variations on the theme of sample size, the calculation usually depends on four parameters. The investigator must designate an acceptable level for type I error (the probability of falsely rejecting a null hypothesis); type II error (the probability of failing to reject a false null hypothesis); variance (the amount of dispersion in the result that would be acceptable); and the effect size (the size of the detectable difference that is deemed important). Cynics will be quick to point out that sample size depends on only one parameter—the amount of money available for the study—but even if true, researchers must still deal with the consequences of the terms so dictated. Because type I and type II error are often set by convention, the investigator must juggle sample size and effect size to produce a study with a priori credibility and ex post facto utility. An important difference among studies is whether or not they are measuring continuous or dichotomous outcomes. In the former case, effect size can be assessed by transformation into units of standard error, and a test of statistical significance is straightforward. Yet, continuous outcomes are rare in STI research. Incidence of STIs is inherently a dichotomous outcome and condom use is typically dichotomised, based on the assumption that consistent (that is, 100%) use is protective against infection whereas lower rates of use are not protective. …
Contrasting Controlled Vocabulary and Tagging: Experts Choose the Right Names to Label the Wrong Things

Social cataloging sites---tagging systems where users tag books---provide us with a rare opportunity to contrast tags to other information organization systems. We contrast tags to a controlled vocabulary, the Library of Congress Subject Headings, which has been developed over several decades. We find that many of the keywords designated by tags and LCSH are similar or the same, but that usage of keywords by annotators is quite different.
Selecting Native Arbuscular Mycorrhizal Fungi to Promote Cassava Growth and Increase Yield under Field Conditions

The use of arbuscular mycorrhizal fungal (AMF) inoculation in sustainable agriculture is now widespread worldwide. Although the use of inoculants consisting of native AMF is highly recommended as an alternative to commercial ones, there is no strategy to allow the selection of efficient fungal species from natural communities. The objective of this study was (i) to select efficient native AMF species (ii) evaluate their impact on nematode and water stresses, and (iii) evaluate their impact on cassava yield, an important food security crop in tropical and subtropical regions. Firstly, native AMF communities associated with cassava rhizospheres in fields were collected from different areas and 7 AMF species were selected, based upon their ubiquity and abundance. Using these criteria, two morphotypes (LBVM01 and LBVM02) out of the seven AMF species selected were persistently dominant when cassava was used as a trap plant. LBVM01 and LBVM02 were identified as Acaulospora colombiana (most abundant) and Ambispora appendicula, respectively, after phylogenetic analyses of LSU-ITS-SSU PCR amplified products. Secondly, the potential of these two native AMF species to promote growth and enhance tolerance to root-knot nematode and water stresses of cassava (Yavo variety) was evaluated using single and dual inoculation in greenhouse conditions. Of the two AMF species, it was shown that A. colombiana significantly improved the growth of the cassava and enhanced tolerance to water stress. However, both A. colombiana and A. appendicula conferred bioprotective effects to cassava plants against the nematode Meloidogyne spp. , ranging from resistance (suppression or reduction of the nematode reproduction) or tolerance (low or no suppression in cassava growth). Thirdly, the potential of these selected native AMF to improve cassava growth and yield was evaluated under field conditions, compared to a commercial inoculant. In these conditions, the A. colombiana single inoculation and the dual inoculation significantly improved cassava yield compared to the commercial inoculant. This is the first report on native AMF species exhibiting multiple benefits for cassava crop productivity, namely improved plant growth and yield, water stress tolerance and nematode resistance.
Genetic and epigenetic architecture of sex-biased expression in the jewel wasps Nasonia vitripennis and giraulti

