Miracle-dz/UniFAR-FTUs huggingface dataset:
Microscopic Surface Textures Created by Interfacial Flow Instabilities

In nature, microscopic surface textures impact useful function, such as the drag reduction of shark skin (Dean & Bhushan, 2010) and superhydrophobicity of the lotus leaf(Pan, Kota, Mabry, & Tuteja, 2013). In this study, we explore these phenomena by re-creating microscopic surface textures via the method of interfacial flow instability in drying polyvinylidene fluoride (PVDF) acetone solutions. In general, PVDF films can be made using either spin coating or electrospray deposition with various weight concentrations in acetone. In order to study the morphology of the porous structure of PVDF films, wet deposition samples were fabricated by spin coating or near-field electrospray. Possible theories are discussed and examined to explain the formation of these porous structures resulting in development of a well-controlled method to create porous PVDF films with various pore sizes and pore densities. All samples are characterized and found to exhibit superhydrophobicity and drag reduction. To connect porous PVDF film morphology to the established field of dry particle fabrication, PVDF particle synthesis by far-field electrospray is also reviewed and discussed. An established method to generate polymer particles of different morphologies in other polymers (Almería-Díez, 2012) by electrospray drying is confirmed using PVDF as well. Due to the ability of scalable and re-configurable electrospray, the microscopic surface textures can be applied to areas of any size to reduce drag or impart waterrepelling properties.
Tetrabutylammonium Iodide–Promoted Thiolation of Oxindoles Using Sulfonyl Chlorides as Sulfenylation Reagents

3-Sulfanyloxindoles were synthesised by triphenylphosphine-mediated transition-metal-free thiolation of oxindoles using sulfonyl chlorides as sulfenylation reagents. The above reaction was promoted by iodide anions, which was ascribed to the in situ conversion of sulfenyl chlorides into the more reactive sulfenyl iodides. Moreover, the thiolation of 3-aryloxindoles was facilitated by bases. The use of a transition-metal-free protocol, readily available reagents, and mild reaction conditions make this protocol more practical for preparing 3-sulfanyloxindoles than traditional methods.
Measuring the Halo Mass of z ~ 3 Damped Lyα Absorbers from the Absorber-Galaxy Cross-Correlation

We test the reliability of a method to measure the mean halo mass of absorption-line systems such as damped Lyα absorbers (DLAs). The method is based on measuring the ratio of the cross-correlation between DLAs and galaxies to the autocorrelation of the galaxies themselves, which is (in linear theory) the ratio of their bias factor b̄. We show that the ratio of the projected cross- and autocorrelation functions [wdg(rθ)/wgg(rθ)] is also the ratio of their bias factor, irrespective of the galaxy distribution, provided that one uses the same galaxies for wdg(rθ) and wgg(rθ). Thus, the method requires only multiband imaging of DLA fields and is applicable to all redshifts. Here, we focus on z = 3 DLAs. We demonstrate that the method robustly constrains the mean DLA halo mass using smoothed particle hydrodynamics (SPH) cosmological simulations that resolve DLAs and galaxies in halos of mass Mh ≳ 5.2 × 1010 M☉. If we use the bias formalism of Mo & White with the DLA and galaxy mass distributions of these simulations, we predict an amplitude ratio wdg/wgg of 0.771. Direct measurement of these correlation functions from the simulations yields wdg/wgg = b̄DLA/b̄gal = 0.73 ± 0.08, in excellent agreement with that prediction. Equivalently, inverting the measured correlation ratio to infer the (logarithmically) averaged DLA halo mass yields ⟨log MDLA(M☉)⟩ = 11.13, in excellent agreement with the true value in the simulations: log MDLA(M☉) = 11.16 is the probability-weighted mean mass of the DLA host halos in the simulations. The cross-correlation method thus appears to yield a robust estimate of the average host halo mass, even though the DLAs and the galaxies occupy a broad mass spectrum of halos and massive halos contain multiple galaxies with DLAs. If we consider subsets of the simulated galaxies with high star formation rates (representing Lyman break galaxies [LBGs]), then both correlations are higher, but their ratio still implies the same DLA host mass, irrespective of the galaxy subsamples, i.e., the cross-correlation technique is also reliable. The inferred mean DLA halo mass, ⟨log MDLA⟩ = 11.13, is an upper limit, since the simulations do not resolve halos less massive than ~1010.5 M☉. Thus, our results imply that the correlation length between DLAs and LBGs is predicted to be at most ~2.85 h-1 Mpc, given that z = 3 LBGs have a correlation length of r0 ≃ 4 h-1 Mpc. While the small size of current observational samples does not allow strong conclusions, future measurements of this cross-correlation can definitively distinguish models in which many DLAs reside in low-mass halos from those in which DLAs are massive disks occupying only high-mass halos.
A Novel Genetic Score Approach Using Instruments to Investigate Interactions between Pathways and Environment: Application to Air Pollution

