Miracle-dz/UniFAR-FTUs huggingface dataset:
Potential application of carbonic anhydrase activity in bioassay and biomarker studies

Carbonic anhydrase (CA) (EC 4.2.1.1), a ubiquitous enzyme in bacteria, plant, and animal kingdoms, catalyses the reversible hydration of CO2 to produce H+ and using zinc as cofactor. CA plays a fundamental role in a number of physiological processes, such as respiration, ionic transport, acid–base regulation, and calcification. The aim of the present work was to investigate the sensitivity of this enzyme to heavy metals with a view to possible future applications of CA activity inhibition measurement in biomonitoring as either an in vitro bioassay or a biomarker. CA activity was determined by modifying a previously described electrometric method: briefly, CA activity units were calculated from the rate of H+ production in the reaction mixture (where CO2 was present as a substrate) against a blank containing the specific CA inhibitor acetazolamide. As regards the possible application as an in vitro bioassay, the sensitivity to heavy metals (cadmium, mercury, and copper) of the commercially available purified carbonic anhydrase (isozyme II) from bovine erythrocyte was tested in vitro. In our experimental set-up, bovine CA activity was significantly inhibited by micromolar concentrations of heavy metals, showing a dose–response behaviour. As regards the possible application as biomarkers, CA was investigated in the filter-feeding Mytilus galloprovincialis, widely used in pollution-monitoring programmes as a sentinel organism. Following in vitro and in vivo exposure to 1.785 μM cadmium chloride as a reference toxicant, mantle CA activity was significant inhibited. In conclusion, the sensitivity to chemical pollutants and low cost and simplicity of the assay method make CA activity measurement suitable for in vitro bioassay of the toxicity of environmental samples and for field biomarker applications in the sentinel organism M. galloprovincialis.
Nest defence in a cuckoo host: great reed warblers risk themselves equally for their own and parasitic chicks

Hosts of the common cuckoo (Cuculus canorus) may foster a foreign chick instead of raising their own progeny, which incurs a significant cost to their fitness. Chick recognition or discrimination is, however, rare in cuckoo hosts and has been investigated exclusively in relation to nestling provisioning. Here we test for the first time whether hosts differ in the willingness of risk-taking when they care for own or parasitic offspring. We investigated nest defence in great reed warblers (Acrocephalus arundinaceus) against three types of nest intruders while controlling for the number of chicks and the length of the nestling period. The most parsimonious linear mixed-effects model showed that the type of intruder and nest identity significantly explained variation in host aggression. Our results demonstrated that the hosts discriminated two predators from an innocuous species and that some nest owners consistently defended their nests more intensely than others. However, the birds did not differ in their responses in relation to the nest contents, indicating that neither the nestling species, nor the length of previous parental investment influenced the intensity of nest defence. Our findings are, therefore, in accordance with the general scarcity of chick discrimination by cuckoo hosts.
Porous semiconductor compounds

In this review paper, we present a comparative analysis of the electrochemical dissolution of III–V (InP, GaAs, GaN), II–VI (ZnSe, CdSe) and SiC semiconductor compounds. The resulting morphologies are discussed, including those of porous layers and networks of low-dimensional structures such as nanowires, nanobelts, and nanomembranes. Self-organized phenomena in anodic etching are disclosed, leading to the formation of controlled porous patterns and quasi-ordered distribution of pores. Results of templated electrochemical deposition of metal nanowires, nanotubes and nanodots are summarized. Porosification of some compounds is shown to improve luminescence characteristics as well as to enhance photoconductivity, second harmonic generation and Terahertz emission. Possible applications of porous semiconductor compounds in various areas are discussed.
The role of plateletcrit and neutrophil lymphocyte ratio in showing the clinical severity of the disease in patients with chronic venous insufficiency

