Miracle-dz/UniFAR-FTUs huggingface dataset:
Natural-Scene Statistics Predict How the Figure–Ground Cue of Convexity Affects Human Depth Perception

The shape of the contour separating two regions strongly influences judgments of which region is “figure” and which is “ground. ” Convexity and other figure–ground cues are generally assumed to indicate only which region is nearer, but nothing about how much the regions are separated in depth. To determine the depth information conveyed by convexity, we examined natural scenes and found that depth steps across surfaces with convex silhouettes are likely to be larger than steps across surfaces with concave silhouettes. In a psychophysical experiment, we found that humans exploit this correlation. For a given binocular disparity, observers perceived more depth when the near surface's silhouette was convex rather than concave. We estimated the depth distributions observers used in making those judgments: they were similar to the natural-scene distributions. Our findings show that convexity should be reclassified as a metric depth cue. They also suggest that the dichotomy between metric and nonmetric depth cues is false and that the depth information provided many cues should be evaluated with respect to natural-scene statistics. Finally, the findings provide an explanation for why figure–ground cues modulate the responses of disparity-sensitive cells in visual cortex.
Combination of density gradient centrifugation and swim-up methods effectively decreases morphologically abnormal sperms

Density gradient centrifugation (DGC) and swim-up techniques have been reported for semen preparation in assisted reproductive techniques in humans. We investigated whether semen preparation using a combination of DGC and swim-up techniques could effectively decrease morphologically abnormal human sperms at the ultrastructural level. Semen samples were obtained from 16 infertile males and fractionated by swim-up following DGC. Ultrastructural abnormalities of sperms obtained from original semen, lower layer of swim-up following DGC, and upper layer of swim-up following DGC were analyzed by transmission electron microscopy. The correlation among ultrastructural head abnormality in sperms from the upper layer of swim-up, fertilization in in vitro fertilization, and pregnancy after embryo transfer was also investigated. Furthermore, sperms with DNA fragmentation in the samples processed via a combination of DGC and swim-up was assessed in a sperm chromatin structure assay. Ultrastructural abnormalities in sperm heads and tails in the upper layer after swim-up following DGC was the lowest among the three groups. Sperms with nuclear vacuoles were the most difficult to eliminate using a combination of DGC and swim-up in all types of head abnormalities. A negative correlation was confirmed between the fertilization rates of intracytoplasmic sperm injection and head abnormality of sperms obtained from the upper layer of the swim-up following DGC. Sperms with DNA fragmentation were effectively decreased using the combination of two techniques. In conclusion, the combination of DGC and swim-up effectively decreased the number of sperms with ultrastructural abnormalities both in the head and in the tail. However, sperms with ultrastructural abnormalities that cannot be completely decreased using a combination of DGC and swim-up may impair fertilization in some cases of intracytoplasmic sperm injection.
Predictive Coding of Dynamical Variables in Balanced Spiking Networks

Two observations about the cortex have puzzled neuroscientists for a long time. First, neural responses are highly variable. Second, the level of excitation and inhibition received by each neuron is tightly balanced at all times. Here, we demonstrate that both properties are necessary consequences of neural networks that represent information efficiently in their spikes. We illustrate this insight with spiking networks that represent dynamical variables. Our approach is based on two assumptions: We assume that information about dynamical variables can be read out linearly from neural spike trains, and we assume that neurons only fire a spike if that improves the representation of the dynamical variables. Based on these assumptions, we derive a network of leaky integrate-and-fire neurons that is able to implement arbitrary linear dynamical systems. We show that the membrane voltage of the neurons is equivalent to a prediction error about a common population-level signal. Among other things, our approach allows us to construct an integrator network of spiking neurons that is robust against many perturbations. Most importantly, neural variability in our networks cannot be equated to noise. Despite exhibiting the same single unit properties as widely used population code models (e.g. tuning curves, Poisson distributed spike trains), balanced networks are orders of magnitudes more reliable. Our approach suggests that spikes do matter when considering how the brain computes, and that the reliability of cortical representations could have been strongly underestimated.
Picture-driven animation