Air pollution has been associated with increased systemic inflammation markers. We developed a new pathway analysis approach to investigate whether gene variants within relevant pathways (oxidative stress, endothelial function, and metal processing) modified the association between particulate air pollution and fibrinogen, C-reactive protein (CRP), intercellular adhesion molecule-1 (ICAM-1), and vascular cell adhesion molecule-1 (VCAM-1). Our study population consisted of 822 elderly participants of the Normative Aging Study (1999–2011). To investigate the role of biological mechanisms and to reduce the number of comparisons in the analysis, we created pathway-specific scores using gene variants related to each pathway. To select the most appropriate gene variants, we used the least absolute shrinkage and selection operator (Lasso) to relate independent outcomes representative of each pathway (8-hydroxydeoxyguanosine for oxidative stress, augmentation index for endothelial function, and patella lead for metal processing) to gene variants. A high genetic score corresponds to a higher allelic risk profile. We fit mixed-effects models to examine modification by the genetic score of the weekly air pollution association with the outcome. Among participants with higher genetic scores within the oxidative stress pathway, we observed significant associations between particle number and fibrinogen, while we did not find any association among participants with lower scores (pinteraction = 0.04). Compared to individuals with low genetic scores of metal processing gene variants, participants with higher scores had greater effects of particle number on fibrinogen (pinteraction = 0.12), CRP (pinteraction = 0.02), and ICAM-1 (pinteraction = 0.08). This two-stage penalization method is easy to implement and can be used for large-scale genetic applications.
Molecular Characterization of a Lysozyme Gene and Its Altered Expression Profile in Crowded Beet Webworm (Loxostege sticticalis)

There is growing evidence that insects living in high-density populations exhibit an increase in immune function to counter a higher risk of disease. This phenomenon, known as density-dependent prophylaxis, has been experimentally tested in a number of insect species. Although density-dependent prophylaxis is especially prevalent in insects exhibiting density-dependent phase polyphenism, the molecular mechanism remains unclear. Our previous study demonstrated that the antibacterial activity of lysozyme is important for this process in the beet webworm Loxostege sticticalis. In this study, a lysozyme cDNA from L. sticticalis was cloned and characterized. The full-length cDNA is 1078 bp long and contains an open reading frame of 426 bp that encodes 142 amino acids. The deduced protein possesses structural characteristics of a typical c-type lysozyme and clusters with c-type lysozymes from other Lepidoptera. LsLysozyme was found to be expressed throughout all developmental stages, showing the highest level in pupae. LsLysozyme was also highly expressed in the midgut and fat body. Elevated LsLysozyme expression was observed in L. sticticalis larvae infected by Beauveria bassiana and in larvae reared under crowding conditions. In addition, the expression level of LsLysozyme in infected larvae reared at a density of 10 larvae per jar was significantly higher compared to those reared at a density of l or 30 larvae per jar. These results suggest that larval crowding affects the gene expression profile of this lysozyme. This study provides additional insight into the expression of an immune-associated lysozyme gene and helps us to better understand the immune response of L. sticticalis under crowding conditions.
Bayesian analysis of multimethod ego‐depletion studies favours the null hypothesis