Aim: Chronic venous insufficiency (CVI) is a common disease and affects approximately 40% of the population. In this study, we aimed to investigate the relationship of neutrophil to lymphocyte ratio (NLR) and plateletcrit (PCT) values with the clinical severity of the disease in patients diagnosed with CVI. Material and Methods: The patients hospitalized to our clinic for treatment with the diagnosis of chronic venous insufficiency between August 2014 and August 2019 were included in the study retrospectively. Patients were divided into two groups as Group 1 including patients with stage C1, C2, C3 disease and Group 2 including patients with stage C4, C5, C6 disease according to the clinical evaluation in CEAP staging. Results: There were 119 patients in Group 1 and their median age was 35 (1866) years. There were 55 patients in Group 2 and their median age was 44 (1965) years. In multivariate logistic regression analysis, the presence of concomitant perforator vein incompetence (Odds ratio(OR): 1.527, CI 95%: 1.481-2.846 p = 0.019), presence of concomitant deep venous insufficiency (OR: 1.978 CI 95%: 1.250-2.979 p = 0.020), NLR (OR: 3.244, CI 95%: 1.384-4.825 p<0.001) and PCT (OR: 5.354 CI 95%: 2.935-8.586, p = 0.001) values were found to be independent predictors in showing the clinical severity of venous disease. Conclusions: We determined that the severity of the clinical condition could be predicted by NLR and PCT values in patients with superficial venous insufficiency, the most common insufficiency in the population.
Systematic palaeontology (vertebrate palaeontology) Using radii-of-curvature for the reconstruction of extinct South African carnivoran masticatory behavior

Paleoanthropologists have hypothesized that, during the evolution of increased carnivory in our lineage, hominins transitioned through a scavenging niche created by certain carnivoran taxa (especially sabertooths) that may have lacked the morphology necessary to utilize all parts of carcasses, thus leaving an open niche of high-quality scavengable remains. In this article, we examine the postcanine dentition of modern and fossil carnivorans using quantifications of occlusal radii-of-curvature (ROC) and correlate this morphology with feeding behavior to deduce the carcass-processing capabilities of the Plio-Pleistocene carnivores of South Africa. ROC data do a good job of separating taxa by dietary category, revealing possible differences in the carcass-processing abilities of fossil and modern members of some extant species, and confirming that Chasmaporthetes was probably a hypercarnivore and not a durophage like the modern hyenas. Contrary to previous hypotheses, sabertooth felids do not appear to have been more hypercarnivorous than modern felids based on these data. To cite this article: A. Hartstone-Rose, S. Wahl, C. R. Palevol 7 (2008).
Extreme RSS Based Indoor Localization for LoRaWAN With Boundary Autocorrelation

The received signal strength (RSS) finger-print-based approaches are widely used for indoor location-based services (LBSs). The emerging long range wide area network (LoRaWAN) is a cost-effective solution for indoor latency-tolerant LBSs attributed to its long-range property. In general, there are serious RSS fluctuations due to fadings along the communication path, thus significantly jeopardizing the localization accuracy. To overcome the challenge, in this article we propose the extreme RSS (ERSS) to stabilize the fingerprint database and formulate boundary autocorrelation to downsize tremendously the searching complexity and thus proliferating localization accuracy. In essence, the RSS fluctuations are modeled as a Bernoulli random process so that the RSS stability can be estimated by a newly defined fluctuation analytic function. To mitigate the impact of the perturbative fluctuation, the ERSS is further defined to cultivate a highly stable and robust fingerprint database which withstands environmental dynamics. In addition, boundary autocorrelation is developed to measure and compare the similarity between the measured RSS values versus the prestored fingerprint database. RSS values with low autocorrelation coefficients are eradicated from the typically lengthy searching. The downsized complexity significantly improves the localization accuracy. Experiments were carried out and the results revealed that the proposed method achieved sub-10-m localization accuracy in indoor environments. Such accuracy is encouraging and superior in contemporary LoRaWAN measurements.
Eigenvalue Statistics and Localization for Random Band Matrices with Fixed Width and Wegner Orbital Model

