Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel AlkB Dioxygenases—Alternative Models for In Silico and In Vivo Studies

Background ALKBH proteins, the homologs of Escherichia coli AlkB dioxygenase, constitute a direct, single-protein repair system, protecting cellular DNA and RNA against the cytotoxic and mutagenic activity of alkylating agents, chemicals significantly contributing to tumor formation and used in cancer therapy. In silico analysis and in vivo studies have shown the existence of AlkB homologs in almost all organisms. Nine AlkB homologs (ALKBH1–8 and FTO) have been identified in humans. High ALKBH levels have been found to encourage tumor development, questioning the use of alkylating agents in chemotherapy. The aim of this work was to assign biological significance to multiple AlkB homologs by characterizing their activity in the repair of nucleic acids in prokaryotes and their subcellular localization in eukaryotes. Methodology and Findings Bioinformatic analysis of protein sequence databases identified 1943 AlkB sequences with eight new AlkB subfamilies. Since Cyanobacteria and Arabidopsis thaliana contain multiple AlkB homologs, they were selected as model organisms for in vivo research. Using E. coli alkB − mutant and plasmids expressing cyanobacterial AlkBs, we studied the repair of methyl methanesulfonate (MMS) and chloroacetaldehyde (CAA) induced lesions in ssDNA, ssRNA, and genomic DNA. On the basis of GFP fusions, we investigated the subcellular localization of ALKBHs in A. thaliana and established its mostly nucleo-cytoplasmic distribution. Some of the ALKBH proteins were found to change their localization upon MMS treatment. Conclusions Our in vivo studies showed highly specific activity of cyanobacterial AlkB proteins towards lesions and nucleic acid type. Subcellular localization and translocation of ALKBHs in A. thaliana indicates a possible role for these proteins in the repair of alkyl lesions. We hypothesize that the multiplicity of ALKBHs is due to their involvement in the metabolism of nucleo-protein complexes; we find their repair by ALKBH proteins to be economical and effective alternative to degradation and de novo synthesis.
Species Diversity and Phylogeographical Affinities of the Branchiopoda (Crustacea) of Churchill, Manitoba, Canada

The region of Churchill, Manitoba, contains a wide variety of habitats representative of both the boreal forest and arctic tundra and has been used as a model site for biodiversity studies for nearly seven decades within Canada. Much previous work has been done in Churchill to study the Daphnia pulex species complex in particular, but no study has completed a wide-scale survey on the crustacean species that inhabit Churchill's aquatic ecosystems using molecular markers. We have employed DNA barcoding to study the diversity of the Branchiopoda (Crustacea) in a wide variety of freshwater habitats and to determine the likely origins of the Churchill fauna following the last glaciation. The standard animal barcode marker (COI) was sequenced for 327 specimens, and a 3% divergence threshold was used to delineate potential species. We found 42 provisional and valid branchiopod species from this survey alone, including several cryptic lineages, in comparison with the 25 previously recorded from previous ecological works. Using published sequence data, we explored the phylogeographic affinities of Churchill's branchiopods, finding that the Churchill fauna apparently originated from all directions from multiple glacial refugia (including southern, Beringian, and high arctic regions). Overall, these microcrustaceans are very diverse in Churchill and contain multiple species complexes. The present study introduces among the first sequences for some understudied genera, for which further work is required to delineate species boundaries and develop a more complete understanding of branchiopod diversity over a larger spatial scale.
OPTICAL PROPERTIES OF GALLIUM PHOSPHIDE (GaP)

Optical properties of Gallium Phosphide (GaP) have been investigated by means of Kramers Kronig method. Optical properties such as refractive index, extinction coefficient, dielectric constant, transmit- tance, absorption coefficient, reflectance, reflection coefficient and optical conductivity are presented in the energy range 1.03 - 6.01eV. The calculated optical properties of GaP indicate promising device applications such as the design of optoelectronic devices, electronic and photonic devices.
Fast Estimation of tr(f(A)) via Stochastic Lanczos Quadrature