Ego-depletion refers to the purported decrease in performance on a task requiring self-control after engaging in a previous task involving self-control, with self-control proposed to be a limited resource. Despite many published studies consistent with this hypothesis, recurrent null findings within our laboratory and indications of publication bias have called into question the validity of the depletion effect. This project used three depletion protocols involved three different depleting initial tasks followed by three different self-control tasks as dependent measures (total n = 840). For each method, effect sizes were not significantly different from zero When data were aggregated across the three different methods and examined meta-analytically, the pooled effect size was not significantly different from zero (for all priors evaluated, Hedges' g = 0.10 with 95% credibility interval of [-0.05, 0.24]) and Bayes factors reflected strong support for the null hypothesis (Bayes factor > 25 for all priors evaluated).
Interest Rate Derivatives at Commercial Banks: An Empirical Investigation

I analyze the effects of bank characteristics and macroeconomic shocks on interest rate risk-management behavior of commercial banks. My findings are consistent with hedging theories based on cost of financial distress and costly external financing. Banks with higher probability of financial distress manage their interest rate risk more aggressively, both by means of on-balance sheet and off-balance sheet instruments. As compared to the derivative users, the derivative non-user banks adopt conservative asset-liability management policies in tighter monetary policy regimes. Finally, I show that the derivative non-user bank's lending volume declines significantly with the contraction in the money supply. Derivative users, on the other hand, remain immune to the monetary policy shocks. My findings suggest that a potential benefit of derivatives usage is to minimize the effect of external shocks on a firm's operating policies
On the Resistance of Neural Nets to Label Noise

We investigate the behavior of convolutional neural networks (CNN) in the presence of label noise. We show empirically that CNN prediction for a given test sample depends on the labels of the training samples in its local neighborhood. This is similar to the way that the K-nearest neighbors (K-NN) classifier works. With this understanding, we derive an analytical expression for the expected accuracy of a K-NN, and hence a CNN, classifier for any level of noise. In particular, we show that K-NN, and CNN, are resistant to label noise that is randomly spread across the training set, but are very sensitive to label noise that is concentrated. Experiments on real datasets validate our analytical expression by showing that they match the empirical results for varying degrees of label noise.
Impaired Attention and Synaptic Senescence of the Prefrontal Cortex Involves Redox Regulation of NMDA Receptors

Young (3–6 months) and middle-age (10–14 months) rats were trained on the five-choice serial reaction time task. Attention and executive function deficits were apparent in middle-age animals observed as a decrease in choice accuracy, increase in omissions, and increased response latency. The behavioral differences were not due to alterations in sensorimotor function or a diminished motivational state. Electrophysiological characterization of synaptic transmission in slices from the mPFC indicated an age-related decrease in glutamatergic transmission. In particular, a robust decrease in N-methyl-d-aspartate receptor (NMDAR)-mediated synaptic responses in the mPFC was correlated with several measures of attention. The decrease in NMDAR function was due in part to an altered redox state as bath application of the reducing agent, dithiothreitol, increased the NMDAR component of the synaptic response to a greater extent in middle-age animals. Together with previous work indicating that redox state mediates senescent physiology in the hippocampus, the results indicate that redox changes contribute to senescent synaptic function in vulnerable brain regions involved in age-related cognitive decline.
Dihydroartemisinin Accentuates the Anti-Tumor Effects of Photodynamic Therapy via Inactivation of NF-κB in Eca109 and Ec9706 Esophageal Cancer Cells

Background: Photodynamic therapy (PDT) is a new treatment for esophageal cancer which has been shown to be effective in the elimination of tumor. However, PDT could induce the activation of nuclear factor-kappa B (NF-κB) in many photosensitizers based PDT, which plays a negative role in PDT. In addition, our previous results have shown that dihydroartemisinin (DHA), which was the most potent one of artemisinin derivatives, has anticancer activity in esophageal cancer cells. Methods: Cell viability was determined by MTT analysis, and apoptosis was evaluated by flow cytometry. Nuclear extract was obtained for determining NF-κB DNA-binding activity, while total protein extract obtained for downstream gene expression by western blot. Results: We demonstrated DHA enhanced PDT-induced growth inhibition and apoptosis in both human esophageal cancer cell lines Eca109 and Ec9706 in vitro. The mechanism was at least partially due to DHA deactivated PDT-induced NF-κB activation, so as to decrease tremendously the expression of its target gene Bcl-2. Conclusion: Our results demonstrate that DHA augments PDT-induced growth inhibition and apoptosis in esophageal cancer cells, and that inactivation of NF-κB activity is a potential mechanism by which DHA sensitizes esophageal cancer cells to PDT-induced growth inhibition and apoptosis.
Transparent Key Integrity (TKI): A Proposal for a Public-Key Validation Infrastructure (CMU-CyLab-12-016)

