Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Chaperones in Ectothermic Marine Animals: Biochemical Function and Gene Expression1

Abstract The intertidal zone has historically functioned as an important natural laboratory for testing ideas about how physical factors such as temperature influence organismal physiology and in turn influence the distribution patterns of organisms. Key to our understanding of how the physical environment helps structure organismal distribution is the identification of physiological processes that have ecological relevance. We have focused on biochemical- and molecular-level physiology that would contribute to thermal tolerance and maintenance of a functional intracellular protein pool in the face of extreme and fluctuating environmental temperatures. Past research has addressed processes central to protein homeostasis (e.g., protein ubiquitination) and the molecular ecology of molecular chaperones, a.k. a. heat shock proteins (Hsps), in ectothermic animals. In this presentation, we focus on two new developments regarding the biology of heat shock proteins as molecular chaperones in intertidal organisms. First, we present data on the functional characteristics of the transcriptional factor, HSF1 and discuss how these data relate to the plasticity of Hsp gene expression observed in intertidal organisms in nature. Second, we present data on the biochemical function of heat shock proteins purified from our non-model study organisms and discuss the temperature relationships of these molecules as they assist in protein folding in situ.
Multiple paternity is a shared reproductive strategy in the live-bearing surfperches (Embiotocidae) that may be associated with female fitness

According to Bateman's principle, female fecundity is limited relative to males, setting the expectation that males should be promiscuous, while females should be choosy and select fewer mates. However, several surfperches (Embiotocidae) exhibit multiple paternity within broods indicating that females mate with multiple males throughout the mating season. Previous studies found no correlation between mating success and reproductive success (i.e., a Bateman gradient). However, by including samples from a broader range of reproductive size classes, we found evidence of a Bateman gradient in two surfperch species from distinct embiotocid clades. Using microsatellite analyses, we found that 100% of the spotfin surfperch families sampled exhibit multiple paternity (Hyperprosopon anale, the basal taxon from the only clade that has not previously been investigated) indicating that this tactic is a shared reproductive strategy among surfperches. Further, we detected evidence for a Bateman gradient in H. anale; however, this result was not significant after correction for biases. Similarly, we found evidence for multiple paternity in 83% of the shiner surfperch families (Cymatogaster aggregata) sampled. When we combine these data with a previous study on the same species, representing a larger range of reproductive size classes and associated brood sizes, we detect a Bateman gradient in shiner surfperch for the first time that remains significant after several conservative tests for bias correction. These results indicate that sexual selection is likely complex in this system, with the potential for conflicting optima between sexes, and imply a positive shift in fertility (i.e., increasing number) and reproductive tactic with respect to the mating system and number of sires throughout the reproductive life history of females. We argue that the complex reproductive natural history of surfperches is characterized by several traits that may be associated with cryptic female choice, including protracted oogenesis, uterine sac complexity, and sperm storage.
Research on Reverse Nearest Neighbor Queries Using Ranked Voronoi Diagram

The reverse nearest neighbor query is a new issue in the spatial and security database theory and application. This paper answers the reverse nearest neighbor queries effectively using the properties of the Voronoi diagram and the space-dividing regions. The reverse nearest neighbors of the given query point can be acquired without computing its nearest neighbors every time by the query and dynamic updating algorithm using the ranked Voronoi diagram. Experiments on typical synthetic data sets confirm the efficiency and scalability of proposed algorithms compared with the Brute Force search and TPL approach.
The Cytochrome P450 Complement (CYPome) of Streptomyces coelicolor A3(2)*

In the present study we describe the complete cytochrome P450 complement, the “CYPome,” of Streptomyces coelicolor A3(2). Eighteen cytochromes P450 (CYP) are described, in contrast to the absence of CYPs in Escherichia coli, and the twenty observed in Mycobacterium tuberculosis. Here we confirm protein identity as cytochromes P450 by heterologous expression in E. coli and measurement of reduced carbon monoxide difference spectra. We also report on their arrangement in the linear chromosome and relatedness to other CYPs in the superfamily. The future development of manipulation of antibiotic pathways and the use of streptomycetes in bioremediation and biotransformations will involve many of the new CYP forms identified here.
Survey on security attacks in Vehicular Ad hoc Networks (VANETs)

