Miracle-dz/UniFAR-FTUs huggingface dataset:
Unreported cases in the 2014-2016 Ebola epidemic: Spatiotemporal variation, and implications for estimating transmission

In the recent 2014–2016 Ebola epidemic in West Africa, non-hospitalized cases were an important component of the chain of transmission. However, non-hospitalized cases are at increased risk of going unreported because of barriers to access to healthcare. Furthermore, underreporting rates may fluctuate over space and time, biasing estimates of disease transmission rates, which are important for understanding spread and planning control measures. We performed a retrospective analysis on community deaths during the recent Ebola epidemic in Sierra Leone to estimate the number of unreported non-hospitalized cases, and to quantify how Ebola reporting rates varied across locations and over time. We then tested if variation in reporting rates affected the estimates of disease transmission rates that were used in surveillance and response. We found significant variation in reporting rates among districts, and district-specific rates of increase in reporting over time. Correcting time series of numbers of cases for variable reporting rates led, in some instances, to different estimates of the time-varying reproduction number of the epidemic, particularly outside the capital. Future analyses that compare Ebola transmission rates over time and across locations may be improved by considering the impacts of differential reporting rates.
- 1-A COMPUTATIONAL FLUID DYNAMICS STUDY OF ‘ CLAP AND FLING ’ IN THE SMALLEST INSECTS

In this paper, we have used the immersed boundary method t o solve the twodimensional Navier-Stokes equations with two immersed wings performing an idealized ‘clap and fling’ stroke and a ‘fling’ half stroke. We calculated lift coefficients as a function of time per wing for a range of Reyn olds numbers between 8 and 128. We also calculated the instantaneous streamlines ar ound each wing throughout the stroke cycle and related the changes in lift to the relative strength and position of the leading and trailing edge vortices.
Patrolling Mechanics of Non-Classical Monocytes in Vascular Inflammation

Non-classical monocytes have emerged as the preeminent vascular housekeepers. Continuous intravascular screening is enabled by slow patrolling on the endothelium and allows a rapid response to local perturbations. Intravital imaging has been crucial to elucidate the molecular mechanisms and migratory phenotype of patrolling. In this review, we discuss technical requirements of intravital microscopy such as imaging modalities, labeling strategies, and data analysis. We further focus on patrolling kinetics and adhesion receptors in different organs and vascular beds including arteries during homeostasis and vascular inflammation and define pertinent questions in the field.
Numerical study of the lateral resolution in electrostatic force microscopy for dielectric samples

We present a study of the lateral resolution in electrostatic force microscopy for dielectric samples in both force and gradient modes. Whereas previous studies have reported expressions for metallic surfaces having potential heterogeneities (Kelvin probe force microscopy), in this work we take into account the presence of a dielectric medium. We introduce a definition of the lateral resolution based on the force due to a test particle being either a point charge or a polarizable particle on the dielectric surface. The behaviour has been studied over a wide range of typical experimental parameters: tip–sample distance (1–20) nm, sample thickness (0–5) µm and dielectric constant (1–20), using the numerical simulation of the equivalent charge method. For potential heterogeneities on metallic surfaces expressions are in agreement with the bibliography. The lateral resolution of samples having a dielectric constant of more than 10 tends to metallic behaviour. We found a characteristic thickness of 100 nm, above which the lateral resolution measured on the dielectric surface is close to that of an infinite medium. As previously reported, the lateral resolution is better in the gradient mode than in the force mode. Finally, we showed that for the same experimental conditions, the lateral resolution is better for a polarizable particle than for a charge, i.e. dielectric heterogeneities should always look ‘sharper’ (better resolved) than inhomogeneous charge distributions. This fact should be taken into account when interpreting images of heterogeneous samples.
Targeting nasopharyngeal carcinoma by artesunate through inhibiting Akt/mTOR and inducing oxidative stress

