Miracle-dz/UniFAR-FTUs huggingface dataset:
Three-Dimensional Structure of Different Functional Forms of the Vibrio cholerae Hemolysin Oligomer: a Cryo-Electron Microscopic Study

ABSTRACT Vibrio cholerae hemolysin (HlyA) is a 65-kDa water-soluble pore-forming toxin that causes lysis of eukaryotic cells by destroying selective permeability of the plasma membrane bilayer. The HlyA monomer self-assembles on the target cell surface to the more stable β-barrel amphipathic heptamer, which inserts into the membrane bilayer to form a diffusion channel. Deletion of the 15-kDa β-prism lectin domain at the C terminus generates a 50-kDa hemolysin variant (HlyA50) with an ∼1,000-fold decrease in hemolytic activity. Because functional differences are eventually dictated by structural differences, we determined three-dimensional structures of 65- and 50-kDa HlyA oligomers, using cryo-electron microscopy and single-particle methods. Our study clearly shows that the HlyA oligomer has sevenfold symmetry but that the HlyA50 oligomer is an asymmetric molecule. The HlyA oligomer has bowl-like, arm-like, and ring-like domains. The bowl-like domain is coupled with the ring-like domain, and seven side openings are present just beneath the ring-like domain. Although a central channel is present in both HlyA and HlyA50 oligomers, they differ in pore size as well as in shape of the molecules and channel. These structural differences may be relevant to the striking difference in efficiencies of functional channel formation by the two toxin forms.
Phosphorylation of Synaptojanin Differentially Regulates Endocytosis of Functionally Distinct Synaptic Vesicle Pools

The rapid replenishment of synaptic vesicles through endocytosis is crucial for sustaining synaptic transmission during intense neuronal activity. Synaptojanin (Synj), a phosphoinositide phosphatase, is known to play an important role in vesicle recycling by promoting the uncoating of clathrin following synaptic vesicle uptake. Synj has been shown to be a substrate of the minibrain (Mnb) kinase, a fly homolog of the dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A); however, the functional impacts of Synj phosphorylation by Mnb are not well understood. Here we identify that Mnb phosphorylates Synj at S1029 in Drosophila. We find that phosphorylation of Synj at S1029 enhances Synj phosphatase activity, alters interaction between Synj and endophilin, and promotes efficient endocytosis of the active cycling vesicle pool (also referred to as exo-endo cycling pool) at the expense of reserve pool vesicle endocytosis. Dephosphorylated Synj, on the other hand, is deficient in the endocytosis of the active recycling pool vesicles but maintains reserve pool vesicle endocytosis to restore total vesicle pool size and sustain synaptic transmission. Together, our findings reveal a novel role for Synj in modulating reserve pool vesicle endocytosis and further indicate that dynamic phosphorylation and dephosphorylation of Synj differentially maintain endocytosis of distinct functional synaptic vesicle pools. SIGNIFICANCE STATEMENT Synaptic vesicle endocytosis sustains communication between neurons during a wide range of neuronal activities by recycling used vesicle membrane and protein components. Here we identify that Synaptojanin, a protein with a known role in synaptic vesicle endocytosis, is phosphorylated at S1029 in vivo by the Minibrain kinase. We further demonstrate that the phosphorylation status of Synaptojanin at S1029 differentially regulates its participation in the recycling of distinct synaptic vesicle pools. Our results reveal a new role for Synaptojanin in maintaining synaptic vesicle pool size and in reserve vesicle endocytosis. As Synaptojanin and Minibrain perturbations are associated with various neurological disorders, such as Parkinson's, autism, and Down syndrome, understanding mechanisms modulating Synaptojanin function provides valuable insights into processes affecting neuronal communication.
Spatial and Temporal Variation in Susceptibility Status of Anopheles arabiensis the Malaria Vector to Insecticides in Khartoum State , Sudan

