Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Determinants of Hepatitis B and D Virus Entry Restriction in Mouse Sodium Taurocholate Cotransporting Polypeptide

ABSTRACT Human hepatitis B virus (HBV) and its satellite virus, hepatitis D virus (HDV), primarily infect humans, chimpanzees, or tree shrews (Tupaia belangeri). Viral infections in other species are known to be mainly restricted at the entry level since viral replication can be achieved in the cells by transfection of the viral genome. Sodium taurocholate cotransporting polypeptide (NTCP) is a functional receptor for HBV and HDV, and amino acids 157 to 165 of NTCP are critical for viral entry and likely limit viral infection of macaques. However, the molecular determinants for viral entry restriction in mouse NTCP (mNTCP) remain unclear. In this study, mNTCP was found to be unable to support either HBV or HDV infection, although it can bind to pre-S1 of HBV L protein and is functional in transporting substrate taurocholate; comprehensive swapping and point mutations of human NTCP (hNTCP) and mNTCP revealed molecular determinants restricting mNTCP for viral entry of HBV and HDV. Remarkably, when mNTCP residues 84 to 87 were substituted by human counterparts, mNTCP can effectively support viral infections. In addition, a number of cell lines, regardless of their species or tissue origin, supported HDV infection when transfected with hNTCP or mNTCP with residues 84 to 87 replaced by human counterparts, highlighting the central role of NTCP for viral infections mediated by HBV envelope proteins. These studies advance our understanding of NTCP-mediated viral entry of HBV and HDV and have important implications for developing the mouse model for their infections.
Progranulin Deficiency Decreases Gross Neural Connectivity But Enhances Transmission at Individual Synapses

Frontotemporal dementia (FTD) has been linked to mutations in the progranulin gene (GRN) that lead to progranulin (PGRN) haploinsufficiency. Thus far, our understanding of the effects of PGRN depletion in the brain has been derived from investigation of gross pathology, and more detailed analyses of cellular function have been lacking. We report that knocking down PGRN levels in rat primary hippocampal cultures reduces neural connectivity by decreasing neuronal arborization and length as well as synapse density. Despite this, the number of synaptic vesicles per synapse and the frequency of mEPSCs are increased in PGRN knockdown cells, suggesting an increase in the probability of release at remaining synapses. Interestingly, we demonstrate that the number of vesicles per synapse is also increased in postmortem brain sections from FTD patients with PGRN haploinsufficiency, relative to controls. Our observations show that PGRN knockdown severely alters neuronal connectivity in vitro and that the synaptic vesicle phenotype observed in culture is consistent with that observed in the hippocampus of FTD patients.
Improvement of energy consumption in cognitive radio by reducing the number of sensed samples

High energy consumption is one of the main challenges faced in cognitive radio (CR) networks, which may limit their implementation especially in battery-powered devices. In these networks, significant part of the energy is consumed in the energy detector during spectrum sensing for possible vacancy for secondary user transmission. In this paper, we have investigated reducing the energy consumption of single cognitive user (CU) by reducing the number of sensed samples. Also we have explained the optimization criteria for improving energy consumption by controlling number of sensed samples, detection probability and threshold of energy detector. The performance of energy detection system is evaluated in AWGN and Rayleigh fading channels. The simulation results show that at Eb/No of 10 dB 50% and 46 % of the energy consumed in detection are saved when the number of sensed samples is reduced by 50% with acceptable loss in detection probability of 5% and 12% in AWGN and Rayleigh channel respectively. The results also shows the impact of changing the threshold of energy detector on energy consumed in spectrum sensing.
The Major Tuber Storage Protein of Araceae Species Is a Lectin (Characterization and Molecular Cloning of the Lectin from Arum maculatum L.)

