Miracle-dz/UniFAR-FTUs huggingface dataset:
Bile acid deoxycholate induces differential subcellular localisation of the PKC isoenzymes beta 1, epsilon and delta in colonic epithelial cells in a sodium butyrate insensitive manner.

Elevated levels of bile acids have been implicated in the abnormal morphogenesis of the colonic epithelium thus contributing to colorectal cancer (CRC). Alternatively sodium butyrate (NaB) produced by anaerobic fermentation of dietary fibre is regarded as being protective against colon cancer. Bile acids such as deoxycholic acid (DCA) are thought to mediate some of their actions by differentially activating protein kinase C (PKC). We examined the effects of DCA on the subcellular localisation of PKC-beta(1), -epsilon and -delta and whether these responses could be modulated by NaB. HCT116 cells endogenously express PKC-epsilon and -delta but not PKC-beta. DCA treatment results in endogenous PKC-epsilon translocation but not PKC-delta after 1 hr. To study the subcellular localisation of PKC isoforms in response to DCA in real time, PKC-beta(1), PKC-epsilon and PKC-delta functionally intact green fluorescent protein (GFP) fusion constructs were used. Stimulation with 300 microM DCA induces rapid translocation of PKC-beta(1)-GFP and PKC-epsilon-GFP but not PKC-delta-GFP from the cytosol to the plasma membrane in 15 min. Interestingly, pretreatment with 4mM NaB does not modify the response of the PKC isoenzymes to DCA as PKC-beta(1)-GFP and PKC-epsilon-GFP translocates to the plasma membrane in 15 min whereas PKC-delta-GFP localisation remains unaltered. Immunofluorescence shows that PKC-beta(1)-GFP and PKC-epsilon-GFP cells treated with DCA colocalise with the cytoskeletal elements actin and tubulin adjacent to the plasma membrane. Our findings demonstrate that the differential activation of the PKC isoenzymes by DCA may be of critical importance for the functional responses of colonic epithelial cells. Supplementary material for this article can be found on the International Journal of Cancer website at http://www.interscience. wiley.com/jpages/0020-7136/suppmat/index.html.
Global Prediction of Tissue-Specific Gene Expression and Context-Dependent Gene Networks in Caenorhabditis elegans

Tissue-specific gene expression plays a fundamental role in metazoan biology and is an important aspect of many complex diseases. Nevertheless, an organism-wide map of tissue-specific expression remains elusive due to difficulty in obtaining these data experimentally. Here, we leveraged existing whole-animal Caenorhabditis elegans microarray data representing diverse conditions and developmental stages to generate accurate predictions of tissue-specific gene expression and experimentally validated these predictions. These patterns of tissue-specific expression are more accurate than existing high-throughput experimental studies for nearly all tissues; they also complement existing experiments by addressing tissue-specific expression present at particular developmental stages and in small tissues. We used these predictions to address several experimentally challenging questions, including the identification of tissue-specific transcriptional motifs and the discovery of potential miRNA regulation specific to particular tissues. We also investigate the role of tissue context in gene function through tissue-specific functional interaction networks. To our knowledge, this is the first study producing high-accuracy predictions of tissue-specific expression and interactions for a metazoan organism based on whole-animal data.
Raman spectroscopy and coherent anti-Stokes Raman scattering imaging: prospective tools for monitoring skeletal cells and skeletal regeneration

The use of skeletal stem cells (SSCs) for cell-based therapies is currently one of the most promising areas for skeletal disease treatment and skeletal tissue repair. The ability for controlled modification of SSCs could provide significant therapeutic potential in regenerative medicine, with the prospect to permanently repopulate a host with stem cells and their progeny. Currently, SSC differentiation into the stromal lineages of bone, fat and cartilage is assessed using different approaches that typically require cell fixation or lysis, which are invasive or even destructive. Raman spectroscopy and coherent anti-Stokes Raman scattering (CARS) microscopy present an exciting alternative for studying biological systems in their natural state, without any perturbation. Here we review the applications of Raman spectroscopy and CARS imaging in stem-cell research, and discuss the potential of these two techniques for evaluating SSCs, skeletal tissues and skeletal regeneration as an exemplar.
Wasserstein Stability of the Entropy Power Inequality for Log-Concave Densities