OF DISSERTATION Eigenvalue Statistics and Localization for Random Band Matrices with Fixed Width and Wegner Orbital Model Abstract: We discuss two models from the study of disordered quantum systems. The first is the Random Band Matrix with a fixed band width and Gaussian or more general disorder. The second is the Wegner n-orbital model. We establish that the point process constructed from the eigenvalues of finite size matrices converge to a Poisson Point Process in the limit as the matrix size goes to infinity. The proof is based on the method of Minami for the Anderson tight-binding model. As a first step, we expand upon the localization results by Schenker and Peled-Schenker-Shamis-Sodin to account for complex energies. We use the fractional moment method of Aizenman-Molchanov to derive these bounds. In addition, we establish convergence and smoothness of the density of states functions by modifying estimates of Dolai-Krishna-Mallick to allow for unbounded random variables. From there we follow the Daley and Vere-Jones criteria for establishing the convergence of the eigenvalue point process to the Poisson Point process. The analysis is first presented for the band matrix with adjustments for the orbital model following after. Other properties of these models such as ergodicity and Lyapunov exponents are discussed.
Estimating Wind Turbine–Caused Bird Mortality

Abstract Mortality estimates are needed of birds and bats killed by wind turbines because wind power generation is rapidly expanding worldwide. A mortality estimate is based on the number of fatalities assumed caused by wind turbines and found during periodic searches, plus the estimated number not found. The 2 most commonly used estimators adjust mortality estimates by rates of searcher detection and scavenger removal of carcasses. However, searcher detection trials can be biased by the species used in the trial, the number volitionally placed for a given fatality search, and the disposition of the carcass on the ground. Scavenger removal trials can be biased by the metric representing removal rate, the number of carcasses placed at once, the duration of the trial, species used, whether carcasses were frozen, whether carcasses included injuries consistent with wind turbine collisions, season, distance from the wind turbines, and general location. I summarized searcher detection rates among reported trials, and I developed models to predict the proportion of carcasses remaining since the last fatality search. The summaries I present can be used to adjust previous and future estimates of mortality to improve comparability. I also identify research directions to better understand these and other adjustments needed to compare mortality estimates among wind farms.
Differentiation between Lactococcus sp. and Leuconostoc sp. based on RFLP analysis of 16S rRNA.

Lactic acid bacteria (LAB) are industrially important microbes that are used all over the world in a large variety of industrial food fermentations [Klaenhammer et al., 2002; Kleerebezem et al., 2002]. LAB are found naturally in a variety of environmental habitats, including dairy, meat, vegetable, cereal and plant environments, where lactic acid fermentation can occur. Historically, the traditional roles for many LAB have been as starter cultures for food and dairy fermentations, leading to their widespread human consumption [Klaenhammer et al., 2005; Yanagida et al., 2005]. Typical LAB are gram-positive, nonsporing, catalasenegative, devoid of cytochromes, anaerobic or aerotolerant cocci or rods that are acid-tolerant and produce lactic acid as the major end product during sugar fermentation [Axelsson, 2004]. Traditionally, lactic acid bacteria have been classified on the basis of phenotypic properties, e.g. morphology, mode of glucose fermentation, growth at different temperatures, lactic acid optical configuration, and fermentation of various carbohydrates [Holzapfel et al., 2001]. Commonly applied identification system API 50CHL for diagnostics of Lactic Acid Bacteria (LAB) may lead to false classification of strains resulting from the same biochemical profiles of two organisms belonging to different genera. This may result in the nonreproducibility of the tests or difficulties in interpretation and therefore limits the use of traditional methods. These difficulties have increased the interest in molecular approaches to identification. In the past decades, several molecular techniques have been applied to identify these bacteria [Gonzalez et al., 2006; Ben-Amor et al., 2007]. Most of these methods use PCR to amplify small-subunit rRNA genes, in particular the 16S rRNA gene, and then PCR amplicons are separated based on differences in DNA sequences of the 16S rRNA genes [Saikaly et al., 2005]. These methods include ribosomal intergenic spacer analysis (RISA), single-strand conformation polymorphism (SSCP), amplified ribosomal DNA restriction analysis (ARDRA), terminal restriction fragment length polymorphism (T-RFLP), denaturing gradient gel electrophoresis (DGGE) and pulsedfield gel electrophoresis (PFGE) [Miteva et al., 2001; Blackwood et al., 2003; Rodas et al., 2005; Randazzo et al., 2009]. Polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) analysis of amplified 16S rRNA fragments was developed by Woese and coworkers [O’Sullivan, 2000]. This is one of the most frequent methods used to differentiate between Lactococcus and Leuconostoc species because it is more discriminatory, faster, and more cost-effective than the phenotypic tests [Randazzo et al., 2004]. 16S rRNA genes contain conserved regions coexisting with variable sequences that make them suitable targets for molecular identification methods. Consequently, modern molecular techniques have become increasingly important for species identification or differentiation of LAB strains.
Tumor suppressor PTEN signaling is up-regulated in mammary epithelial cells by soy isoflavone genistein: implications for breast cancer protection.