A new lectin was purified from tubers of Arum maculatum L. by affinity chromatography on immobilized asialofetuin. Although this lectin is also retained on mannose-Sepharose 4B, under the appropriate conditions free mannose is a poor inhibitor of its agglutination activity. Pure preparations of the Arum lectin apparently yielded a single polypeptide band of approximately 12 kD upon sodium dodecyl sulfate-polyacrylamide gel electrophoresis. However, N-terminal sequencing of the purified protein combined with molecular cloning of the lectin have shown that the lectin is composed of two different 12-kD lectin subunits that are synthesized on a single large precursor translated from and mRNA of approximately 1400 nucleotides. Lectins with similar properties were also isolated from the Araceae species Colocasia esculenta (L.) Schott, Xanthosoma sagittifolium (L.) Schott, and Dieffenbachia sequina Schott. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and gel filtration of the different Araceae lectins have shown that they are tetrameric proteins composed of lectin subunits of 12 to 14 kD. Interestingly, these lectins are the most prominent proteins in the tuber tissue. Evidence is presented that a previously described major storage protein of Colocasia tubers corresponds to the lectin.
ON THE EVALUATION OF PERCEPTUAL SIMILARITY MEASURES FOR MUSIC

Several applications in the field of content-based interaction with music repositories rely on measures which estimate the perceived similarity of music. These applications include automatic genre recognition, playlist generation, and recommender systems. In this paper we study methods to evaluate the performance of such measures. We compare five measures which use only the information extracted from the audio signal and discuss how these measures can be evaluated qualitatively and quantitatively without resorting to large scale listening tests.
Vascular endothelial growth factor induces MEF2C and MEF2-dependent activity in endothelial cells.

PURPOSE Vascular endothelial growth factor is a key regulator of physiological and pathologic angiogenesis. Although much is known about the major upstream signaling pathways of VEGF in endothelial cells, less is known about key transcription factors involved in VEGF action. The transcription factor myocyte enhancer factor (MEF)-2C is thought to play an important role in vasculogenesis and angiogenesis during vascular development. The purpose of this study was to investigate the regulation of MEF2C expression and MEF2-dependent activity in endothelial cells by VEGF. METHODS Expression of MEF2C in human retinal endothelial cells and human umbilical vein endothelial cells was assayed by real-time PCR and Western blot. VEGF regulation of MEF2-dependent transcription was studied using an MEF2-luciferase reporter construct containing three copies of a high-affinity MEF2 binding site. The effect of MEF2 on endothelial cell migration was evaluated using a dominant-negative MEF2C mutant. RESULTS VEGF induced MEF2C expression in a dose- and time-dependent fashion. This induction was completely abrogated by the inhibition of protein kinase C and was partially blocked by the inhibition of PKC-beta and PKC-delta. In addition to regulating MEF2C expression, VEGF stimulated transcription from an MEF2-dependent promoter. VEGF stimulation of transcription was significantly reduced by the inhibition of calcineurin, CaMKII, p38 MAPK, and PKC, but not by the inhibition of ERK1/2 or BMK1/ERK5. Transfection of a dominant-negative mutant of MEF2C significantly inhibited VEGF-stimulated endothelial cell migration. CONCLUSIONS These results implicate VEGF as a key regulator of MEF2C and suggest that MEF2 may be an important mediator of VEGF in endothelial cells.
Extracting latent structures in numerical classification: an investigation using two factor models

We investigate the use of SVD based two factor models for numerical data classification. Motivations for such a study include the widespread success of such models (e.g, LSI) in textual information retrieval, emerging connections with well established statistical techniques and the increasing occurrence of mixed mode (text-and-numeric) data. A direct extension as well as an efficient modification of the LSI model applied to numerical data problems are presented and the associated problems and likely remedies discussed. The techniques under investigation are shown to perform competitively with respect to popular existing numerical classification techniques on a range of synthetic and real world benchmark data. In particular, we show that the modified LSI proposed in this work avoids confronting the optimal subspace selection problem yet generalizes well and remains computationally efficient for large data.
Cell swelling activates ATP-dependent voltage-gated chloride channels in M-1 mouse cortical collecting duct cells