The problem of estimating the trace of matrix functions appears in applications ranging from machine learning and scientific computing, to computational biology. This paper presents an inexpensive method to estimate the trace of $f(A)$ for cases where $f$ is analytic inside a closed interval and $A$ is a symmetric positive definite matrix. The method combines three key ingredients, namely, the stochastic trace estimator, Gaussian quadrature, and the Lanczos algorithm. As examples, we consider the problems of estimating the log-determinant ($f(t)=\log(t)$), the Schatten $p$-norms ($f(t)=t^{p/2}$), the Estrada index ($f(t)=e^{t}$), and the trace of the matrix inverse ($f(t)=t^{-1}$). We establish multiplicative and additive error bounds for the approximations obtained by this method. In addition, we present error bounds for other useful tools such as approximating the log-likelihood function in the context of maximum likelihood estimation of Gaussian processes. Numerical experiments illustrate the performan.
Trophic cascades promote threshold-like shifts in pelagic marine ecosystems

Fisheries can have a large impact on marine ecosystems, because the effects of removing large predatory fish may cascade down the food web. The implications of these cascading processes on system functioning and resilience remain a source of intense scientific debate. By using field data covering a 30-year period, we show for the Baltic Sea that the underlying mechanisms of trophic cascades produced a shift in ecosystem functioning after the collapse of the top predator cod. We identified an ecological threshold, corresponding to a planktivore abundance of ≈17 × 1010 individuals, that separates 2 ecosystem configurations in which zooplankton dynamics are driven by either hydroclimatic forces or predation pressure. Abundances of the planktivore sprat above the threshold decouple zooplankton dynamics from hydrological circumstances. The current strong regulation by sprat of the feeding resources for larval cod may hinder cod recovery and the return of the ecosystem to a prior state. This calls for the inclusion of a food web perspective in management decisions.
Identification and Re-Evaluation of Freshwater Catfishes through DNA Barcoding

Background Catfishes are globally demanded as human food, angling sport and aquariums keeping thus are highly exploited all over the world. North-East India possess high abundance of catfishes and are equally exploited through decades. The strategies for conservation necessitate understanding the actual species composition, which is hampered due to sporadic descriptions of the species through traditional taxonomy. Therefore, actual catfish diversity in this region is important to be studied through the combined approach of morphological and molecular technique of DNA barcoding. Methodology/Principal Findings Altogether 75 native catfish specimens were collected from across the North-East India and their morphological features were compared with the taxonomic keys. The detailed taxonomic study identified 25 species belonging to 17 genera and 9 families. The cytochrome oxidase c subunit-I gene fragment were then sequenced from the samples in accordance with the standard DNA barcoding protocols. The sequences were compared with public databases, viz., GenBank and BOLD. Sequences developed in the current study and from databases of the same and related taxa were analyzed to calculate the congeneric and conspecific genetic divergences using Kimura 2-parameter distance model, and a Neighbor Joining tree was created using software MEGA5.1. The DNA barcoding approach delineated 21 distinct species showing 4.33 folds of difference between the nearest congeners. Four species, viz., Amblyceps apangi, Glyptothorax telchitta, G. trilineatus and Erethistes pusillus, showed high conspecific divergence; hence their identification through molecular approach remained inconclusive. On the other hand, the database sequences for three species, viz., Mystus horai, Bagarius yarrelli and Clarias batrachus, appeared mislabeled. Conclusion The efficiency of DNA barcoding was reaffirmed from its success by easily identifying the major share (84%) of the studied catfish into 21 distinct species. The study contributed 27 new barcodes for 7 species and confirmed the range expansion of 2 important species in NE India.
Artificial neural networks for automatic modelling of the pectus excavatum corrective prosthesis