Spatial and temporal variation in the susceptibility status of Anopheles arabiensis to five insecticides were investigated during 2011-2013 in nine sentinel sites in Khartoum State. Field-collected larvae and pupae Anopheles in three seasons (cold dry, hot dry and wet seasons) were reared to adult stages. Standard WHO diagnostic bioassay for 4% DDT, 5% malathion, 0.1% propoxur, 0.75% permethrin and 0.05% deltamethrin were used to test the susceptibility 1 Corresponding author: Tagwa.salah1@hotmail.com, Tagwa@sustech.edu Tagwa Salah Ahmed Mohammed, Khalid Awadelkareem Ahmed, Ali Alamin Nasir, Mo’awia Mukhtar HassanSpatial and Temporal Variation in Susceptibility Status of Anopheles arabiensis the Malaria Vector to Insecticides in Khartoum State, Sudan EUROPEAN ACADEMIC RESEARCH Vol. III, Issue 8 / November 2015 9406 of adults An. arabiensis. A total of 6275 females of An. arabiensis were exposed to the aforementioned insecticides. Resistances in An. arabiensis to all insecticides were recorded in most of the sites investigated. Most of the populations of An. arabiensis were resistant to malathion, DDT and pyrethroids (permethrin and deltamethrin). The results of overall revealed a clear difference pattern between the seasons in the susceptibility status of An. arabiensis exposed to 4% DDT and 0.1% propoxur. However, the seasonal variations in susceptibility status in An. arabiensis from the sentinel sites did not follow clear trends. In contrast, a significant difference were observed between the seasons in mortality of An. arabiensis from the urban and periurban areas exposed to 4% DDT and 5% malathion respectively. The current study provides useful information on the distribution and seasonal variations in the susceptibility status in An. arabiensis populations from Khartoum State. The mortality rate in An. arabiensis exposed to these insecticides has increased in the wet season which can be explained by the selective insecticide pressures from the agricultural and malaria control programme activities.
Efficiency in Learning: Evidence-Based Guidelines to Manage Cognitive Load

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Dietary flavonoids as intracellular substrates for an erythrocyte trans-plasma membrane oxidoreductase activity

The plasma membrane oxidoreductase (PMOR) activity, which mainly utilises ascorbate as intracellular electron donor, represents a major mechanism for cell-dependent reduction of extracellular oxidants and might be an important process used by the erythrocytes to keep a reduced plasma environment. We previously reported that in human erythrocytes, myricetin and quercetin act as intracellular substrates of a PMOR showing a novel mechanism whereby these flavonoids could exert beneficial effects under oxidative stress conditions. Here, we evaluated the ability of different flavonoids (quercetin, myricetin, morin, kaempferol, fisetin, catechin, luteolin, apigenin, acacetin, rutin, taxifolin, naringenin, genistein) and of two in vivoO-methylated metabolites of quercetin (isorhamnetin and tamarixetin) to be substrates of PMOR, by comparing their antioxidant capacity (i.e. direct interaction with the oxidant ferricyanide or with the free radical 1,1-diphenyl-2-picryl-hydrazil) with their ability to penetrate the erythrocytes and donate electrons to the PMOR. The results obtained indicate that, although most of the flavonoids display significant antioxidant activities, only those (quercetin, myricetin, fisetin) that combine the cathecol structure of the B ring (responsible for the reducing activity) with the 2,3 double bond and 4-oxo function of the C ring (responsible for the uptake by erythrocytes) can act as intracellular substrates for PMOR. It is of note that the metabolites of quercetin enter erythrocytes and donate electrons to the PMOR as the parent compound. The present data show a relationship between the flavonoid structures and their ability to provide electrons to the PMOR, suggesting an additional mechanism whereby dietary flavonoids may exert beneficial effects in man.
Expert ranking using reputation and answer quality of co-existing users