Vehicular Ad hoc Networks (VANETs) are emerging mobile ad hoc network technologies incorporating mobile routing protocols for inter-vehicle data communications to support intelligent transportation systems. Among others security and privacy are major research concerns in VANETs due to the frequent vehicles movement, time critical response and hybrid architecture of VANETs that make them different than other Ad hoc networks. Thus, designing security mechanisms to authenticate and validate transmitted message among vehicles and remove adversaries from the network are significantly important in VANETs. This paper presents several existing security attacks and approaches to defend against them, and discusses possible future security attacks with critical analysis and future research possibilities.
Seasonal variation of bacterial endophytes in urban trees

Bacterial endophytes, non-pathogenic bacteria residing within plants, contribute to the growth and development of plants and their ability to adapt to adverse conditions. In order to fully exploit the capabilities of these bacteria, it is necessary to understand the extent to which endophytic communities vary between species and over time. The endophytes of Acer negundo, Ulmus pumila, and Ulmus parvifolia were sampled over three seasons and analyzed using culture dependent and independent methods (culture on two media, terminal restriction fragment length polymorphism, and tagged pyrosequencing of 16S ribosomal amplicons). The majority of culturable endophytes isolated were Actinobacteria, and all the samples harbored Bacillus, Curtobacterium, Frigoribacterium, Methylobacterium, Paenibacilllus, and Sphingomonas species. Regardless of culture medium used, only the culturable communities obtained in the winter for A. negundo could be distinguished from those of Ulmus spp. In contrast, the nonculturable communities were dominated by Proteobacteria and Actinobacteria, particularly Erwinia, Ralstonia, and Sanguibacter spp. The presence and abundance of various bacterial classes and phyla changed with the changing seasons. Multivariate analysis on the culture independent data revealed significant community differences between the endophytic communities of A. negundo and Ulmus spp. , but overall season was the main determinant of endophytic community structure. This study suggests studies on endophytic populations of urban trees should expect to find significant seasonal and species-specific community differences and sampling should proceed accordingly.
An Analysis of the Variation in the RED Algorithm

We explore a toy model for the RED congestion control mechanism. A sample estimator for our parameter of interest is presented and a limiting inequality is derived which suggests that the order of our estimator is at most O( 1 T ). Plots are provided which feature simulated observations of our sample estimator and give a strong indication that the order of our parameter is in fact O( 1 T ). In the final two sections, we look at the problem of finding a traffic independent bound on the variance in average queue length for a RED queue and establish a methodology for estimating the variance in average queue length for a RED controlled queue.
A Formalism for Relating Lexical and Pragmatic Information: Its Relevance to Recognition and Generation

Clearly, (I) and (2) are "pragmatic" in nature and are not limited to natural language processing, while (3) and (4) may be viewed as special cases of (I) and (2) respectively. One of our main goals is to show how both pragmatic and semantic issues may be approached in a formal framework. We have chosen to study the area of "speech acts" (conversational activities like "request," "command," "promise," .) as this area is especially rich in interactions among the four areas.
A compact starburst ring traced by clumpy OH megamaser emission