Significance This paper provides a comprehensive analysis of sex differential gene expression in haplodiploid jewel wasps. Between two closely related species, 75% of genes display differential expression, despite males having half the genetic complement of females, with no sex chromosomes. These differences are not directly mediated by sex-specific methylation because almost no sex differences in methylation were observed. Genes with sex-specific expression show low frequency of methylation. However, the majority of female-biased genes are methylated (in both sexes), whereas male-biased ones are mostly nonmethylated in either sex. We conclude that female-biased genes are more likely to be recruited from conserved methylated genes over evolutionary time, whereas most male-biased genes are from genes after recent duplication events that are not methylated. There is extraordinary diversity in sexual dimorphism (SD) among animals, but little is known about its epigenetic basis. To study the epigenetic architecture of SD in a haplodiploid system, we performed RNA-seq and whole-genome bisulfite sequencing of adult females and males from two closely related parasitoid wasps, Nasonia vitripennis and Nasonia giraulti. More than 75% of expressed genes displayed significantly sex-biased expression. As a consequence, expression profiles are more similar between species within each sex than between sexes within each species. Furthermore, extremely male- and female-biased genes are enriched for totally different functional categories: male-biased genes for key enzymes in sex-pheromone synthesis and female-biased genes for genes involved in epigenetic regulation of gene expression. Remarkably, just 70 highly expressed, extremely male-biased genes account for 10% of all transcripts in adult males. Unlike expression profiles, DNA methylomes are highly similar between sexes within species, with no consistent sex differences in methylation found. Therefore, methylation changes cannot explain the extensive level of sex-biased gene expression observed. Female-biased genes have smaller sequence divergence between species, higher conservation to other hymenopterans, and a broader expression range across development. Overall, female-biased genes have been recruited from genes with more conserved and broadly expressing “house-keeping” functions, whereas male-biased genes are more recently evolved and are predominately testis specific. In summary, Nasonia accomplish a striking degree of sex-biased expression without sex chromosomes or epigenetic differences in methylation. We propose that methylation provides a general signal for constitutive gene expression, whereas other sex-specific signals cause sex-biased gene expression.
A long-term retrospective study of young women with essential thrombocythemia.

OBJECTIVE To describe presenting clinical manifestations, long-term disease complications, prognostic indicators, and outcome of pregnancy for women younger than 50 years with essential thrombocythemia. PATIENTS AND METHODS We retrospectively reviewed the records of all patients with essential thrombocythemia evaluated at Mayo Clinic, Rochester, Minn, between 1969 and 1991 and identified 74 young women (median age, 35 years; range, 18-48 years) with essential thrombocythemia. The diagnosis was based on previously established criteria. Median follow-up was 9.2 years (range, 0.2-26.2 years). RESULTS Overall survival was similar to that of an age- and sex-matched control population. Thrombotic events (except superficial thrombophlebitis) occurred at and after diagnosis in 11 patients (15%) and 13 patients (18%), respectively. A history of thrombosis at diagnosis was significantly associated with recurrent thrombosis (P = .03). A platelet count higher than 1500 x 10(9)/L at diagnosis was significantly associated with gastrointestinal tract bleeding and subsequent development of venous (but not arterial) thrombosis (P = .04). Major hemorrhagic events occurred in only 3 patients (4%) after diagnosis. Only 1 patient developed acute leukemia. Thirty-four pregnancies occurred in 18 patients. Of these, 17 (50%) resulted in live births. Of the 17 patients with unsuccessful pregnancies, 14 had spontaneous abortions, 1 had an ectopic pregnancy, and 2 had elective abortions. Preconception platelet count, thrombotic history, or specific therapy was not useful in predicting pregnancy outcome. CONCLUSION Young women with essential thrombocythemia can expect long survival with a low incidence of life-threatening thrombohemorrhagic complications or acute leukemia. There is an increased incidence of first-trimester miscarriages that may not be influenced by specific therapy.
Carotid Sinus Baroreceptor Reflex Control of Respiration

We have studied the effect of the carotid sinus baroreceptor reflex on respiration in 10 vagotomized, spontaneously breathing, pentobarbital anesthetized dogs. The carotid body chemoreceptor reflex response was eliminated by surgically excluding the carotid bodies from the carotid sinus baroreceptor area. Steady state frequency, tidal volume, and minute ventilation were measured after 25 mm Hg step changes in intrasinus pressure between 50 and 200 mm Hg. Over this range, the step decreases in intrasinus pressure caused concomitant increases in mean arterial pressure from 86 to 182 mm Hg. All of the respiratory response curves were sigmoidal in shape. Decreasing intrasinus pressure from 200 to 50 mm Hg caused respiratory frequency to increase from 4.8 to 9.7/min, and tidal volume to decrease from 704 to 515 ml. The calculated total ventilation, however, increased from 3180 to 4530 ml/min. The time of inspiration decreased from 3.7 to 2.4 seconds, and the time of expiration decreased from 9.8 to 4.1 seconds. These ventilatory responses are shown to be baroreceptor reflex mediated, and not secondary to changes in arterial pressure. These findings indicate that not only does the carotid sinus baroreceptor reflex control arterial pressure, but it also simultaneously influences ventilation, through changes in both respiratory frequency and tidal volume.
A real-time learning algorithm for a multilayered neural network based on the extended Kalman filter