"Animation is the graphic art which occurs in time. Whereas a static image (such as a Picasso or a complex graph) may convey complex information through a single picture, animation conveys equivalently complex information through a sequence of images seen in time. It is characteristic of this medium, as opposed to static imagery, that the actual graphical information at any given instant is relatively slight. The source of information for the viewer of animation is implicit in picture change: change in relative position, shape, and dynamics. Therefore, a computer is ideally suited to making animation "possible" through the fluid refinement of these changes. "
The Anticancer Drug Ellipticine Is a Potent Inducer of Rat Cytochromes P450 1A1 and 1A2, Thereby Modulating Its Own Metabolism

Ellipticine is an antineoplastic agent whose mode of action is based mainly on DNA intercalation, inhibition of topoisomerase II, and formation of covalent DNA adducts mediated by cytochromes P450 (P450s) and peroxidases. Here, this drug was found to induce CYP1A1 and/or 1A2 enzymes and their enzymatic activities in livers, lungs, and kidneys of rats treated (i.p.) with ellipticine. The induction is transient. In the absence of repeated administration of ellipticine, the levels and activities of the induced CYP1A decreased almost to the basal level 2 weeks after treatment. The ellipticine-mediated CYP1A induction increases the DNA adduct formation by the compound. When microsomal fractions from livers, kidneys, and lungs of rats treated with ellipticine were incubated with ellipticine, DNA adduct formation, measured by 32P-postlabeling analysis, was up to 3.8-fold higher in incubations with microsomes from pretreated rats than with controls. The observed stimulation of DNA adduct formation by ellipticine was attributed to induction of CYP1A1 and/or 1A2-mediated increase in ellipticine oxidative activation to 13-hydroxy- and 12-hydroxyellipticine, the metabolites generating two major DNA adducts in human and rat livers. In addition to these metabolites, increased formation of the excretion products 9-hydroxy- and 7-hydroxyellipticine was also observed in microsomes of rats treated with ellipticine. Taken together, these results demonstrate for the first time that by inducing CYP1A1/2, ellipticine increases its own metabolism, leading both to an activation of this drug to reactive species-forming DNA adducts and to detoxication metabolites, thereby modulating to some extent its pharmacological and/or genotoxic potential.
Compression of Data Streams Down to Their Information Content

According to the Kolmogorov complexity, every finite binary string is compressible to a shortest code—its information content—from which it is effectively recoverable. We investigate the extent to which this holds for the infinite binary sequences (streams). We devise a new coding method that uniformly codes every stream <inline-formula> <tex-math notation="LaTeX">$X$ </tex-math></inline-formula> into an algorithmically random stream <inline-formula> <tex-math notation="LaTeX">$Y$ </tex-math></inline-formula>, in such a way that the first <inline-formula> <tex-math notation="LaTeX">$n$ </tex-math></inline-formula> bits of <inline-formula> <tex-math notation="LaTeX">$X$ </tex-math></inline-formula> are recoverable from the first <inline-formula> <tex-math notation="LaTeX">$I(X \upharpoonright _{n})$ </tex-math></inline-formula> bits of <inline-formula> <tex-math notation="LaTeX">$Y$ </tex-math></inline-formula>, where <inline-formula> <tex-math notation="LaTeX">$I$ </tex-math></inline-formula> is any partial computable information content measure that is defined on all prefixes of <inline-formula> <tex-math notation="LaTeX">$X$ </tex-math></inline-formula>, and where <inline-formula> <tex-math notation="LaTeX">$X \upharpoonright _{n}$ </tex-math></inline-formula> is the initial segment of <inline-formula> <tex-math notation="LaTeX">$X$ </tex-math></inline-formula> of length <inline-formula> <tex-math notation="LaTeX">$n$ </tex-math></inline-formula>. As a consequence, if <inline-formula> <tex-math notation="LaTeX">$g$ </tex-math></inline-formula> is any computable upper bound on the initial segment prefix-free complexity of <inline-formula> <tex-math notation="LaTeX">$X$ </tex-math></inline-formula>, then <inline-formula> <tex-math notation="LaTeX">$X$ </tex-math></inline-formula> is computable from an algorithmically random <inline-formula> <tex-math notation="LaTeX">$Y$ </tex-math></inline-formula> with oracle-use at most <inline-formula> <tex-math notation="LaTeX">$g$ </tex-math></inline-formula>. Alternatively (making no use of such a computable bound <inline-formula> <tex-math notation="LaTeX">$g$ </tex-math></inline-formula>), one can achieve an the oracle-use bounded above by <inline-formula> <tex-math notation="LaTeX">$K(X \upharpoonright _{n})+\log n$ </tex-math></inline-formula>. This provides a strong analogue of Shannon’s source coding theorem for the algorithmic information theory.
Molecular Biology of Liver Cancer Stem Cells