Abstract We model the OH megamaser emission from the luminous infrared galaxy IIIZw35 as arising from a narrow rotating starburst ring of radius 22 pc enclosing a mass of 7×106M⊙. We show how both the compact and apparently diffuse maser emission from this ring can arise from a single phase of unsaturated maser clouds amplifying background radio continuum. The masering clouds are estimated to have a diameter of <0.7 pc and internal velocity dispersion of ∽20 kms−1. We find that the clouds are neither self-gravitating nor pressure confined, and they could be magnetically confined or freely expanding. Their dispersal lifetimes may set the vertical thickness of the ring. For an estimated internal density of 3×103cm−3, cloud masses are of order 24 M⊙. The observed spectral features and velocity gradients indicate that the clouds must be outflowing and escaping the nucleus. The cloud mass outflow rate is estimated to be 0.8 M⊙yr−1, while the star formation rate is ∽19 M⊙yr−1. Associated ionised gas, possibly generated from dissipated clouds, provides free-free absorption along the source axis, explaining the observed East-West asymmetries. We show that the clumpiness of a maser medium can have a dramatic effect on what is observed even in a relatively low gain OH megamaser. Specifically, in IIIZw35 our clumpy maser model naturally explains the large line to continuum ratios, the large 1667MHz:1665MHz line ratios and the wide velocity dispersions seen in the compact maser spots. Other astrophysical masers showing both compact and apparently diffuse emission might be explained by similar clumpy structures.
Energy Consumption Analysis of Ad hoc Routing Protocols for Different Energy Models in MANET

In Mobile Ad hoc Networks (MANETs), energy conservation is a critical issue as the nodes are powered by the batteries which have limited energy reservoir. Hence the power level of the nodes is a problematical factor that extensively affects the performance and efficiency of ad hoc routing protocols. The rapidly changing traffic pattern the mobility of the nodes and the lack of fixed infrastructure makes routing in a MANET a challenging issue. So one of the main issues in MANET routing protocols is the development of energy efficient and QoS aware routing protocols which requires the energy analysis of routing protocols so that some modifications can be suggested. This paper presents performance comparison of three categories of mobile ad hoc routing protocols i.e. proactive, reactive and hybrid. The performance analysis is based on different metrics of Physical Layer such as Power Consumed in Transmit Mode, Power Consumed in Receive and Idle Modes, and metrics of application layer like Average End to End Delay, Average Jitter, Throughput and Packet Delivery Ratio based on the simulation analysis. Simulation analysis is performed over well known network simulator QualNet 6.1. Keywords - MANET, AODV, DYMO, OLSR, PDR.
On Hamiltonian Cycles in Trees

We present a simple algorithm for constructing Hamiltonian cycles on trees together with additional edges between leaves, compute the number of such additional edges required for complete k-ary trees of given depth, show this number is minimal over all Hamiltonian cycles, and present an algorithm that determines the successor of each node in the cycle from the node index alone. We discuss the applications of these algorithms to parallel computing.
Design and evaluation of a new multi-path incremental routing algorithm on software routers

In this paper we analyze intra-domain routing protocols improvements to support new features required by realtime services. In particular we introduce OSPF fast convergence and highlight the advantage of using a dynamic algorithm instead of the Dijkstra one to compute the shortest paths. Then we propose a new multi-path dynamic algorithm which uses multipath information to make a fast determination about the new shortest paths when a link failure occurs, reducing this way the network re-convergence time. To evaluate the proposed algorithm performance we have implemented it in the OSPF code of the Quagga open-source routing software. We compare our own algorithm with three different dynamic algorithms, like the one implemented in Cisco routers and the two others, well known in literature, proposed by Narvaez and Ramalingam-Reps. We show how, by exploiting multi-path information, our algorithm performs, in many case studies, better than the above algorithms, especially in a link failure scenario.
Molecular Mechanisms of Bipolar Disorder: Progress Made and Future Challenges

Bipolar disorder (BD) is a chronic and progressive psychiatric illness characterized by mood oscillations, with episodes of mania and depression. The impact of BD on patients can be devastating, with up to 15% of patients committing suicide. This disorder is associated with psychiatric and medical comorbidities and patients with a high risk of drug abuse, metabolic and endocrine disorders and vascular disease. Current knowledge of the pathophysiology and molecular mechanisms causing BD is still modest. With no clear biological markers available, early diagnosis is a great challenge to clinicians without previous knowledge of the longitudinal progress of illness. Moreover, despite recommendations from evidence-based guidelines, polypharmacy is still common in clinical treatment of BD, reflecting the gap between research and clinical practice. A major challenge in BD is the development of effective drugs with low toxicity for the patients. In this review article, we focus on the progress made and future challenges we face in determining the pathophysiology and molecular pathways involved in BD, such as circadian and metabolic perturbations, mitochondrial and endoplasmic reticulum (ER) dysfunction, autophagy and glutamatergic neurotransmission; which may lead to the development of new drugs.
C-Reactive-Protein-Associated Increase in Myocardial Infarct Size After Ischemia/Reperfusion