The extended Kalman filter (EKF) is well known as a state estimation method for a nonlinear system, and can be used as a parameter estimation method by augmenting the state with unknown parameters. A multilayered neural network is a nonlinear system having a layered structure, and its learning algorithm is regarded as parameter estimation for such a non- linear system. In this paper, a new real-time learning algorithm for a mul- tilayered neural network is derived from the EKF. Since this EKF-based learning algorithm approximately gives the mini- mum variance estimate of the linkweights, the convergence performance is improved in comparison with the backwards error propagation algorithm using the steepest descent tech- niques. Furthermore, tuning parameters which crucially gov- ern the convergence properties are not included, which makes its application easier. Simulation results for the XOR and par- ity problems are provided.
Amplified in Breast Cancer 1 in Human Epidermal Growth Factor Receptor–Positive Tumors of Tamoxifen-Treated Breast Cancer Patients

Purpose: Amplified in breast cancer 1 (AIB1) is a member of the p160/steroid receptor coactivators family and is involved in estrogen-dependent gene transcription by reducing the antagonistic activity of tamoxifen-bound estrogen receptor-α (ER-α). The present study was carried out to test the hypothesis that AIB1 protein expression and/or gene amplification mediates tamoxifen resistance in breast cancer. Experimental Design: Immunohistochemistry using AIB1 antibody and fluorescence in situ hybridization using probes specific for AIB1 and chromosome 20 was done on 402 ER-α–positive tamoxifen-treated breast cancers. Results: AIB1 overexpression was not associated with relapse during treatment with tamoxifen. In contrast, high AIB1 expression in patients with human epidermal growth factor receptor (HER) 2– and HER3-overexpressing tumors or tumors expressing one or more of HER1, HER2, or HER3 (HER1-3 positive) was associated with an increased risk of relapse on tamoxifen [hazard ratio, 2.20; 95% confidence interval, 1.07-3.52 (P = 0.0416); hazard ratio, 2.42; 95% confidence interval, 1.32-4.43 (P = 0.0030), respectively]. AIB1 gene amplification was observed in 18 of 362 (5%) patients. High AIB1 gene copy number had no effect on overall or disease-free survival. Conclusions: Data presented here support a role for AIB1 expression on relapse during tamoxifen treatment in hormone-responsive HER-expressing clinical breast cancers and support clinical evidence, suggesting a cross-talk between ER-α and growth factor receptor pathways through changes in expression of specific coactivator proteins, such as AIB1. This study highlights the potential that tumor profiling, using multiple markers of treatment response, may improve patient selection for endocrine treatment, such as tamoxifen or aromatase inhibitors.
Effects and Tolerance of Silymarin (Milk Thistle) in Chronic Hepatitis C Virus Infection Patients: A Meta-Analysis of Randomized Controlled Trials

Objective. This study aimed to evaluate the efficacy and safety of silymarin on chronic hepatitis C virus- (HCV-) infected patients. Methods. Randomized controlled trials (RCTs) of silymarin in chronic HCV-infected patients up to April 1, 2014 were systematically identified in PubMed, Ovid, Web of Science, and Cochrane Library databases. Results. A total of 222 and 167 patients in five RCTs were randomly treated with silymarin (or intravenous silibinin) and placebo, respectively. Serum HCV RNA relatively decreased in patients treated with silymarin compared with those administered with placebo, but no significance was found (P = 0.09). Meta-analysis of patients orally treated with silymarin indicated that the changes of HCV RNA are similar in the two groups (P = 0.19). The effect on alanine aminotransferase (ALT) of oral silymarin is not different from that of placebo (P = 0.45). Improvements in quality-of-life (Short Form-36) in both silymarin and placebo recipients were impressive but relatively identical (P = 0.09). Conclusion. Silymarin is well tolerated in chronic HCV-infected patients. However, no evidence of salutary effects of oral silymarin has yet been reported based on intermediate endpoints (ALT and HCV RNA) in this population. Moreover, intravenous administration of silymarin should be further studied.
Hardness of routing with congestion in directed graphs