Online discussion forums provide knowledge sharing facilities to online communities. Usage of online discussion forums has increased tremendously due to the variety of services and their ability of common users to ask question and provide answers. With the passage of time, these forums can accumulate huge contents. Some of these posted discussions may not contain quality contents and may reflect users’ personal opinions about topic which may contradict with a relevant answer. These low quality discussions indicate the existence of unprofessional users. Therefore, it is imperative to rank an expert in online forums. Most of the existing expert-ranking techniques consider only user’s social network authority and content relevancy features as parameters of evaluating user expertise. But user reputation as a group member of thread repliers is not considered. In this context a novel solution of expert ranking in online discussion forums is proposed. We proposed two expert ranking techniques: The first technique is based on user and their co-existing user’s reputation in different threaded discussions, and the second technique is based on user answers’ quality and their category specialty features. Furthermore, we extended a technique expertise rank with our proposed features sets. The experimental study based on real dataset shows that the following proposed techniques perform better than existing techniques.
The incidence and risk factors of hepatocellular carcinoma in patients with nonalcoholic steatohepatitis

Nonalcoholic steatohepatitis (NASH) is a well‐recognized cause of cirrhosis and has been increasingly associated with the development of hepatocellular carcinoma (HCC). The aims of this study were to (1) estimate the incidence of HCC in patients with NASH‐related cirrhosis, (2) compare incidence in NASH‐related cirrhosis with hepatitis C virus (HCV)‐related cirrhosis, and (3) identify risk factors of HCC in patients with NASH‐related cirrhosis compared with HCV‐related cirrhosis. Adult patients with cirrhosis secondary to chronic HCV (n = 315) or NASH (n = 195) were evaluated at our hepatobiliary clinic between 2003 and 2007. To assess for HCC development, all patients were monitored using serial abdominal computed tomography and serum alpha‐fetoprotein every 6 months. Kaplan‐Meier analysis was performed to estimate the cumulative incidence of HCC. Descriptive statistics were computed for all factors. Univariate and multivariate Cox regression analysis were used to assess associations between HCC and factors of interest. The median follow‐up was 3.2 years (25th percentile [P25], 75th percentile [P75]: 1.7, 5.7) during which 25/195 (12.8%) of NASH‐cirrhotic and 64/315 (20.3 %) of HCV‐cirrhotic patients developed HCC (P = 0.03). Yearly cumulative incidence of HCC was found to be 2.6% in patients with NASH‐cirrhosis, compared with 4.0% in patients with HCV cirrhosis (P = 0.09). Multivariate regression analysis revealed that older age (P = 0.006) and alcohol consumption (P = 0.002) were independent variables associated with development of HCC in patients with NASH‐cirrhosis. Compared with nondrinkers, patients who reported any regular alcohol consumption were at greater risk for HCC development (hazard ratio: 3.6; P25, P75: 1.5, 8.3). Conclusion: Patients with NASH cirrhosis have a greatly increased risk of liver cancer. Alcohol consumption, a modifiable risk factor, appears to be the most significant factor associated with risk of HCC development in our study population. (Hepatology 2010;)
Beamforming in Dual-Hop Fixed Gain Relaying Systems

The performance of beamforming in dual-hop co-operative networks with fixed-gain relays is investigated. These kinds of relays offer low complexity and ease of deployment when compared with variable-gain relays. In our analysis, the source and destination nodes are equipped with multiple antennas, whereas the relay is assumed to be a single-antenna device. Closed-form expressions for the outage probability (OP), probability density function (PDF), moment generating function (MGF), and generalized moments of the end-to-end signal-to-noise ratio (SNR) are obtained. It is shown that when the same antenna configurations are considered at the source and destination sides, the power imbalance between the hops may be either beneficial or detrimental for the overall system performance. In addition, depending on whether the average SNR of the second hop is equal, lower, or higher than that of the first hop, an increase of the number of antennas may not necessarily result in a substantial improvement in performance.
Widely Tunable Narrow-Linewidth Monolithically Integrated External-Cavity Semiconductor Lasers

We theoretically analyze, design, and measure the performance of a semiconductor laser with a monolithically integrated external cavity. A ~4 cm long on-chip cavity is made possible by a low-loss silicon waveguide platform. We show tuning in excess of 54 nm in the O-band as well as significant reduction in laser linewidth due to controlled feedback from the external cavity. The measured linewidth in full tuning range is below 100 kHz and the best results are around 50 kHz. Approaches to further improve the performance of such laser architectures are described.
PROBABILISTIC FORECASTS OF SOLAR INSOLATION