In the present study we used whole-cell patch clamp recordings to investigate swelling-activated Cl-currents (ICl-swell) in M-1 mouse cortical collecting duct (CCD) cells. Hypotonic cell swelling reversibly increased the whole-cell Cl- conductance by about 30-fold. The I-V relationship was outwardly-rectifying and ICl-swell displayed a characteristic voltage-dependence with relatively fast inactivation upon large depolarizing and slow activation upon hyperpolarizing voltage steps. Reversal potential measurements revealed a selectivity sequence SCN- > I- > Br- > Cl- > > gluconate. ICl-swell was inhibited by tamoxifen, NPPB (5-nitro-2(3-phenylpropylamino)-benzoate), DIDS (4,4'-diisothiocyanostilbene-2,2'-disulphonic acid), flufenamic acid, niflumic acid, and glibenclamide, in descending order of potency. Extracellular cAMP had no significant effect. ICl-swell was Ca2+ independent, but current activation depended on the presence of a high- energy gamma-phosphate group from intracellular ATP or ATP gamma S. Moreover, it depended on the presence of intracellular Mg2+ and was inhibited by staurosporine, which indicates that a phosphorylation step is involved in channel activation. Increasing the cytosolic Ca2+ concentration by using ionomycin stimulated Cl- currents with a voltage dependence different from that of ICl-swell. Analysis of whole-cell current records during early onset of ICl-swell and during final recovery revealed discontinuous step-like changes of the whole-cell current level which were not observed under nonswelling conditions. A single-channel I-V curve constructed using the smallest resolvable current transitions detected at various holding potentials and revealed a slope conductance of 55, 15, and 8 pS at +120, 0, and -120 mV, respectively. The larger current steps observed in these recordings had about 2, 3, or 4 times the size of the putative single-channel current amplitude, suggesting a coordinated gating of several individual channels or channel subunits. In conclusion we have functionally characterized ICl-swell in M-1 CCD cells and have identified the underlying single channels in whole-cell current recordings.
(l1, ..., lq)-diversity for Anonymizing Sensitive Quasi-Identifiers

A lot of studies of privacy-preserving data mining have been proposed. Most of them assume that they can separate quasi-identifiers (QIDs) from sensitive attributes. For instance, they assume that address, job, and age are QIDs but not sensitive attributes, and that a disease name is a sensitive attribute but not a QID. However, all of these attributes can have features that are both sensitive attributes and QIDs depending on the persons in practice. In this paper, we refer to these attributes as sensitive QIDs, and we propose a novel privacy definition (l1, ., lq)-diversity and a method that can treat sensitive QIDs. Our method is composed of two algorithms: an anonymization algorithm and a reconstruction algorithm. The anonymization algorithm, which is conducted by data holders, is simple but effective, whereas the reconstruction algorithm, which is conducted by data users, can be conducted according to each data user's objective. Our proposed method is experimentally evaluated using real datasets.
Ice-nucleating bacteria control the order and dynamics of interfacial water

Specialized bacteria trigger ice formation by controlling the molecular structure and energy transfer in interfacial water. Ice-nucleating organisms play important roles in the environment. With their ability to induce ice formation at temperatures just below the ice melting point, bacteria such as Pseudomonas syringae attack plants through frost damage using specialized ice-nucleating proteins. Besides the impact on agriculture and microbial ecology, airborne P. syringae can affect atmospheric glaciation processes, with consequences for cloud evolution, precipitation, and climate. Biogenic ice nucleation is also relevant for artificial snow production and for biomimetic materials for controlled interfacial freezing. We use interface-specific sum frequency generation (SFG) spectroscopy to show that hydrogen bonding at the water-bacteria contact imposes structural ordering on the adjacent water network. Experimental SFG data and molecular dynamics simulations demonstrate that ice-active sites within P. syringae feature unique hydrophilic-hydrophobic patterns to enhance ice nucleation. The freezing transition is further facilitated by the highly effective removal of latent heat from the nucleation site, as apparent from time-resolved SFG spectroscopy.
Price Competition with the Attraction Demand Model: Existence of Unique Equilibrium and Its Stability

We show the existence of Nash equilibria in a Bertrand oligopoly price competition game using a possibly asymmetric attraction demand model with convex costs under mild assumptions. We show that the equilibrium is unique and globally stable. To our knowledge, this is the first paper to show the existence of a unique equilibrium with both nonlinear demand and nonlinear costs. In addition, we guarantee the linear convergence rate of tatonnement. We illustrate the applicability of this approach with several examples arising from operational considerations that are often ignored in the economics literature.
Interactive segmentation with seed expansion