Drug repurposing has become an alternative therapeutic strategy for cancer treatment given the known pharmacokinetics and toxicity. The inhibitory effects of artesunate have been reported in various cancers. In this work, we investigated the effects of artesunate in nasopharyngeal carcinoma (NPC). We demonstrate that artesunate significantly inhibits proliferation via arresting NPC cells at G2/M phase. It also induces apoptosis through caspase‐dependent and mitochondria‐independent pathways in multiple NPC cell lines. The combination of artesunate and cisplatin is synergistic in targeting NPC cells in in vitro cellular culture system and in vivo xenograft tumor models. Artesunate inhibits phosphorylation of essential molecules involved in Akt/mTOR pathway in NPC cells, such as Akt, mTOR, and 4EBP1, and its inhibitory effects are partially abolished by overexpression of constitutively active Akt. In addition, artesunate also induces mitochondrial dysfunction and oxidative stress via inhibiting mitochondrial respiration, increasing levels of mitochondrial superoxide and cellular reactive oxygen species (ROS), leading to decreased ATP levels. Two ROS scavengers partially abolish the inhibitory effects of artesunate in NPC cells. These data suggest that both inhibition of Akt/mTOR pathway and induction of ROS are required for the action of artesunate in NPC cells. Our work demonstrates that artesunate is a potential candidate for NPC treatment. Our work also highlights the critical roles of Akt/mTOR pathway and mitochondrial function in NPC cells.
A Better Facet of Dynamic Information Flow Control

Multiple Facets (MF) is a dynamic enforcement mechanism which has proved to be a good fit for implementing information flow security for JavaScript. It relies on multi executing the program, once per each security level or view, to achieve soundness. By looking inside programs, MF encodes the views to reduce the number of needed multi-executions. In this work, we extend Multiple Facets in three directions. First, we propose a new version of MF for arbitrary lattices, called Generalised Multiple Facets, or GMF. GMF strictly generalizes MF, which was originally proposed for a specific lattice of principals. Second, we propose a new optimization on top of GMF that further reduces the number of executions. Third, we strengthen the security guarantees provided by Multiple Facets by proposing a termination sensitive version that eliminates covert channels due to termination.
Dihydropyridine Receptors and Type 1 Ryanodine Receptors Constitute the Molecular Machinery for Voltage-Induced Ca2+ Release in Nerve Terminals

Ca2+ stores were studied in a preparation of freshly dissociated terminals from hypothalamic magnocellular neurons. Depolarization from a holding level of −80 mV in the absence of extracellular Ca2+ elicited Ca2+ release from intraterminal stores, a ryanodine-sensitive process designated as voltage-induced Ca2+ release (VICaR). The release took one of two forms: an increase in the frequency but not the quantal size of Ca2+ syntillas, which are brief, focal Ca2+ transients, or an increase in global [Ca2+]. The present study provides evidence that the sensors of membrane potential for VICaR are dihydropyridine receptors (DHPRs). First, over the range of −80 to −60 mV, in which there was no detectable voltage-gated inward Ca2+ current, syntilla frequency was increased e-fold per 8.4 mV of depolarization, a value consistent with the voltage sensitivity of DHPR-mediated VICaR in skeletal muscle. Second, VICaR was blocked by the dihydropyridine antagonist nifedipine, which immobilizes the gating charge of DHPRs but not by Cd2+ or FPL 64176 (methyl 2,5 dimethyl-4[2-(phenylmethyl)benzoyl]-1H-pyrrole-3-carboxylate), a non-dihydropyridine agonist specific for L-type Ca2+ channels, having no effect on gating charge movement. At 0 mV, the IC50 for nifedipine blockade of VICaR in the form of syntillas was 214 nm in the absence of extracellular Ca2+. Third, type 1 ryanodine receptors, the type to which DHPRs are coupled in skeletal muscle, were detected immunohistochemically at the plasma membrane of the terminals. VICaR may constitute a new link between neuronal activity, as signaled by depolarization, and a rise in intraterminal Ca2+.
Osteopontin deletion drives hematopoietic stem cell mobilization to the liver and increases hepatic iron contributing to alcoholic liver disease