Meteorological forecasts of incident solar radiation are valuable for solar resource owners and others. Most previously described forecast methods provide a single predicted value. However, a well-calibrated forecast probability distribution is more useful in that it could be used to make optimum decisions under any decision rule. We demonstrate methods of constructing and evaluating probabilistic forecasts of cloudiness (as observed from geostationary satellites) for a given location by combining climatology with weather prediction model output. We use metrics from information theory for forecast skill assessment. We consider two locations, New York City (representing a moist temperate climate) and Nevada (representing a sunny desert climate). We find that probabilistic forecasts conditioned on weather prediction model output improve on climatology at both locations. At Nevada the key limitation for accurate forecasts appears to be the weather model’s representation of cloudiness, while at New York weather predictability is also important.
The changing paradigm in pulmonary hypertension trials: longer duration, new endpoints

Purpose of review Approved therapies for pulmonary arterial hypertension (PAH) currently consist of 12 agents, the majority of which were approved following short-term randomized clinical trials using change in 6 minute walk distance (6MWD) as the primary outcome. However, there is growing concern that significant improvements in this measure do not translate into morbidity and mortality benefits. Recent findings As a result of data questioning the association between improvements in 6 minute walk distance and improvements in outcome, PAH clinical trial design is increasingly utilizing morbidity and mortality events as a composite primary outcome. This concept was recently illustrated in the published phase 3 trial of macitentan versus placebo, during which the clinical worsening event rate was decreased by 45%. Several additional unpublished trials have been similarly designed, all of which will require extended blinded treatment time in order to accrue sufficient event rates. The definition of morbidity events has varied across clinical studies; further standardization of this parameter is necessary. Summary Although multiple direct and surrogate outcomes have been studied in PAH clinical research, rate of clinical worsening events, using prolonged, event-driven trial design, has emerged as the new standard.
2-Methylcarbamoyl-4-{4-[3-(trifluoromethyl)benzamido]phenoxy}pyridinium 4-methylbenzenesulfonate monohydrate

The asymmetric unit of the title compound, C21H17F3N3O3 +·C7H7O3S−·H2O, contains two formula units. In one of the cations, the pyridinium and trifluoromethyl benzene rings form dihedral angles of 87.42 (8) and 45.92 (8)°, respectively, with the central benzene ring [79.56 (8) and 43.52 (8)° in the other cation]. In the crystal structure, N—H⋯O, O—H⋯O and C—H⋯O hydrogen bonds link the ions and water molecules, forming a three-dimensional network.
The Traveling Salesman Problem with Distances One and Two

We present a polynomial-time approximation algorithm with worst-case ratio 7/6 for the special case of the traveling salesman problem in which all distances are either one or two. We also show that this special case of the traveling salesman problem is MAX SNP-hard, and therefore it is unlikely that it has a polynomial-time approximation scheme.
An electrophysiological correlate of Eating Attitudes Test scores in female college students

Synopsis Eating Attitudes Test (EAT) scores of forty female college students were compared to their electrodermal activity (EDA) responses when offered a plate of chocolate chip cookies. A significant positive correlation was detected between the EAT scores and the skin conductivity measures associated with the presentation of food. Women with the highest EAT scores also exhibited the greatest sympathetic nervous system responses to a plate of cookies. This finding supports the conclusion that the EAT is capable of identifying individuals who are preoccupied with food or anxious about eating.
Does ice drive early Maastrichtian eustasy

A large (30–40 m), rapid (≪1 m.y.), earliest Maastrichtian sea-level drop inferred from New Jersey sequence stratigraphic records correlates with synchronous δ18O increases in deep-water benthic and low-latitude surface-dwelling planktonic foraminifera. The coincidence of these events argues for the development of a moderate-sized ice sheet during the early Maastrichtian.
Downlink FTP Performance of Heterogeneous Networks for LTE-Advanced