Pectus excavatum is the most common deformity of the thorax and usually comprises Computed Tomography (CT) examination for pre-operative diagnosis. Aiming at the elimination of the high amounts of CT radiation exposure, this work presents a new methodology for the replacement of CT by a laser scanner (radiation-free) in the treatment of pectus excavatum using personally modeled prosthesis. The complete elimination of CT involves the determination of ribs external outline, at the maximum sternum depression point for prosthesis placement, based on chest wall skin surface information, acquired by a laser scanner. The developed solution resorts to artificial neural networks trained with data vectors from 165 patients. Scaled Conjugate Gradient, Levenberg-Marquardt, Resilient Back propagation and One Step Secant gradient learning algorithms were used. The training procedure was performed using the soft tissue thicknesses, determined using image processing techniques that automatically segment the skin and rib cage. The developed solution was then used to determine the ribs outline in data from 20 patient scanners. Tests revealed that ribs position can be estimated with an average error of about 6.82±5.7 mm for the left and right side of the patient. Such an error range is well below current prosthesis manual modeling (11.7±4.01 mm) even without CT imagiology, indicating a considerable step forward towards CT replacement by a 3D scanner for prosthesis personalization.
Drought and reproductive effort interact to control growth of a temperate broadleaved tree species (Fagus sylvatica)

Interannual variation in radial growth is influenced by a range of physiological processes, including variation in annual reproductive effort, although the importance of reproductive allocation has rarely been quantified. In this study, we use long stand-level records of annual seed production, radial growth (tree ring width) and meteorological conditions to analyse the relative importance of summer drought and reproductive effort in controlling the growth of Fagus sylvatica L. , a typical masting species. We show that both summer drought and reproductive effort (masting) influenced growth. Importantly, the effects of summer drought and masting were interactive, with the greatest reductions in growth found in years when high reproductive effort (i.e., mast years) coincided with summer drought. Conversely, mast years that coincided with non-drought summers were associated with little reduction in radial growth, as were drought years that did not coincide with mast years. The results show that the strength of an inferred trade-off between growth and reproduction in this species (the cost of reproduction) is dependent on environmental stress, with a stronger trade-off in years with more stressful growing conditions. These results have widespread implications for understanding interannual variability in growth, and observed relationships between growth and climate.
Bayesian approach to multilayer stochastic blockmodel and network changepoint detection

Abstract Network scholars commonly encounter multiple networks, each of which is possibly governed by distinct generation rules while sharing a node group structure. Although the stochastic blockmodeling—detecting such latent group structures with group-specific connection profiles—has been a major topic of recent research, the focus has been given to the assortative group discovery of a single network. Despite its universality, concepts, and techniques for simultaneous characterization of node traits of multilayer networks, constructed by stacking multiple networks into layers, have been limited. Here, we propose a Bayesian multilayer stochastic blockmodeling framework that uncovers layer-common node traits and factors associated with layer-specific network generating functions. Without assuming a priori layer-specific generation rules, our fully Bayesian treatment allows probabilistic inference of latent traits. We extend the approach to detect changes in block structures embedded in temporal layers of network time series. We demonstrate the method using synthetic multilayer networks with assortative, disassortative, core-periphery, and overlapping community structures. Finally, we apply the method to empirical social network datasets, and find that it detects significant latent traits and structural changepoints. In particular, we uncover endogenous historical regimes associated with distinct constellations of states in United States Senate roll call vote similarity patterns.
Predicting mobile apps spread: An epidemiological random network modeling approach

The mobile applications business is a really big market, growing constantly. In app marketing, a key issue is to predict future app installations. The influence of the peers seems to be very relevant when downloading apps. Therefore, the study of the evolution of mobile apps spread may be approached using a proper network model that considers the influence of peers. Influence of peers and other social contagions have been successfully described using models of epidemiological type. Hence, in this paper we propose an epidemiological random network model with realistic parameters to predict the evolution of downloads of apps. With this model, we are able to predict the behavior of an app in the market in the short term looking at its evolution in the early days of its launch. The numerical results provided by the proposed network are compared with data from real apps. This comparison shows that predictions improve as the model is fed back. Marketing researchers and strategy business managers can benefit from the proposed model since it can be helpful to predict app behavior over the time anticipating the spread of an app.
Associations of overweight/obesity and socioeconomic status with hypertension prevalence across racial and ethnic groups