We establish quantitative stability results for the entropy power inequality (EPI). Specifically, we show that if uniformly log-concave densities nearly saturate the EPI, then they must be close to Gaussian densities in the quadratic Wasserstein distance. Further, if one of the densities is log-concave and the other is Gaussian, then the deficit in the EPI can be controlled in terms of the $L^1$-Wasserstein distance. As a counterpoint, an example shows that the EPI can be unstable with respect to the quadratic Wasserstein distance when densities are uniformly log-concave on sets of measure arbitrarily close to one. Our stability results can be extended to non-log-concave densities, provided certain regularity conditions are met. The proofs are based on optimal transportation.
Mirtazapine in Comorbid Major Depression and Alcohol Use Disorder: A Long-Term Follow-Up Study.

BACKGROUND/OBJECTIVE To date, pharmacotherapy trials of depressed alcoholics (MDD/AUD) have focused on SSRI medications, with disappointing results, so effective treatments for that comorbid population are lacking. Mirtazapine is an FDA-approved medication for treating MDD with a unique pharmacological profile whose efficacy may exceed that of SSRIs. Results from our recent open label study suggest robust acute phase efficacy for mirtazapine for decreasing both the depression and the drinking of that population. However, to date, no studies have evaluated the longer-term efficacy of mirtazapine in that population. We now report findings from a first long-term (two-year) naturalistic follow-up evaluation involving subjects from the acute phase trial. We hypothesized that the improvements would persist at follow-up. METHODS An eight-week open label study of mirtazapine and motivation therapy was conducted involving persons 18 to 55 years of age with DSM-IV diagnoses of comorbid MDD/AD. Two years after entry into the acute phase study, a long-term evaluation was conducted using the same instruments that had been used at baseline to assess whether the improvements seen during the acute phase trial had persisted. RESULTS Ten of the twelve patients who entered the acute phase study participated in the follow-up study. The large magnitude improvements (p<.01) in depressive symptoms (BDI), drinking (TLFB), and sleep disturbance (HDRS) persisted at the follow-up evaluation. Two of the subjects demonstrated MDD on structured interview at follow-up, while all ten had demonstrated MDD at baseline. Six of the ten used antidepressants during the follow-up period. At baseline, three were employed, while at follow-up seven were employed. CONCLUSIONS These findings suggest long-term efficacy for mirtazapine for decreasing the drinking and depression of depressed alcoholics. Double-blind, placebo-controlled studies are warranted to clarify the efficacy of mirtazapine in depressed alcoholics.
Reconstructability Analysis as a Tool for Identifying Gene-Gene Interactions in Studies of Human Diseases

There are a number of common human diseases for which the genetic component may include an epistatic interaction of multiple genes. Detecting these interactions with standard statistical tools is difficult because there may be an interaction effect, but minimal or no main effect. Reconstructability analysis (RA) uses Shannon's information theory to detect relationships between variables in categorical datasets. We applied RA to simulated data for five different models of gene-gene interaction, and find that even with heritability levels as low as 0.008, and with the inclusion of 50 non-associated genes in the dataset, we can identify the interacting gene pairs with an accuracy of ? 80%. We applied RA to a real dataset of type 2 non-insulin-dependent diabetes (NIDDM) cases and controls, and closely approximated the results of more conventional single SNP disease association studies. In addition, we replicated prior evidence for epistatic interactions between SNPs on chromosomes 2 and 15.
Author ' s personal copy Biased samples not mode of presentation : Re-examining the apparent underweighting of rare events in experience-based choice q