This paper discusses the need and enabling mechanisms for a heterogeneous deployment model in LTE networks, where lower power nodes are deployed in a macro network. Cell range expansion, enabled through cell biasing and adaptive resource partitioning, is seen as an effective method to balance the load among the nodes in the network and to improve overall trunking efficiency. Interference cancellation receiver plays a crucial role to ensure acquisition of weak cells and reliability of control and data reception in the presence of legacy signal. System simulations results for an FTP traffic model indicate that, for a pico cell deployment with density of 4 picos per macro cell, 40% or more performance gain can be achieved when techniques enabling cell range expansion are deployed.
Deletion of the RNA Polymerase Subunit RPB4 Acts as a Global, Not Stress-specific, Shut-off Switch for RNA Polymerase II Transcription at High Temperatures*

We used whole genome expression analysis to investigate the changes in the mRNA profile in cells lacking theSaccharomyces cerevisiae RNA polymerase II subunit RPB4 (ΔRPB4). Our results indicated that an essentially complete shutdown of transcription occurs upon temperature shift of this conditionally lethal mutant; 98% of mRNA transcript levels decrease at least 2-fold, 96% at least 4-fold. This data was supported by in vivo experiments that revealed a rapid and greater than 5-fold decline in steady state poly(A) RNA levels after the temperature shift. Expression of several individual genes, measured by Northern analysis, was also consistent with the whole genome expression profile. Finally we demonstrated that the loss of RNA polymerase II activity causes secondary effects on RNA polymerase I, but not RNA polymerase III, transcription. The transcription phenotype of the ΔRPB4 mutant closely mirrors that of the temperature-sensitive rpb1-1mutant frequently implemented as a tool to inactivate the RNA polymerase II in vivo. Therefore, the ΔRPB4 mutant can be used to easily design strains that enable the study of distinct post-transcriptional cellular processes in the absence of RNA polymerase II transcription.
Support vector regression based autoassociative models for time series classification

There are two paradigms for modeling varying length time series data, namely, modeling the sequence of feature vectors and modeling the sets of vectors. In this paper, we propose a regression based autoassociative model for modeling sets of vectors for time series data. We also propose a hybrid framework where a regression based autoassociative model is used for representing varying length time series data and then a discriminative model is used for classification. The proposed approach applied to speech emotion recognition task gives a better performance than the conventional methods.
Recovering the Manhattan Frame from a single RGB-D image by using orientation relevance

Most man-made indoor and urban scenes are composed of a set of orthogonal and parallel planes. In robotics and computer vision, these scenes typically represented by the Manhattan-World model. The accurate estimation of the Manhattan Frame, which consists of three orthogonal directions being used to represent the Manhattan-World, plays an important role in many applications, such as SLAM, scene understanding and 3D reconstruction. In this paper, a new method for accurately recovering the Manhattan frame from a single RGB-D image by using the orientation relevance is proposed. It first extracts planes from the input single RGB-D image. Then three orthogonal dominant planes are determined by introducing the concept of orientation relevance. Finally, the Manhattan Frame can be easily recovered from the obtained three orthogonal dominant planes. Experiments with open dataset validate the proposed method. The overall performance of the proposed method, which takes both accuracy and speed into account, is superior to that of the state-of-the-art methods. It is also applied on the application of scene annotation to confirm its applicability.
Effect of two-times 24 hour exposures to 60 GHz millimeter-waves on neurite outgrowth in PC12VG cells in consideration of polarization

We investigated the effects of millimeter-wave (MMW) electromagnetic fields on neurite outgrowth in PC12VG cells in vitro. We examined the average length of neurites of 160 cells exposed or sham-exposed to 60 GHz MMWs with circular and linear polarizations at average power density of 1 mW/cm2 for two-times of 24 hour exposure. Four parameters, namely the power density, inhomogeneity of the induced distribution, polarization characteristics, and induced temperature increase due to MMW absorption, were determined and analyzed to characterize exposure conditions extensively. Our results suggested that MMW exposure under these exposure conditions has no significant effect on neurite outgrowth in PC12VG cells.