Recent trends in public-key infrastructure research explore the tradeoff between decreased trust in certificate authorities (CAs), the level of security achieved, the communication overhead (bandwidth and latency) for setting up a secure connection (e.g., verified via SSL/ TLS), and the availability with respect to verifiability of public key information. In this paper, we propose TKI as a new public-key validation infrastructure, where we reduce the level of trust in any CA and increase the security by achieving increased robustness in the case of CA key compromise. Compared to other proposals, we reduce the communication overhead associated with certificate validation during the existing SSL/TLS connection handshake and provide site owners with an optional time window to review potentially malicious key changes. Our design deters CA misbehavior by using a public log that records all certificate events, thereby enabling CAs’ accountability for their actions. TKI will help reduce the trust in the hundreds of currently trusted CAs, reduce exposure to CA compromise, and enhance the security of SSL/TLS connection establishment.
Antiviral RNA Interference Responses Induced by Semliki Forest Virus Infection of Mosquito Cells: Characterization, Origin, and Frequency-Dependent Functions of Virus-Derived Small Interfering RNAs

ABSTRACT RNA interference (RNAi) is an important mosquito defense mechanism against arbovirus infection. In this paper we study the processes underlying antiviral RNAi in Aedes albopictus-derived U4.4 mosquito cells infected with Semliki Forest virus (SFV) (Togaviridae; Alphavirus). The production of virus-derived small interfering RNAs (viRNAs) from viral double-stranded RNA (dsRNA) is a key event in this host response. dsRNA could be formed by RNA replication intermediates, by secondary structures in RNA genomes or antigenomes, or by both. Which of these dsRNAs is the substrate for the generation of viRNAs is a fundamental question. Here we used deep sequencing of viRNAs and bioinformatic analysis of RNA secondary structures to gain insights into the characteristics and origins of viRNAs. An asymmetric distribution of SFV-derived viRNAs with notable areas of high-level viRNA production (hot spots) and no or a low frequency of viRNA production (cold spots) along the length of the viral genome with a slight bias toward the production of genome-derived viRNAs over antigenome-derived viRNAs was observed. Bioinformatic analysis suggests that hot spots of viRNA production are rarely but not generally associated with putative secondary structures in the SFV genome, suggesting that most viRNAs are derived from replicative dsRNA. A pattern of viRNAs almost identical to those of A. albopictus cells was observed for Aedes aegypti-derived Aag2 cells, suggesting common mechanisms that lead to viRNA production. Hot-spot viRNAs were found to be significantly less efficient at mediating antiviral RNAi than cold-spot viRNAs, pointing toward a nucleic acid-based viral decoy mechanism to evade the RNAi response.
In vitro inhibitory effects of dihydromyricetin on human liver cytochrome P450 enzymes

Abstract Context: Dihydromyricetin (DHM) is the most abundant and active flavonoid component isolated from Ampelopsis grossedentata (Hand-Mazz) W.T. Wang (Vitaceae) and it possesses numerous pharmacological activities. However, whether DHM affects the activity of human liver cytochrome P450 (CYP) enzymes remains unclear. Materials and methods: The inhibitory effects of DHM on eight human liver CYP isoforms (i.e., 1A2, 3A4, 2A6, 2E1, 2D6, 2C9, 2C19 and 2C8) were investigated in vitro using human liver microsomes (HLMs). Results: The results showed that DHM could inhibit the activity of CYP3A4, CYP2E1 and CYP2D6, with IC50 values of 14.75, 25.74 and 22.69 μM, respectively, but that other CYP isoforms were not affected. Enzyme kinetic studies showed that DHM was not only a non-competitive inhibitor of CYP3A4 but also a competitive inhibitor of CYP2E1 and CYP2D6, with Ki values of 6.06, 9.24 and 10.52 μM, respectively. In addition, DHM is a time-dependent inhibitor for CYP3A4 with KI/Kinact value of 12.17/0.057 min−1 μM−1. Discussion and conclusion: The in vitro studies of DHM with CYP isoforms indicate that DHM has the potential to cause pharmacokinetic drug interactions with other co-administered drugs metabolized by CYP3A4, CYP2E1 and CYP2D6. Further clinical studies are needed to evaluate the significance of this interaction.
The effect of the financial crisis on physical health: Perceived impact matters