Hepatocellular carcinoma (HCC) is one of the most common and lethal cancers worldwide. The concept of cancer stem cells (CSCs) is based primarily on the clinical and experimental observations that indicate the existence of a subpopulation of cells with the capacity to self-renew and differentiate as well as show increased resistance to radiation and chemotherapy. They are considered as the factors responsible for the cases of tumor relapse. Hepatic progenitor cells (HPCs) could form the basis of some hepatocellular carcinomas (HCC) and cholangiocarcinomas. Liver CSCs have been reported in multiple subtypes of HCC and are considered as the master regulators of HCC initiation, tumor metastasis, and progression. HPCs activators such as epithelial cell adhesion molecule (EpCAM), Wnt/β-catenin, transforming growth factor-beta (TGF-β), Notch and Hedgehog signaling systems expedite tumorigenesis or conversely, serve as a powerful cancer-prevention tool. Recent work has also identified Sal-like protein 4 (SALL4) and some epigenetic regulations as important molecules, while several therapeutic drugs that directly control HPCs have been tested both in vivo and in vitro. However, liver CSCs clearly have a complex pathogenesis, with the potential for considerable crosstalk and redundancy in signaling pathways. Hence, the targeting of single molecules or pathways may have limited benefit for treatment. In addition to the direct control of liver CSCs, many other factors are needed for CSC maintenance including angiogenesis, vasculogenesis, invasion and migration, hypoxia, immune evasion, multiple drug resistance, and radioresistance. Here, we provide a brief review of molecular signaling in liver CSCs and present insights into new therapeutic strategies for their targeting.
A Pilot Study on Cortical Auditory Evoked Potentials in Children: Aided CAEPs Reflect Improved High-Frequency Audibility with Frequency Compression Hearing Aid Technology

Background. This study investigated whether cortical auditory evoked potentials (CAEPs) could reliably be recorded and interpreted using clinical testing equipment, to assess the effects of hearing aid technology on the CAEP. Methods. Fifteen normal hearing (NH) and five hearing impaired (HI) children were included in the study. NH children were tested unaided; HI children were tested while wearing hearing aids. CAEPs were evoked with tone bursts presented at a suprathreshold level. Presence/absence of CAEPs was established based on agreement between two independent raters. Results. Present waveforms were interpreted for most NH listeners and all HI listeners, when stimuli were measured to be at an audible level. The younger NH children were found to have significantly different waveform morphology, compared to the older children, with grand averaged waveforms differing in the later part of the time window (the N2 response). Results suggest that in some children, frequency compression hearing aid processing improved audibility of specific frequencies, leading to increased rates of detectable cortical responses in HI children. Conclusions. These findings provide support for the use of CAEPs in measuring hearing aid benefit. Further research is needed to validate aided results across a larger group of HI participants and with speech-based stimuli.
Blindness in schoolchildren: importance of heredity, congenital cataract, and prematurity

Of 99 children in the Royal Blind School, Edinburgh (which serves Scotland and part of N E England), 15 had optic atrophy (hydrocephalus 4, intracranial haemorrhage 2, prematurity 2, fetal distress 2, birth asphyxia 2, cerebral atrophy 1, cardiac arrest during hernia operation 1, and leukaemia 1). Fourteen had congenital cataract, 12 congenital retinal aplasia (Leber's congenital amaurosis) and 11 retinopathy of prematurity. There were small numbers in many other diagnostic categories, including three with non-accidental head injury. Mental retardation, spasticity, and nystagmus were frequent other correlates in all diagnostic categories. 'Very probably hereditary' was a conservative attribution in 36, while 'probable' seemed appropriate for 12-that is, almost 48% were hereditary. Only about 11 cases might have been prevented through genetic counselling, which testifies to the frequency of autosomal recessive hereditary disease, although no parents were consanguineous.
Postnatal Development of Metabolic Flexibility and Enhanced Oxidative Capacity After Prenatal Undernutrition