C-Reactive protein (CRP), a marker for acute inflammation, is associated with increased risk of cardiovascular events. The mechanism underlying this association is uncertain. An acute inflammatory response was induced in rabbits by subcutaneous injection of croton oil (CO) 1 to 3 days before 30 min of regional myocardial ischemia/180 min of reperfusion. CO treatment increased plasma CRP from below the limit of detection to 2.5 ± 0.5 mg/dl and was associated with an increase in infarct size expressed as percentage of risk region [32 ± 6% vehicle controls (n = 7) to 47 ± 9% CO-treated rabbits (n = 7;P < 0.05]. After 10 min of ischemia and 180 min reperfusion, no infarct was found in controls; however, an infarct of 7 ± 1% was found in CO-treated rabbits (P < 0.05; CRP, 2.3 ± 0.4 mg/dl). The CRP-related increase in infarct size was not observed in croton oil-treated, C6-deficient rabbits (n = 5/group), indicating the involvement of complement. In these rabbits, infarct size was 22 ± 2% (P < 0.05) despite having plasma CRP of 4.3 ± 0.4 mg/dl. The CRP-associated increase in infarct size was ameliorated by pretreatment with heparin (n = 7; infarct size 33 ± 3%; CRP, 2.3 ± 0.3 mg/dl;P < 0.05) or N-acetylheparin (n = 7; infarct size 23 ± 4%; CRP, 3.1 ± 0.5 mg/dl; P < 0.05). These observations may explain why increased serum CRP is associated with an augmented risk for cardiovascular events.
What Is the Connection Principle

The Connection Principle (hereafter, CP) says that there is some kind of internal relation between a state's having intentional content ("aspectual shape") and its being (at least potentially) conscious. Searle's argument for the principle is just that potential consciousness is the only thing he can think of that would distinguish original intentionality from ersatz (Searle, 1992, pp. 84, 155 and passim. All Searle references are to 1992). Cognitivists have generally found this argument underwhelming given the empirical successes recently enjoyed by linguistic and psychological theories with which, according to Searle, CP is not reconcilable. Our primary interest in this paper is not, however, to decide whether CP is true, but just to get as clear as we can about what exactly it asserts. Finding a reasonable formulation of the principle turns out to be harder than Searle appears to suppose; or so we claim.
Compton-thick X-ray absorption in the Seyfert galaxies Tololo 0109-383 and ESO 138-G1

We present analyses of the ASCA X-ray spectra of two Seyfert galaxies, Tololo 0109– 383 and ESO 138–G1. In both cases, spectral ﬁtting reveals two statistically acceptable continuum models: Compton reﬂection and partial covering. Both spectra have strong iron K α lines, with equivalent widths greater than 1.5 keV. These large equivalent widths are suggestive of heavier obscuration than that directly indicated by the partial-covering models ( ≈ 2 × 10 23 cm − 2 ), with the actual column densities being ‘Compton-thick’ (i.e. N H > ∼ 1 . 5 × 10 24 cm − 2 ). We use the hard X-ray/[O iii ] ﬂux correlation for Seyferts and data from the literature to provide additional support for this hypothesis. Since Tololo 0109–383 is known to have optical type 1 characteristics such as broad Balmer line components and Fe ii emission, this result marks it as a notable object.
On Modeling, Complexities, and Automatic Configuration of Wireless Industrial Control Networks

We propose a mathematical model for wireless industrial control systems and analyze the engineering challenge of co-scheduling networking and control in this context. We demonstrate the use of the model using a small case study and explain how our modelling approach allows for self-configuring and self-adapting systems. The main theoretical contribution of the paper is a mathematical formulation of the computational problem of synthesizing a co-design of scheduling and control for wireless industrial control systems and a mathematical proof that this problem is computationally hard. We also identify relevant special network topologies for which the problem can be efficiently solved.
The radio luminosity function of cluster radio halos