In this paper, we address the problem of interactive image segmentation which segments an image based on user-supplied scribbles. For this purpose, we propose a novel framework that provides consistent performance robust to the location of input seeds. Most of the existing methods, especially random walk-based approaches, strongly depend on initial seed positions, which differ from one user to another. To overcome this drawback, the proposed algorithm incorporates the seed expansion step, in which robust seed information is secured and improved. We also address the computation issue using a coarse-to-fine random walk technique. We evaluate our algorithm using challenging datasets, such as Grabcut, PASCAL VOC and Alpha matting datasets. Our algorithm produces a more accurate segmentation results than the existing methods.
Seminal plasma transforming growth factor-β, activin A and follistatin fluctuate within men over time.

STUDY QUESTION Do seminal plasma transforming growth factor-β (TGFB) cytokines vary within individuals over time, and does this relate to sperm parameters, age or prior abstinence? SUMMARY ANSWER Activin A and follistatin, and to a lesser extent TGFB1, TGFB2 and TGFB3, vary within individuals over time, in association with duration of abstinence. WHAT IS ALREADY KNOWN Seminal plasma TGFB cytokines can influence sperm function and reproductive success through interactions with the female reproductive tract after coitus. Over time, individual sperm parameters fluctuate considerably. Whether seminal fluid TGFB cytokines vary similarly, and the determinants of any variance, is unknown. STUDY DESIGN, SIZE, DURATION Between two and seven semen samples were collected from each of 14 fertile donors at 6-10 week intervals over the course of 12 months, then seminal plasma cytokines and sperm parameters were measured. PARTICIPANTS/MATERIALS, SETTING AND METHOD The concentrations and total amounts per ejaculate of TGFB1, TGFB2, TGFB3, activin A and follistatin were determined using commercial assays. Sperm parameters were assessed according to WHO IV standards. Mixed model analysis was utilised to determine the relative contribution of between- and within-individual factors to the variance. Relationships between cytokines and sperm parameters, as well as effect of age and duration of abstinence, were investigated by correlation analysis. MAIN RESULTS AND THE ROLE OF CHANCE Within-individual variability contributed to the total variance for all cytokines and sperm parameters, and was a stronger determinant than between-individual variability for activin A and follistatin as well as for total sperm concentration and sperm motility. Positive correlations between each of the three TGFB isoforms, and activin and follistatin, suggest co-regulation of synthesis. Duration of abstinence influenced total content of TGFB1, TGFB2, activin A and follistatin. TGFB1 correlated inversely with age. LIMITATIONS, REASONS FOR CAUTION A limited number of donors from a single clinic were investigated. Clinical information on BMI, nutrition, smoking and other lifestyle factors was unavailable. Further studies are required to determine whether the findings can be generalised to larger populations and different ethnicities. WIDER IMPLICATIONS OF THE FINDINGS These data reveal substantial variation over time in seminal fluid cytokines and indicate that repeated analyses are required to gain precise representative data on an individual's status. Within-individual variation in seminal fluid components should be taken into account when investigating seminal fluid cytokines. STUDY FUNDING/COMPETING INTERESTS This study was supported by grants from the National Health and Medical Research Council of Australia, ID453556 and APP1041332. The authors have no competing interests to disclose.
The JPEG still picture compression standard

For the past few years, a joint ISO/CCITT committee known as JPEG (Joint Photographic Experts Group) has been working to establish the first international compression standard for continuous-tone still images, both grayscale and color. JPEG’s proposed standard aims to be generic, to support a wide variety of applications for continuous-tone images. To meet the differing needs of many applications, the JPEG standard includes two basic compression methods, each with various modes of operation. A DCT-based method is specified for “lossy’’ compression, and a predictive method for “lossless’’ compression. JPEG features a simple lossy technique known as the Baseline method, a subset of the other DCT-based modes of operation. The Baseline method has been by far the most widely implemented JPEG method to date, and is sufficient in its own right for a large number of applications. This article provides an overview of the JPEG standard, and focuses in detail on the Baseline method.
A power-gated MPU with 3-microsecond entry/exit delay using MTJ-based nonvolatile flip-flop