The aim of this study was to investigate the role of osteopontin (OPN) in hematopoietic stem cell (HPSC) mobilization to the liver and its contribution to alcoholic liver disease (ALD). We analyzed young (14‐16 weeks) and old (>1.5 years) wild‐type (WT) littermates and global Opn knockout (Opn−/−) mice for HPSC mobilization to the liver. In addition, WT and Opn−/− mice were chronically fed the Lieber–DeCarli diet for 7 weeks. Bone marrow (BM), blood, spleen, and liver were analyzed by flow cytometry for HPSC progenitors and polymorphonuclear neutrophils (PMNs). Chemokines, growth factors, and cytokines were measured in serum and liver. Prussian blue staining for iron deposits and naphthol AS‐D chloroacetate esterase staining for PMNs were performed on liver sections. Hematopoietic progenitors were lower in liver and BM of young compared to old Opn−/− mice. Granulocyte colony‐stimulating factor and macrophage colony‐stimulating factor were increased in Opn−/− mice, suggesting potential migration of HPSCs from the BM to the liver. Furthermore, ethanol‐fed Opn−/− mice showed significant hepatic PMN infiltration and hemosiderin compared to WT mice. As a result, ethanol feeding caused greater liver injury in Opn−/− compared to WT mice. Conclusion: Opn deletion promotes HPSC mobilization, PMN infiltration, and iron deposits in the liver and thereby enhances the severity of ALD. The age‐associated contribution of OPN to HPSC mobilization to the liver, the prevalence of PMNs, and accumulation of hepatic iron, which potentiates oxidant stress, reveal novel signaling mechanisms that could be targeted for therapeutic benefit in patients with ALD. (Hepatology Communications 2018;2:84–98)
Gesture Interface for the Blind Using the Leap Motion Controller

The aim of described preliminary studies was the evaluation of prototype gesture user interface using the Leap Motion controller. Provided experiment used a modified version of the file explorer that was supported by gesture controller and synthesized voice feedback. Obtained results shows that visual disability does not have a significant influence on the correctness of controlling the application using the proposed contact-free interface.
Experimental and procedural pain responses in primary dysmenorrhea: a systematic review

Primary dysmenorrhea (PD) has been the focus of a number of experimental pain studies. Although a number of reviews exist, few have critically evaluated the existing body of research on PD and experimental and procedural pain. Data from 19 published research articles that include women with PD and responses to an experimental or procedural pain stimulus (or stimuli) suggest that women with PD may have elevated pain reactivity, as compared to women without PD. This pattern appears to be true across different phases of the menstrual cycle. However, there is an abundance of conflicting findings, which may be due to significant methodological issues such as inconsistent definitions of PD, wide variation in experimental pain methodologies, and inaccurate assessment of the menstrual cycle. Future research should focus on identifying specific symptoms (i.e., pain threshold ratings) to more clearly define what constitutes PD, establish reliable and valid laboratory testing protocols, and assess the menstrual cycle with greater precision.
i2kit: A Tool for Immutable Infrastructure Deployments based on Lightweight Virtual Machines specialized to run Containers

Container technologies, like Docker, are becoming increasingly popular. Containers provide exceptional developer experience because containers offer lightweight isolation and ease of software distribution. Containers are also widely used in production environments, where a different set of challenges arise such as security, networking, service discovery and load balancing. Container cluster management tools, such as Kubernetes, attempt to solve these problems by introducing a new control layer with the container as the unit of deployment. However, adding a new control layer is an extra configuration step and an additional potential source of runtime errors. The virtual machine technology offered by cloud providers is more mature and proven in terms of security, networking, service discovery and load balancing. However, virtual machines are heavier than containers for local development, are less flexible for resource allocation, and suffer longer boot times. This paper presents an alternative to containers that enjoy the best features of both approaches: (1) the use of mature, proven cloud vendor technology; (2) no need for a new control layer; and (3) as lightweight as containers. Our solution is i2kit, a deployment tool based on the immutable infrastructure pattern, where the virtual machine is the unit of deployment. The i2kit tool accepts a simplified format of Kubernetes Deployment Manifests in order to reuse Kubernetes' most successful principles, but it creates a lightweight virtual machine for each Pod using Linuxkit. Linuxkit alleviates the drawback in size that using virtual machines would otherwise entail, because the footprint of Linuxkit is approximately 60MB. Finally, the attack surface of the system is reduced since Linuxkit only installs the minimum set of OS dependencies to run containers, and different Pods are isolated by hypervisor technology.
Witten Conditioning Cholinergic Interneurons Control Local Circuit Activity and Cocaine