Most experimental investigations of risky choice provide participants with a description of the probabilities and outcomes for each option, and observe that small probabilities are overweighted. However, when payoffs are learned from repeated experience of outcomes (as in many real-world decisions), different patterns of choice are observed—consistent with underweighting rare events. We re-examined this phenomenon to determine whether biased sampling and recency effects in experience-based choice could account for this description–experience gap. Two hundred and forty paid participants made choices for 12 pairs of simple gambles. In the objective description condition, probabilities and outcomes were specified. In the free sampling condition, participants observed repeated plays of each gamble before choosing. Participants in four yoked conditions received the same information as the free sampling participants—either described or experienced. Differences between objective description and free sampling were consistent with underweighting rare events in experience-based choice. However, consistent with a biased sampling account, patterns of choice in the yoked conditions barely differed from the free sampling condition: given identical information, presentation mode has no effect. Recency effects in choice occurred only when outcomes were actively sampled, and were unaffected by working memory capacity. The absence of recency for passive observation implies actor–observer differences in forming expectations or testing hypotheses. The results provide no support for the claim that decisions from description and decisions from experience require separate descriptive theories. 2008 Elsevier Inc. All rights reserved.
Expression and localization of three G protein α subunits, Go, Gq, and Gs, in adult antennae of the silkmoth (Bombyx mori)

In insect olfactory receptor neurons, rapid and transient increases in inositol triphosphate (IP3) and Ca2+ are detected upon stimulation with pheromone or nonpheromonal odorants. This suggests that heterotrimeric guanine nucleotide binding proteins (G proteins) may transduce some odorant responses in insects. We obtained cDNA clones encoding three classes of G protein α subunits, Bm Go, Bm Gq, and Bm Gs, from the antennae of the adult male silkmoth (Bombyx mori). RT‐PCR experiments showed that the mRNA of these G protein α subunits was also present in the various tissues of adult and larval insects. We used immunocytochemistry to localize these G protein α subunits in adult male and female antennae. In the adult male antennae, anti‐Go antiserum stained the nerve bundles. In contrast, anti‐Gq and anti‐Gs antisera stained the inner and outer dendritic segments of the putative olfactory receptor neuron. The localizations of Bm Go, Bm Gq, and Bm Gs in the female antennae were the same as in the male antennae. The localizations of Bm Gq and Bm Gs suggest that each subunit mediates a subset of the odorant response. J. Comp. Neurol. 485:143–152, 2005. © 2005 Wiley‐Liss, Inc.
Difference in Aneurysm Characteristics Between Ruptured and Unruptured Aneurysms in Patients With Multiple Intracranial Aneurysms

Background and Purpose— Prediction of the risk of rupture of unruptured intracranial aneurysms is mainly based on aneurysm size and location. Previous studies identified features of aneurysm shape and flow angles as additional risk factors for aneurysm rupture, but these studies were at risk for confounding by patient-specific risk factors such as hypertension and age. In this study, we avoided this risk by comparing characteristics of ruptured and unruptured aneurysms in patients with both aneurysmal subarachnoid hemorrhage and multiple intracranial aneurysms. Methods— We included patients with aneurysmal subarachnoid hemorrhage and multiple aneurysms who presented to our hospital between 2003 and 2013. We identified the ruptured aneurysm based on bleeding pattern on head computed tomography or surgical findings. Aneurysm characteristics (size, location, shape, aspect ratio [neck-to-dome length / neck-width], flow angles, sidewall or bifurcation type, and contact with bone) were evaluated on computed tomographic angiograms. We calculated odds ratios with 95% confidence intervals with conditional univariable logistic regression analysis. Analyses were repeated after adjustment for aneurysm size and location. Results— The largest aneurysm had not ruptured in 36 (29%) of the 124 included patients with 302 aneurysms. Odds ratios for aspect ratio ≥1.3 was 3.3 (95% confidence intervals [1.3–8.4]) and odds ratios for irregular shape was 3.0 (95% confidence intervals [1.0–8.8]), both after adjustment for aneurysm size and location. Conclusions— Aspect ratio ≥1.3 and irregular shape are associated with aneurysm rupture independent of aneurysm size and location, and independent of patient characteristics. Additional studies need to assess to what extent these factors increase the risks of rupture of small aneurysms in absolute terms.
Two-body relaxation in cosmological simulations