Metabolic flexibility is the body’s ability to adapt to changing energy demand and nutrient supply. Maternal undernutrition causes growth restriction at birth and subsequent obesity development. Intriguingly, metabolic flexibility is maintained due to adaptations of muscle tissue. The aim of the present study was to investigate developmental pathways of these adaptive changes. Wistar rats received standard chow at either ad libitum (AD) or 30% of ad libitum intake (UN) throughout pregnancy. At all ages, metabolic status indicated similar insulin sensitivity in AD and UN offspring despite the development of adiposity in UN offspring at weaning. Type IIA fiber size was reduced in soleus muscle of UN offspring at weaning and they had a higher percentage of type I fibers in adulthood with a concomitantly higher oxidative capacity. Plasticity of muscle was present during the postnatal period and proposes novel pathways for the dynamic development of metabolic flexibility throughout postnatal life.
Peripherally Inserted Central Venous Catheter–Associated Bloodstream Infections in Hospitalized Adult Patients

Background. Limited data on the risk of peripherally inserted central venous catheter-associated bloodstream infections (PICC BSIs) in hospitalized patients are available. In 2007, dedicated intravenous therapy nurses were no longer available to place difficult peripheral intravenous catheters or provide PICC care Barnes-Jewish Hospital. Objectives. To determine the hospital-wide incidence of PICC BSIs and to assess the effect of discontinuing intravenous therapy service on PICC use and PICC BSI rates. Setting. A 1,252-bed tertiary care teaching hospital. Methods. A 31-month retrospective cohort study was performed. PICC BSIs were defined using National Healthcare Safety Network criteria. Results. In total, 163 PICC BSIs were identified (3.13 BSIs per 1,000 catheter-days). PICC use was higher in intensive care units (ICUs) than non-ICU areas (PICC utilization ratio, 0.109 vs 0.059 catheter-days per patient-day for ICU vs non-ICU; rate ratio [RR], 1.84 [95% confidence interval {CI}, 1.78-1.91]). PICC BSI rates were higher in ICUs (4.79 vs 2.79 episodes per 1,000 catheter-days; RR, 1.7 [95% CI, 1.10-2.61]). PICC use increased hospital-wide after the intravenous therapy service was discontinued (0.049 vs 0.097 catheter-days per patient-day; P = .01), but PICC BSI rates did not change (2.68 vs 3.63 episodes per 1,000 catheter-days; P = .06). Of PICC BSIs, 73% occurred in non-ICU patients. Conclusions. PICC use and PICC BSI rates were higher in ICUs; however, most of the PICC BSIs occurred in non-ICU areas. Reduction in intravenous therapy services was associated with increased PICC use across the hospital, but PICC BSI rates did not increase.
Ajents: towards an environment for parallel, distributed and mobile Java applications

The rapid proliferation of the World-Wide Web has been due to the seamless access it provides to information that is distributed both within organizations and around the world. In this paper, we describe the design and implementation of a system, called Ajents, which provides the software infrastructure necessary to support a similar level of seamless access to organization-wide or world-wide heterogeneous computing resources. Ajents introduces class libraries which are written entirely in Java and that run on any standard compliant Java virtual machine. These class libraries implement and combine several important features that are essential to supporting distributed and parallel computing using Java. These features include: the ability to easily create objects on remote hosts, to interact with those objects through either synchronous or asynchronous remote method invocations, and to freely migrate objects to heterogeneous hosts. While some of these features have been implemented in other systems, Ajents provides support for the combination of all of these features using techniques that permit them to operate together in a fashion that is more transparent and/or and less restrictive than existing systems. Our experimental results show that in our test environment: we are able to achieve good speedup on a sample parallel application; the overheads introduced by our implementation do not adversely a ect remote method invocation times; and (somewhat surprisingly) the cost of migration does not greatly impact the execution time of an example application.
Bibliometric analysis of Traffic Medicine – related publications: 2008 – 2015