, 1677 (2010); 330 Science et al. Ilana B. Witten Conditioning Cholinergic Interneurons Control Local Circuit Activity and Cocaine This copy is for your personal, non-commercial use only. clicking here. colleagues, clients, or customers by , you can order high-quality copies for your If you wish to distribute this article to others here. following the guidelines can be obtained by Permission to republish or repurpose articles or portions of articles ): September 19, 2014 www.sciencemag. org (this information is current as of The following resources related to this article are available online at http://www.sciencemag. org/content/330/6011/1677.full. html version of this article at: including high-resolution figures, can be found in the online Updated information and services, http://www.sciencemag. org/content/suppl/2010/12/14/330.6011. 1677.DC1. html can be found at: Supporting Online Material http://www.sciencemag. org/content/330/6011/1677.full. html#ref-list-1 , 16 of which can be accessed free: cites 40 articles This article http://www.sciencemag. org/content/330/6011/1677.full. html#related-urls 31 articles hosted by HighWire Press; see: cited by This article has been http://www.sciencemag. org/cgi/collection/neuroscience Neuroscience subject collections: This article appears in the following
Depletion of keratin 8/18 modulates oncogenic potential by governing multiple signaling pathways

Keratin 8/18, the predominant keratin pair of simple epithelia, is often aberrantly expressed in various squamous cell carcinomas (SCCs) including skin SCC. Its aberrant expression is correlated with increased invasiveness and poor prognosis of the same, although the underlying mechanism is still unclear. A previous report from our laboratory has shown K8‐mediated regulation of α6β4 integrin signaling and thereby tumorigenic potential of oral SCC‐derived cells. Another study on transgenic mouse model has shown that during skin carcinogenesis, K8 favors conversion of papillomas toward malignancy. In order to understand the role of K8 and allied mechanism in skin SCC, K8 was stably knocked down in a skin epidermoid carcinoma‐derived A431 cells. K8 downregulation significantly reduced the tumorigenic potential of these cells. In agreement with our phenotypic data, differential quantitative proteomics followed by IPA analysis showed altered expression of many proteins associated with biological functions including ‘Cancer’, ‘Cellular movement’, ‘Cell death and survival’, and ‘Cellular morphology’. Some of these proteins were TMS1, MARCKSL1, RanBP1, 14‐3‐3γ, Rho‐GDI2, etc. Furthermore, to our surprise, there was a significant reduction in K17 protein stability upon loss of K8, probably due to its caspase‐mediated degradation. This was supported by altered TMS1‐NF‐κB signaling, leading to increased apoptotic sensitivity of A431 cells which in turn affected ‘Cell death and survival’. Moreover, MARCKSL1‐Paxillin1‐Rac axis was found to be deregulated bestowing a possible mechanism behind altered ‘Cellular movement’ pathway. Altogether our study unravels a much broader regulatory role of K8, governing multiple signaling pathways and consequently regulating oncogenic potential of skin SCC‐derived cells.
Adding Recognition Discriminability Index to the Delayed Recall Is Useful to Predict Conversion from Mild Cognitive Impairment to Alzheimer's Disease in the Alzheimer's Disease Neuroimaging Initiative