CTRC-AACR San Antonio Breast Cancer Symposium: 2008 Abstracts Abstract #4069 Breast cancer is the second leading cause of death in the Western hemisphere affecting one of eight women in their lifetime. In addition to chromosomal and genetic alterations, nutrition is considered a risk determinant for breast cancer. Prevailing evidence suggests a negative correlation between intake of soy-rich foods and breast cancer incidence. Epidemiological and case control studies have shown a two-to eight fold lower occurrence of the disease in Asian women whose early intake of soy products is 20-25 times higher than their American counterparts. Previous work from our group has shown diet-induced protection against DMBA- and NMU-induced mammary tumors in vivo , with decreased tumor incidence and increased tumor latency in rats exposed to dietary soy protein isolate (SPI) or casein (CAS) supplemented with the major soy isoflavone genistein (GEN) when compared to those fed the control casein (CAS) diet. We also have shown that GEN enhanced apoptosis in mammary epithelial cells in vivo and in vitro (MCF-7 cells), attendant with increased expression of the tumor suppressor PTEN and several pro-apoptotic genes Bax, Bok, and p21. Here, we test the hypothesis that GEN induction of PTEN expression and nuclear localization in mammary epithelial cells result in decreased cellular proliferation and enhanced cellular differentiation, to confer protection from mammary tumorigenesis. Using the non-tumor human mammary epithelial cell line MCF-10A, we show that GEN at physiologically relevant concentrations (40 nM, 2 µM) increased PTEN mRNA and protein levels and enhanced nuclear accumulation of active (non-phosphorylated) PTEN. GEN induction of PTEN transcript levels was lost with the inclusion of the transcription inhibitor actinomycin D, suggesting PTEN is a direct GEN target. Further, cells treated with GEN for 6 days had lower cell viability when compared to control cells, concomitant with decreased expression of cyclin D1 and of the PTEN regulated gene pleiotrophin. Interestingly, GEN up-regulation of PTEN expression was accompanied by similar effects on another tumor suppressor p53, which co-localized with PTEN in the nuclei of GEN-treated cells. PTEN siRNA targeting, which decreased basal PTEN expression by 60%, significantly increased cyclin D1 but not p53 expression. Our findings provide support to the hypothesis that the protective effects of GEN in the mammary epithelium may be mediated by PTEN to enhance differentiation and inhibit cellular proliferation, and suggest the participation of another key tumor suppressor p53. Funding by USDA-CRIS 6251-5100002-06S. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 4069.
Ex Ovo Culture System for Avian Embryos and its Application

Ex ovo culture of avian embryos can be applied not only to embryology but also to various fields of basic research such as embryo manipulation, toxicology, and regenerative medicine. The windowing method, which facilitates various manipulations and observations by opening a hole in one part of the eggshell, and culture systems using surrogate eggshells, are widely used. Despite this, biology lessons in high schools cover shell-less culture systems, which involve the development of avian embryos in artificial vessels, such as rice bowls, without using surrogate eggshells. However, as embryo development stops at its early stages in this method, it is not possible to continuously observe the development of the embryo. This led to attempts to develop an embryo culture method using a complete artificial culture vessel that does not use surrogate eggshells, and Kamihira et al. (1998) succeeded in hatching quail embryos in an artificial culture vessel using polytetrafluoroethylene membranes. In addition, Tahara succeeded in hatching chick embryos in artificial culture vessels that used cling film made of polymethylpentene and reported their detailed methodology (Tahara and Obara, 2014). These technologies are being applied not only to school education but also to various fields of research.
Prediction of Specific Subtypes and Common Markers of Non-Small Cell Lung Cancer Based on Competing Endogenous RNA Network