We propose a novel power-gated microprocessor unit (MPU) using a nonvolatile flip-flop (NV-F/F) with magnetic tunnel junction (MTJ). By using the NV-F/F to store the MPU's internal state, this MPU realizes power-gating operation with a small 3-microsecond entry/exit delay penalty in power-on/power-off, which is one order of magnitude faster than a conventional MPU's deep power down mode. To achieve this short entry/exit delay, an appropriate NV-F/F circuit, which can perform stable high speed store/recall operations, has been developed. The MPU will help in the realization of low power systems because of its easy controllability for the power gating mode.
Generation of DC corona discharge in supercritical CO/sub 2/ for environment protection purpose

The generation of dc corona discharges in supercritical CO/sub 2/ using a point-plane electrode is studied experimentally. The results reveal a bizarre situation for CO/sub 2/ breakdown voltages, which is much lower in near the supercritical point than the measured in the normal high pressure gas. An explanation is probably because of the extensive cluster formation under the supercritical fluid condition. Therefore, it can be concluded that corona discharge in supercritical fluid condition may be generated with very low voltage.
Regular Repair of Specifications

What do you do if a computational object (e.g. program trace) fails a specification? An obvious approach is to perform \emph{repair}: modify the object minimally to get something that satisfies the constraints.In this paper we study repair of temporal constraints, given as automata or temporal logic formulas. We focus on determining the number of repairs that must be applied to a word satisfying a given input constraint in order to ensure that it satisfies a given target constraint. This number may well be unbounded, one of our main contributions is to isolate the complexity of the ``bounded repair problem'', based on a characterization of the pairs of regular languages that admit such a repair. Weconsider this in the setting where the repair strategy is unconstrained and also when the strategy is restricted to use finite memory. Although the streaming setting is quite different from the general setting, we find that there are surprising connections between streaming and non-streaming, as well as within variants of the streaming problem.
An online EEG BCI based on covert visuospatial attention in absence of exogenous stimulation

Objective. In this work we present—for the first time—the online operation of an electroencephalogram (EEG) brain–computer interface (BCI) system based on covert visuospatial attention (CVSA), without relying on any evoked responses. Electrophysiological correlates of pure top-down CVSA have only recently been proposed as a control signal for BCI. Such systems are expected to share the ease of use of stimulus-driven BCIs (e.g. P300, steady state visually evoked potential) with the autonomy afforded by decoding voluntary modulations of ongoing activity (e.g. motor imagery). Approach. Eight healthy subjects participated in the study. EEG signals were acquired with an active 64-channel system. The classification method was based on a time-dependent approach tuned to capture the most discriminant spectral features of the temporal evolution of attentional processes. The system was used by all subjects over two days without retraining, to verify its robustness and reliability. Main results. We report a mean online accuracy across the group of 70.6 ± 1.5%, and 88.8 ± 5.8% for the best subject. Half of the participants produced stable features over the entire duration of the study. Additionally, we explain drops in performance in subjects showing stable features in terms of known electrophysiological correlates of fatigue, suggesting the prospect of online monitoring of mental states in BCI systems. Significance. This work represents the first demonstration of the feasibility of an online EEG BCI based on CVSA. The results achieved suggest the CVSA BCI as a promising alternative to standard BCI modalities.
Dwarf Novae with Newly Determined Parallaxes: Model Analyses of VY Aquarii, RU Pegasi, and T Leonis

Using newly determined parallaxes for dwarf novae, we have derived outburst accretion rates for VY Aqr, RU Peg, and T Leo, and for T Leo during quiescence. The two short‐period dwarf novae, VY Aqr and T Leo, show good agreement with optically thick steady‐state accretion disks in outburst, whereas RU Peg shows a significant departure from a steady‐state disk. We have determined that the white dwarf in T Leo has Teff = 16,000 ± 1000 K, a value consistent with long‐term compressional heating when gravitational‐wave emission drives mass transfer. The white dwarf in T Leo has a temperature in the same narrow range as other WZ Sge–like dwarf novae.