Racial/ethnic disparities in the prevalence of diagnosed hypertension are persistent but may be partially explained by racial/ethnic differences in weight category and neighborhood socioeconomic status. The authors compared hypertension prevalence rates among 4 060 585 adults with overweight or obesity across 10 healthcare systems by weight category and neighborhood education level in geographically and racially diverse individuals. Data were obtained from electronic health records. Hypertension was defined as at least two outpatient visits or one inpatient hospitalization with a coded diagnosis. Logistic regression, adjusted for age, sex, and site, with two‐way interactions between race/ethnicity and weight category or neighborhood education, was used to examine the association between hypertension and race/ethnicity, with whites as the reference. Results documented that odds ratios for hypertension prevalence were greater for blacks, American Indians/Alaskan Natives, Asians, and Native Hawaiians/other Pacific Islanders compared with whites and lower for Hispanics in similar weight categories and neighborhood education levels. Although two‐way interactions were statistically significant, the magnitude of the odds of hypertension compared with whites did not substantially vary across weight or neighborhood education. Hypertension odds were almost double relative to whites for blacks and Native Hawaiians/other Pacific Islanders across most weight categories and all neighborhood education levels. Odds of hypertension were about 50% greater for Asians relative to whites across weight categories. Results suggest that other factors might be associated with racial/ethnic disparities in hypertension. More research is needed to understand the many factors that may contribute to variation in diagnosed hypertension across racial/ethnic groups with overweight or obesity.
Insomnia and the Risk of Breast Cancer: The HUNT Study

Objective The association of insomnia with subsequent breast cancer risk is largely unknown. Therefore, we assessed whether different symptoms of insomnia and their combination are associated with incident breast cancer in a large population-based study. Methods In a prospective cohort study, 33,332 women were followed to monitor the occurrence of their first invasive breast cancer identified by the Cancer Registry of Norway. Insomnia symptoms including (1) nonrestorative sleep and (2) difficulty initiating and (3) maintaining sleep were self-reported using a study specific measure reflecting the current Diagnostic and Statistical Manual of Mental Disorders criteria. Hazard ratios and 95% confidence intervals were calculated using multiadjusted Cox proportional hazards models. Results A total of 862 incident breast cancer cases occurred during a mean follow-up of 14.7 years. No consistent association was observed between the individual insomnia symptoms and breast cancer risk. However, compared to women reporting no insomnia complaints, those who reported having all three aspects of insomnia simultaneously were at increased risk (hazard ratio, 2.38; 95% confidence interval = 1.11–5.09). Conclusion Our results suggest that having only some aspects of insomnia may not predispose someone to breast cancer. In contrast, experiencing all insomnia symptoms simultaneously might confer considerable excess risk.
Production of carbon nanotubes

First, the historical fact of the discovery of carbon nanotubes is reviewed. Then, production of high crystallinity multi-walled carbon nanotubes by DC arc discharge evaporation of pure graphite rod in pure hydrogen gas is discussed. The smallest carbon nanotubes included in the core of the multi-walled carbon nanotubes are shown. Carbon chain included in the core of the multi-walled carbon nanotubes and their special Raman peaks near 1850cm-1 also are discussed.
Another Nail in the Coffin for Learning Styles? Disparities among Undergraduate Anatomy Students’ Study Strategies, Class Performance, and Reported VARK Learning Styles