Background: A pproximately 1.25 million deaths annually due to road traffic accidents (RTA). Research has proven to improve traffic safety. Therefore, this study was carried out to analyze data in the field of traffic medicine to endorse and support the Decade of Action for Road Safety plan, and to enrich the literature in the field of RTA. Method: Scopus database was used to retrieve relevant data, then it was refined to traffic medicine field. Bibliometric indicators were presented and data visualization was carried out using VOSviewer and ArcGIS10.1 Results: A total of 2029 traffic medicine–related publications were retrieved, with h -index of 46. The relative growth rate declined from 0.63 in 2008 to 0.18 in 2015 while doubling time increased from 1.1 in 2008 to 3.55 in 2015. In 2008, traffic medicine-related publications were approximately 70% of total publications on traffic accidents and dropped to approximately 67% in 2015. Retrieved documents had a total of 8,478 authors, from 101 different countries with the USA having the largest share (498; 25.54%). Sweden, the UK and Canada had the highest percentage of inter-country collaboration. The most active institution was the University of Toronto (36 documents). Accident Analysis and Prevention was the most preferred for publishing RTA documents. Conclusion: The study period was characterized by slow growth of traffic medicine – related publications, which may suggest relative lack of interest or funding. To reverse fatalities due to RTA and injuries, researchers need to be more involved in RTA research to present solutions for better safety.
Diffusion Tensor Imaging in Alzheimer’s Disease and Mild Cognitive Impairment

Structural magnetic resonance imaging (MRI) studies of Alzheimer’s disease and mild cognitive impairment (MCI) have focused on the hippocampus and entorhinal cortex; gray matter structures in the medial temporal lobe. Few studies have investigated the integrity of white matter in patients with AD or MCI. Diffusion tensor imaging (DTI) is a MRI technique that allows for the interrogation of the microstructural integrity of white matter. Based on increases in translational diffusion (mean diffusivity: MD) and decreases directional diffusion (fractional anisotropy: FA) damage to white matter can be assessed. Studies have identified regions of increased MD and decreased FA in patients with AD and MCI in all lobes of the brain, as well as medial temporal lobe structures including the hippocampus, entorhinal cortex and parahippocampal white matter. The pattern of white matter integrity disruption tends to follow an anterior to posterior gradient with greater damage noted in posterior regions in AD and MCI. Recent studies have exploited inter-voxel directional similarities to develop models of white matter pathways, and have used these models to assess the integrity of inter-cerebral connections. Particular focus has been applied to the parahippocampal white matter (including the perforant path) and the posterior cingulum. Although many studies have found DTI indicators of impaired white matter in AD and MCI, other studies have failed to detect any differences in MD or FA between the groups, demonstrating the need for large replicative studies. DTI is an evolving technique and advances in its application ought to provide new insights into AD and MCI.
HIV-1 Nef Interacts with Inositol Trisphosphate Receptor to Activate Calcium Signaling in T Cells

HIV-1 pathogenicity factor Nef has been shown to modulate calcium signaling in host cells, but the underlying molecular mechanisms have remained unclear. Here we show that calcium/calcineurin-dependent activation of nuclear factor of activated T cells (NFAT) by Nef in Jurkat T cells requires the endoplasmic reticulum-resident inositol trisphosphate receptor (IP3R), but yet does not involve increase in phospholipase-Cγ1 (PLCγ1)-catalyzed production of IP3 or depletion of IP3-regulated intracellular calcium stores. Nef could be coprecipitated with endogenous IP3R type-1 (IP3R1) from Nef-transfected Jurkat T cells as well as from HIV-infected primary human peripheral mononuclear cells. Thus, the Nef/IP3R1-interaction defines a novel T cell receptor–independent mechanism by which Nef can promote T cell activation, and appears to involve atypical IP3R-triggered activation of plasma membrane calcium influx channels in a manner that is uncoupled from depletion of intracellular calcium stores.