It is logically possible that early two-body relaxation in simulations of cosmological clustering influences the final structure of massive clusters. Convergence studies in which mass and spatial resolution are simultaneously increased cannot eliminate this possibility. We test the importance of two-body relaxation in cosmological simulations with simulations in which there are two species of particles. The cases of two mass ratios, √2:1 and 4:1, are investigated. Simulations are run with both a spatially fixed softening length and adaptive softening using the publicly available codes gadget and mlapm, respectively. The effects of two-body relaxation are detected in both the density profiles of haloes and the mass function of haloes. The effects are more pronounced with a fixed softening length, but even in this case they are not so large as to suggest that results obtained with one mass species are significantly affected by two-body relaxation. The simulations that use adaptive softening are less affected by two-body relaxation and produce slightly higher central densities in the largest haloes. They run about three times faster than the simulations that use a fixed softening length.
DEADSouth protein localizes to germ plasm and is required for the development of primordial germ cells in Xenopus laevis

Summary DEADSouth mRNA is a component of germ plasm in Xenopus laevis and encodes a DDX25 DEAD-box RNA helicase. To determine the intracellular localization of DEADSouth protein, we injected mRNA encoding DEADSouth tagged with mCherry fluorescent protein into fertilized eggs from transgenic Xenopus expressing EGFP fused with a mitochondrial targeting signal. The DEADSouth-mCherry fusion protein was localized to the germ plasm, a mitochondria-rich region in primordial germ cells (PGCs). DEADSouth overexpression resulted in a reduction of PGC numbers after stage 20. Conversely, DEADSouth knockdown using an antisense locked nucleic acid gapmer inhibited movement of the germ plasm from the cortex to the perinuclear region, resulting in inhibition of PGC division at stage 12 and a decrease in PGC numbers at later stages. The knockdown phenotype was rescued by intact DEADSouth mRNA, but not mutant mRNA encoding inactive DEADSouth helicase. Surprisingly, it was also rescued by mouse vasa homolog and Xenopus vasa-like gene 1 mRNAs that encode DDX4 RNA helicases. The rescue was dependent on the 3′ untranslated region (3′UTR) of DEADSouth mRNA, which was used for PGC-specific expression. The 3′UTR contributed to localization of the injected mRNA to the germ plasm, resulting in effective localization of DEADSouth protein. These results demonstrate that localization of DEADSouth helicase to the germ plasm is required for proper PGC development in Xenopus laevis.
Role of core polarization curvature of screw dislocations in determining the Peierls stress in bcc Ta: A criterion for designing high-performance materials

We use a family of embedded atom model potentials all based on accurate quantum-mechanical calculations to study the relation between Peierls stress and core properties of the 1/2 a^111& screw dislocation in bcc tantalum ~Ta! We find that the Peierls stress (s P) is a function of the core-polarization curvature~P! near the equilibrium core configuration. Our results suggest that the computationally available quantity P is a useful criterion for designing high-performance materials. Determining the fundamental atomistic mechanisms that underlie plastic deformations of macroscopic materials is a key, enabling step toward designing materials with improved and tailored properties. This is particularly important for bcc metals, which are the basis of some of the highestperforming alloys, but whose behavior is more complex than fcc and hcp materials. 1 Computer simulations could be used to investigate the individual and collective dislocation motions in these materials and guide the development of highperformance materials. 2 At low temperatures, plasticity in bcc metals is governed by low mobility screw dislocations with Burgers vector b 51/2a^111&. It is generally believed that the core structure of these dislocations is a controlling factor of their mobility. 3 Theoretical studies on these dislocations have led to two types of core structures: asymmetric 3‐5 core and symmetric core. 5‐ 8 In differential displacement ~DD! maps, 3 the asymmetric core @Fig. 1~a! # spreads in three ^112& directions on $110% planes, while the symmetric core @Fig. 1~b! # is compact. The main differences between these two types of cores are the relative displacements in the ^111& direction of the two sets of three atoms in the core @atoms $A, C, E% and $B, D, F% in Fig. 1~c! #. The ‘‘polarization’’ 9 of the dislocation core can be used to distinguish different core configurations and is defined by Eq.~1! , p5 udBC2dABu1udDE2dCDu1udFA2dEFu b , ~1!
State Contract Law and Debt Contracts