The impact of the financial crisis on health was investigated (N = 312). Intraindividual intercept, slope, and quadratic parameters capturing trends in income, subjective financial situation, and perceived stress across the period predicted physical health, controlling for baseline health. For those experiencing a decline in financial situation, a decrease in financial situation and an increase in perceived stress predicted poorer health; neither financial situation nor perceived stress predicted health in those not experiencing this decline. Although we cannot intervene in contextual factors like the financial crisis, health outcomes may be improved by targeting perceived impact and stress levels in those who feel affected.
Notes on Decomposition Methods

Decomposition is a general approach to solving a problem by breaking it up into smaller ones and solving each of the smaller ones separately, either in parallel or sequentially. (When it is done sequentially, the advantage comes from the fact that problem complexity grows more than linearly.) Problems for which decomposition works in one step are called (block) separable, or trivially parallelizable. As a general example of such a problem, suppose the variable x can be partitioned into subvectors x1;:::;xk, the objective is a sum of functions of xi, and each constraint involves only variables from one of the subvectors xi. Then evidently we can solve each problem involving xi separately (and in parallel), and then re-assemble the solution x. Of course this is a trivial, and not too interesting, case. A more interesting situation occurs when there is some coupling or interaction between the subvectors, so the problems cannot be solved independently. For these cases there are techniques that solve the overall problem by iteratively solving a sequence of smaller problems. There are many ways to do this; in this note we consider some simple examples that illustrate the ideas. Decomposition is an old idea, and appears in early work on large-scale LPs from the 1960s [DW60]. A good reference on decomposition methods is chapter 6 of Bertsekas [Ber99].
A high-throughput small molecule screen identifies synergism between DNA methylation and Aurora kinase pathways for X reactivation

Significance In mammalian female cells, nearly all genes are silenced on one of two X chromosomes. Heterozygous females with “dominant” X-linked diseases, such as Rett syndrome, may benefit from pharmacological reactivation of the silent, healthy allele in affected organs. Toward establishing proof of concept, here we carry out a primed screen of a large library of small molecules for compounds that can reactivate expression from the inactive X (Xi). We identify a combination of compounds that inhibits the DNA methylation and Aurora kinase pathways and demonstrate that the two pathways act synergistically to repress genes on the Xi, including genes involved in X-linked disease. X-chromosome inactivation is a mechanism of dosage compensation in which one of the two X chromosomes in female mammals is transcriptionally silenced. Once established, silencing of the inactive X (Xi) is robust and difficult to reverse pharmacologically. However, the Xi is a reservoir of >1,000 functional genes that could be potentially tapped to treat X-linked disease. To identify compounds that could reactivate the Xi, here we screened ∼367,000 small molecules in an automated high-content screen using an Xi-linked GFP reporter in mouse fibroblasts. Given the robust nature of silencing, we sensitized the screen by “priming” cells with the DNA methyltransferase inhibitor, 5-aza-2′-deoxycytidine (5azadC). Compounds that elicited GFP activity include VX680, MLN8237, and 5azadC, which are known to target the Aurora kinase and DNA methylation pathways. We demonstrate that the combinations of VX680 and 5azadC, as well as MLN8237 and 5azadC, synergistically up-regulate genes on the Xi. Thus, our work identifies a synergism between the DNA methylation and Aurora kinase pathways as being one of interest for possible pharmacological reactivation of the Xi.