Given as input a directed graph on n vertices and a set ofsource-destination pairs, we study the problem of routing themaximum possible number of source-destination pairs on paths, suchthat at most c(N) paths go through any edge. We show that theproblem is hard to approximate within an NΩ(1/c(N)) factoreven when we compare to the optimal solution that routes pairs onedge-disjoint paths, assuming NP doesn't have NO(log logN)-time randomized algorithms. Here the congestion c(N) can beany function in the range 1 ≤ c(N) ≤ α log N/log log N for some absolute constant α > 0. The hardness result is in the right ballpark since a factor NO(1/c(N)) approximation algorithm is known for this problem, viarounding a natural multicommodity-flow relaxation. We also give asimple integrality gap construction that shows that themulticommodity-flow relaxation has an integrality gap of NΩ(1/c) for c ranging from 1 to Θ((log n)/(log log n)). A solution to the routing problem involves selecting which pairs tobe routed and what paths to assign to each routed pair. Two naturalrestrictions can be placed on input instances to eliminate one ofthese aspects of the problem complexity. The first restriction is toconsider instances with perfect completeness; an optimalsolution is able to route all pairs with congestion 1 in suchinstances. The second restriction to consider is the uniquepaths property where each source-destination pair has a unique pathconnecting it in the instance. An important aspect of our result isthat it holds on instances with any one of these tworestrictions. Our hardness construction with the perfectcompleteness restriction allows us to conclude that the directedcongestion minimization problem, where the goal is to route allpairs with minimum congestion, is hard to approximate to within afactor of Ω(log N/log log N). On the other hand, thehardness construction with unique paths property allows us toconclude an NΩ(1/c) inapproximability bound also for theall-or-nothing flow problem. This is in a sharp contrast to theundirected setting where the all-or-nothing flow problem is known tobe approximable to within a poly-logarithmic factor.
Human Papillomavirus 16 / 18 E 6 Oncoprotein Is Expressed in Lung Cancer and Related with p 53 Inactivation

Inactivation of p53 by human papillomavirus 16/18 E6 plays a crucial role in cervical tumorigenesis. To investigate the involvement of HPV16/18 in lung tumorigenesis, the association between HPV16 or HPV18 E6 and p53 protein expression in 122 lung tumors was evaluated by immunohistochemistry, and data showed that HPV16/18 E6 expression correlated inversely with p53 expression, which was further confirmed by tissue in situ immunostaining. Real-time reverse transcription-PCR analysis indicated that E6-positive tumors had lower p21 and mdm2 mRNA levels than E6-negative tumors. To elucidate the role of E6 in p53 inactivation, we successfully established lung adenocarcinoma cell lines with or without HPV16 infection from patients’ pleural effusions. Western blotting showed that E6 protein was indeed expressed in HPV16-infected cells and a lower level of p53 protein was observed in E6-positive cells compared with E6-negative cells. Moreover, the levels of p21 and mdm2 mRNA in E6positive cells were lower than in E6-negative cells. The interaction of E6 with p53 protein was revealed by immunoprecipitation assay showing that p53 could be inactivated by E6 protein. Conversely, p53 proteins and p21 and mdm2 mRNA expressions were restored in E6-knockdown cells by RNA interference compared with control cells. These results reveal that HPV16/18 E6 may be partially involved in p53 inactivation to down-regulate p21 and mdm2 transcription. In conclusion, HPV16/18 E6 is indeed expressed in HPV DNA–positive lung tumors and is involved in p53 inactivation to contributing to HPV-mediated lung tumorigenesis. [Cancer Res 2007;67(22):10686–93]