This paper examines the relationship between debt contracts and state contract law. We first develop an index to evaluate whether each state’s law is favorable or unfavorable to lenders. We then analyze how the contract terms, the frequency of covenant violations, and the repercussions of covenant violations vary across states. We find that cash collateral is most likely to be used when the contract is governed by law that is favorable to debtors and that out-of-state borrowers who use favorable law pay higher yield spreads. In addition, when the law is favorable to lenders, there are significantly fewer covenant violations, and the repercussions of covenant violations—measured as changes in the borrower’s investment policy—are more severe. We also compare the characteristics of relevant parties across states, and the results provide support for the theory that there is a market for contracts similar to the market for incorporations.
Theory of order statistic filters and their relationship to linear FIR filters

Necessary and/or sufficient conditions on both the filter coefficients and the signal process are derived in order that nonrecursive order statistic (OS) and linear filtering are equivalent operations. The results indicate that an understanding of OS filters hinges on a better understanding of the properties of signals containing logically monotonic components. The results extend a number of previous theories characterizing the well-known median and ranked-order filters to a broader class of filters and input signals. >
Mid-Air Fingertip-Based User Interaction in Mixed Reality

With data growing at a huge rate, there arises a need for advanced data visualization techniques. Visualizing these data sets in Mixed Reality(MR) mode provides an immersive experience to the user in the context of the real world applications. Most of the existing works can only be used with inordinately priced devices such as Microsoft HoloLens, Meta Glass that use proprietary hardware for data visualization and user interaction through hand gestures. In this paper, we demonstrate a cost-effective solution for data visualization using frugal devices such as Google Cardboard, VR Box etc. in MR mode. However, these devices still employ only primitive modes of interaction such as the magnetic trigger, conductive lever and have a limited user-input capability. To interact with visualizations and facilitate rich user experience, we propose the use of intuitive pointing fingertip gestural interface in the user's Field of View(FoV). The proposed pointing hand gesture recognition framework is driven by cascade of state-of-the-art deep learning model - Faster RCNN for localizing the hand followed by a proposed regression CNN for fingertip localization. We conducted both objective and subjective evaluation to demonstrate the performance of our proposed method. Objective metrics are fingertip recognition accuracy and computational time. The subjective evaluation includes user comfort and effectiveness of fingertip interaction that is proposed.
Thermodynamic Modeling of Hydrogen Storage Capacity in Mg-Na Alloys

Thermodynamic modeling of the H-Mg-Na system is performed for the first time in this work in order to understand the phase relationships in this system. A new thermodynamic description of the stable NaMgH3 hydride is performed and the thermodynamic models for the H-Mg, Mg-Na, and H-Na systems are reassessed using the modified quasichemical model for the liquid phase. The thermodynamic properties of the ternary system are estimated from the models of the binary systems and the ternary compound using CALPHAD technique. The constructed database is successfully used to reproduce the pressure-composition isotherms for MgH2 + 10 wt. % NaH mixtures. Also, the pressure-temperature equilibrium diagram and reaction paths for the same composition are predicted at different temperatures and pressures. Even though it is proved that H-Mg-Na does not meet the DOE hydrogen storage requirements for onboard applications, the best working temperatures and pressures to benefit from its full catalytic role are given. Also, the present database can be used for thermodynamic assessments of higher order systems.
Is Maternal Obesity a Risk Factor for Anencephaly and Spina Bifida?

&NA; To determine whether the risk of having an infant with anencephaly or spina bifida is greater among obese women than among average‐weight women, we compared 307 Atlanta‐area women who gave birth to a liveborn or stillborn infant with anencephaly or spina bifida (case group) with 2,755 Atlantaarea women who gave birth to an infant without birth defects (control group). The infants of control women were randomly selected from birth certificates and frequency‐matched to the case group by race, birth hospital, and birth period from 1968 through 1980. After adjusting for maternal age, education, smoking status, alcohol use, chronic illness, and vitamin use, we found that, compared with average‐weight women, obese women (pregravid body mass index greater than 29) had almost twice the risk of having an infant with spina bifida or anencephaly (odds ratio = 1.9; 95% confidence limits = 1.1, 3.4). A woman's risk increased with her body mass index: adjusted odds ratios ranged from 0.6 (95% confidence limits = 0.3, 2.1) for very underweight women to 1.9 for obese women.