The concept and existence of learning styles has been fraught with controversy, and recent studies have thrown their existence into doubt. Yet, many students still hold to the conventional wisdom that learning styles are legitimate, and may adapt their outside of class study strategies to match these learning styles. Thus, this study aims to assess if undergraduate anatomy students are more likely to utilize study strategies that align with their hypothetical learning styles (using the VARK analysis from Fleming and Mills, , Improve Acad. 11:137–155) and, if so, does this alignment correlate with their outcome in an anatomy course. Relatedly, this study examines whether students’ VARK learning styles are correlated with course outcomes regardless of the students’ study strategies, and whether any study strategies are correlated with course outcomes, regardless of student‐specific VARK results. A total of 426 anatomy students from the 2015 and 2016 Fall semesters completed a study strategies survey and an online VARK questionnaire. Results demonstrated that most students did not report study strategies that correlated with their VARK assessment, and that student performance in anatomy was not correlated with their score in any VARK categories. Rather, some specific study strategies (irrespective of VARK results), such as use of the virtual microscope, were found to be positively correlated with final class grade. However, the alignment of these study strategies with VARK results had no correlation with anatomy course outcomes. Thus, this research provides further evidence that the conventional wisdom about learning styles should be rejected by educators and students alike. Anat Sci Educ. © 2018 American Association of Anatomists.
The Role of Perfusion Computed Tomography in the Prediction of Cerebral Hyperperfusion Syndrome

Background Hyperperfusion syndrome (HPS) following carotid angioplasty with stenting (CAS) is associated with significant morbidity and mortality. At present, there are no reliable parameters to predict HPS. The aim of this study was to clarify whether perfusion computed tomography (CT) is a feasible and reliable tool in predicting HPS after CAS. Methodology/Principal Findings We performed a retrospective case-control study of 54 patients (11 HPS patients and 43 non-HPS) with unilateral severe stenosis of the carotid artery who underwent CAS. We compared the prevalence of vascular risk factors and perfusion CT parameters including regional cerebral blood volume (rCBV), regional cerebral blood flow (rCBF), and time to peak (TTP) within seven days prior to CAS. Demographic information, risk factors for atherosclerosis, and perfusion CT parameters were evaluated by multivariable logistic regression analysis. The rCBV index was calculated as [(ipsilateral rCBV - contralateral rCBV)/contralateral rCBV], and indices of rCBF and TTP were similarly calculated. We found that eleven patients had HPS, including five with intracranial hemorrhages (ICHs) of whom three died. After a comparison with non-HPS control subjects, independent predictors of HPS included the severity of ipsilateral carotid artery stenosis, 3-hour mean systolic blood pressure (3 h SBP) after CAS, pre-stenting rCBV index >0.15 and TTP index >0.22. Conclusions/Significance The combination of severe ipsilateral carotid stenosis, 3 h SBP after CAS, rCBV index and TTP index provides a potential screening tool for predicting HPS in patients with unilateral carotid stenosis receiving CAS. In addition, adequate management of post-stenting blood pressure is the most important treatable factor in preventing HPS in these high risk patients.
Ion Channel Expression and Characterization in Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes

Background Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) are providing new possibilities for the biological study, cell therapies, and drug discovery. However, the ion channel expression and functions as well as regulations in hiPSC-CMs still need to be fully characterized. Methods Cardiomyocytes were derived from hiPS cells that were generated from two healthy donors. qPCR and patch clamp techniques were used for the study. Results In addition to the reported ion channels, INa, ICa-L, ICa-T, If, INCX, IK1, Ito, IKr, IKs IKATP, IK-pH, ISK1–3, and ISK4, we detected both the expression and currents of ACh-activated (KACh) and Na+-activated (KNa) K+, volume-regulated and calcium-activated (Cl-Ca) Cl−, and TRPV channels. All the detected ion currents except IK1, IKACh, ISK, IKNa, and TRPV1 currents contribute to AP duration. Isoprenaline increased ICa-L, If, and IKs but reduced INa and INCX, without an effect on Ito, IK1, ISK1–3, IKATP, IKr, ISK4, IKNa, ICl-Ca, and ITRPV1. Carbachol alone showed no effect on the tested ion channel currents. Conclusion Our data demonstrate that most ion channels, which are present in healthy or diseased cardiomyocytes, exist in hiPSC-CMs. Some of them contribute to action potential performance and are regulated by adrenergic stimulation.