A significant fraction of galaxy clusters exhibits cluster-wide radio halos. We give a simple prediction of the local and higher redshift radio halo luminosity function (RHLF) on the basis of (i) an observed and a theoretical X-ray cluster luminosity function (XCLF) (ii) the observed radio-X-ray luminosity correlation (RXLC) of galaxy clusters with radio halos (iii) an assumed fraction of frh ≈ 1 galaxy clusters to have radio halos as supported by observations. We then find 300-700 radio halos with S 1.4 GHz > 1mJy, and 10 5 -10 6 radio halos with S 1.4 GHz > 1 µJy should be visible on the sky. 14% of the S 1.4 GHz > 1mJy and 56% of the S 1.4 GHz > 1 µJy halos are located at z > 0.3. Subsequently, we give more realisticpredictions taking into account (iv) a refined estimate of the radio halo fraction as a function of redshift and cluster mass, and (v) a decrease in intrinsic radio halo luminosity with redshift due to increased inverse Compton electron energy losses on the Cosmic Microwave Background (CMB). We find that this reduces the radio halo counts from the simple prediction by only 30 % totally, but the high redshift (z > 0.3) counts are more strongly reduced by 50-70%. These calculations show that the new generation of sensitive radio telescopes, including LOFAR, ATA, EVLA, SKA and the already-operating GMRT should be able to detect large numbers of radio halos and will provide unique information for studies of galaxy cluster merger rates and associated non-thermal processes.
Increased c-fos expression in spinal neurons after irritation of the lower urinary tract in the rat

This study utilized neuronal c-fos expression to examine the spinal pathways involved in processing nociceptive and non-nociceptive afferent input from the lower urinary tract (LUT) of the urethane- anesthetized rat. C-fos protein was detected immunocytochemically in only a small number of cells (< 2 cells/L6 section) in control animals. However, chemical irritation with 1% acetic acid or mechanical stimulation of the LUT markedly increased the number of c-fos-positive neurons (56–180 cells/L6 section) in four regions of the caudal lumbosacral (L6-S1) spinal cord: medial dorsal horn (MDH), lateral dorsal horn, dorsal commissure (DCM), and sacral parasympathetic nucleus (SPN). Only small numbers of c-fos-positive cells were detected in rostral lumbar segments, a region that is thought to receive nociceptive input from the LUT via afferent pathways in sympathetic nerves. The distribution of c-fos-positive cells in the L6 spinal cord varied according to the stimulus (i.e., urethral catheter, bladder distension, or chemical irritation). Distension of the urinary bladder increased the number of c-fos-positive cells mainly in DCM and SPN regions of the cord. In contrast, irritation of the LUT increased c-fos expression largely in DCM and MDH areas. Spinal cord transection (T8 level) did not alter the c-fos expression induced by a catheter or chemical irritation, indicating that gene expression was mediated by spinal pathways. Denervation experiments showed that c-fos expression was induced by activation of afferent pathways in the pelvic and pudendal nerves. These results suggest that neurons in several regions of the spinal cord are involved in processing afferent input from different parts of the LUT. Neurons in the DCM appear to have an important role since they respond to both nociceptive and non- nociceptive inputs and to visceral (pelvic nerve) and somatic (pudendal nerve) afferent pathways. Thus, these neurons may be involved in the mechanisms of visceral-somatic referred pain.
Back to the Future: How Today's Neurocognitive Techniques Substantiate Predictions Made 50 Years Ago

Back to the Future: How Today's Neurocognitive Techniques Substantiate Predictions Made 50 Years Ago Naomi Ellemers To cite this article: Naomi Ellemers (2016) Back to the Future: How Today's Neurocognitive Techniques Substantiate Predictions Made 50 Years Ago, Psychological Inquiry, 27:4, 290-293, DOI: 10.1080/1047840X.2016. 1215210 To link to this article: http://dx.doi. org/10.1080/1047840X.2016. 1215210