Background There are various pathological types of lung cancer, including squamous cell carcinoma and adenocarcinoma. Although both of them are lung cancers, there are significant differences in diagnosis, pathogenesis, location, imaging, metastasis, and treatment. According to the competing endogenous RNA (ceRNA) theory, long non-coding RNAs (lncRNAs) compete with encoding protein genes (mRNAs) to connect with miRNAs, thus affecting the level of mRNA. Material/Methods First, using the t test, we identified mRNAs and lncRNAs that have different expressions (fold change >2, P<0.01) in normal samples and in tumor samples. We calculated the significance of the shared miRNAs for mRNAs and lncRNAs by hypergeometric test (P<0.01). Further, mRNA and lncRNA pairs with co-expression relationships in cancer samples were used to establish ceRNA networks. Then, the random walk algorithm was used to optimize the specific ceRNA networks and identify potential prognostic markers of survival. Finally, we built a common ceRNA network to find markers of non-small-cell lung cancer. Results We identified some potential key markers, such as PVT1, LINC00472, CDKN2A, and FAM83B, in LUSC and HOXA11-AS, HNF1A-AS1, LINC00511, and HOTAIR in LUAD by analyzing the ceRNA networks. Moreover, a number of common ceRNA pairs, such as CDC25C/CDK1/RRM2-LINC00355, have been found, and they are also significant markers for tumor survival and prognosis. Conclusions In summary, the present study provides a comparative analysis in 2 kinds of lung cancer ceRNA networks. Some specific and common markers we predicted that may be of great importance for clinical diagnosis and treatment.
Grist to the mill of subversion: strikes and coups in counterinsurgencies

Why are acts of organized resistance associated with coups? Inspired by the Arab Spring, a large literature suggests that militaries confronted with civil resistance tend to side with protesters and oust their government. In the historically most coup-prone environment of insurgencies, however, alliances between the military and protesters are implausible because soldiers suspect insurgents behind social dissent. Disentangling different types of resistance, this article analyzes whether and how strikes, demonstrations, riots, and guerrilla attacks affect the military’s disposition and ability to stage a coup during counterinsurgencies. We argue that only strikes trigger coup attempts. Soldiers interpret strikes as manifestations of a strengthening subversive enemy that threatens their victory over insurgents, while economic elites support a coup in the hope that the military will terminate costly walkouts. This interest alignment fosters military takeovers. We provide case-study evidence from Cold War Argentina and Venezuela to show our suggested mechanism at work. Demonstrating the scope of our argument, we quantitatively analyze coup attempts in counterinsurgency worldwide (1950–2005). Results show that strikes increase wartime coup risk, whereas demonstrations, riots, and guerrilla attacks do not. The findings highlight the backfiring potential of nonviolent resistance with important implications for post-coup political orders and democratization prospects.
Broadband Finite Frequency Ambient Noise Tomography: A Case Study in the Western United States Using USArray Stations

We demonstrate the feasibility of finite frequency ambient noise tomography (ANT) in mapping broadband surface wave phase velocities in the western United States using data from the USArray. We obtain cross‐correlation functions (CCFs) of ambient noise data between pairs of stations and then construct a 2‐D phase sensitivity kernel for each CCF between a pair of stations by treating one station as a “virtual” point source and the other as the receiver. Based on a standard, iterative, linearized inversion technique, we develop a finite frequency ANT method and use this method to construct phase velocity maps. These phase velocity maps are very similar to other reported maps generated by established tomography methods based on ray theory at short periods. At intermediate and long periods (>40 s), phase velocity maps based on finite frequency ANT significantly differ from those based on ray theory ANT; however, they are similar with those based on Helmholtz tomography which uses earthquake surface wave data and considers finite frequency effects of surface waves. Our results suggest that finite frequency effects need to be considered in intermediate‐ and long‐period ANT if one intends to resolve upper‐mantle structures with subwavelength scales using ANT.