Background: Ongoing research is focusing on the identification of those individuals with mild cognitive impairment (MCI) who are most likely to convert to Alzheimer's disease (AD). We investigated whether recognition memory tasks in combination with delayed recall measure of episodic memory and CSF biomarkers can predict MCI to AD conversion at 24-month follow-up. Methods: A total of 397 amnestic-MCI subjects from Alzheimer's disease Neuroimaging Initiative were included. Logistic regression modeling was done to assess the predictive value of all RAVLT measures, risk factors such as age, sex, education, APOE genotype, and CSF biomarkers for progression to AD. Estimating adjusted odds ratios was used to determine which variables would produce an optimal predictive model, and whether adding tests of interaction between the RAVLT Delayed Recall and recognition measures (traditional score and d-prime) would improve prediction of the conversion from a-MCI to AD. Results: 112 (28.2%) subjects developed dementia and 285 (71.8%) subjects did not. Of the all included variables, CSF Aβ1-42 levels, RAVLT Delayed Recall, and the combination of RAVLT Delayed Recall and d-prime were predictive of progression to AD (χ2 = 38.23, df = 14, p < 0.001). Conclusions: The combination of RAVLT Delayed Recall and d-prime measures may be predictor of conversion from MCI to AD in the ADNI cohort, especially in combination with amyloid biomarkers. A predictive model to help identify individuals at-risk for dementia should include not only traditional episodic memory measures (delayed recall or recognition), but also additional variables (d-prime) that allow the homogenization of the assessment procedures in the diagnosis of MCI.
Slow-Wave Sleep Is Associated With Incident Hypertension: The Sleep Heart Health Study

We sought to quantify the association between slow-wave (stage N3) sleep and hypertension in a large cohort of middle-aged men and women. Data from 1850 participants free of baseline hypertension from the Sleep Heart Health Study were analyzed. The primary exposure was percentage of N3 sleep on baseline in-home polysomnography and the primary outcome was incident hypertension, defined as systolic blood pressure ≥ 140 mm Hg, diastolic blood pressure ≥ 90 mm Hg, and/or use of any blood pressure lowering medications at follow-up. Multivariable logistic regression models were adjusted for study site, age, sex, race, waist circumference, tobacco use, alcohol use, apnea-hypopnea index, nocturnal oxygen desaturation, sleep duration, sleep efficiency, and arousal index. Mean age was 59.4 ± 10.1 years and 55.5% were female. The mean baseline systolic and diastolic blood pressure was 118.8 and 70.6 mm Hg, respectively. Approximately 30% of the sample developed hypertension during a mean follow-up of 5.3 years. In the multi-adjusted model, participants in quartiles 1 (<9.8%) and 2 (9.8%-17.7%) of N3 sleep had significantly greater odds of incident hypertension compared with those in quartile 3 (17.7%-25.2%) (OR 1.69, 95% CI 1.21-2.36, p = .002 and OR 1.45, 95% CI 1.04-2.00, p = .03, respectively). No significant effect modification by sex on the N3-hypertension association was observed. In conclusion, compared with intermediate levels of N3 sleep (overlapping the "normal" adult range), lower levels of percent N3 sleep are associated with increased odds of incident hypertension in both men and women, independent of potential confounders, including indices of sleep apnea and sleep fragmentation.
Fluid‐driven interfacial instabilities and turbulence in bacterial biofilms

Biofilms are thin layers of bacteria embedded within a slime matrix that live on surfaces. They are ubiquitous in nature and responsible for many medical and dental infections, industrial fouling and are also evident in ancient fossils. A biofilm structure is shaped by growth, detachment and response to mechanical forces acting on them. The main contribution to biofilm versatility in response to physical forces is the matrix that provides a platform for the bacteria to grow. The interaction between biofilm structure and hydrodynamics remains a fundamental question concerning biofilm dynamics. Here, we document the appearance of ripples and wrinkles in biofilms grown from three species of bacteria when subjected to high-velocity fluid flows. Linear stability analysis suggested that the ripples were Kelvin-Helmholtz Instabilities. The analysis also predicted a strong dependence of the instability formation on biofilm viscosity explaining the different surface corrugations observed. Turbulence through Kelvin-Helmholtz instabilities occurring at the interface demonstrated that the biofilm flows like a viscous liquid under high flow velocities applied within milliseconds. Biofilm fluid-like behavior may have important implications for our understanding of how fluid flow influences biofilm biology since turbulence will likely disrupt metabolite and signal gradients as well as community stratification.