Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of Disulfide Bridges Formed in the Luminal Domain of ATF6 in Sensing Endoplasmic Reticulum Stress

ABSTRACT ATF6 is a membrane-bound transcription factor activated by proteolysis in response to endoplasmic reticulum (ER) stress to induce the transcription of ER chaperone genes. We show here that, owing to the presence of intra- and intermolecular disulfide bridges formed between the two conserved cysteine residues in the luminal domain, ATF6 occurs in unstressed ER in monomer, dimer, and oligomer forms. Disulfide-bonded ATF6 is reduced upon treatment of cells with not only the reducing reagent dithiothreitol but also the glycosylation inhibitor tunicamycin, and the extent of reduction correlates with that of activation. Although reduction is not sufficient for activation, fractionation studies show that only reduced monomer ATF6 reaches the Golgi apparatus, where it is cleaved by the sequential action of the two proteases S1P and S2P. Reduced monomer ATF6 is found to be a better substrate than disulfide-bonded forms for S1P. ER stress-induced reduction is specific to ATF6 as the oligomeric status of a second ER membrane-bound transcription factor, LZIP/Luman, is not changed upon tunicamycin treatment and LZIP/Luman is well cleaved by S1P in the absence of ER stress. This mechanism ensures the strictness of regulation, in that the cell can only process ATF6 which has experienced the changes in the ER.
Relative Importance of the Free and Fixed Bacterial Community in Three Lacustrine Ecosystems having Different Trophic Status

The present work consists in determining the total bacterial densities and biomasses and the relative importance of free and fixed bacterioplankton in three lacustrine environments with different trophic status: Pavin lake, oligomesotrophe, and the Villerest reservoir, eutrophe (two French ecosystems) and the dam Allal Fassi, mesotrophe (Morocco). Along the water column, the results obtained showed bacterial densities that ranged from 0.60 to 7 x 105 cells.ml-1 at Pavin Lake, from 1.01 to 9.86 x 106 cells.ml-1 in the Allal Fassi dam reservoir and from 0.70 to 12.90 x 106 cells.ml-1 in the Villerest reservoir. The average recorded bacterial biomass ranged from 0.73 to 1.92 mugC.l-1 in Pavin Lake, from 10.50 to 81.10 mugC.l-1 in the Allal Fassi dam and from 29.40 to 60.52 mugC.l-1 in the Villerest reservoir. Seasonal variations show fluctuations in bacterial densities for the three environments. The proportion of free and fixed bacteria revealed high percentages of the fraction of free bacteria with 96.10% 90.50% 87.90% at the surface layers respectively at Pavin Lake, Villerest Reservoir and Allal Fassi Reservoir. Mean recorded values ​​of fixed bacteria at all depths were 4.26% 10.35% 17.13% of the total bacterial density respectively in Pavin Lake, Villerest Reservoir and Allal Fassi Reservoir.
A characterization of max-min SIR-balanced power allocation with applications

We consider a power-controlled wireless network with an established network topology in which the communication links (transmitter-receiver pairs) are subject to some constraints on transmit powers and corrupted by the cochannel interference and background noise. The interference is completely determined by a so-called gain matrix. Assuming irreducibility of the gain matrix, we provide an elegant characterization of the max-min SIR-balanced power allocation under general power constraints. This characterization gives rise to two types of algorithms for computing the max-min SIR-balanced power allocation. It also allows for an interesting saddle point characterization of the Perron root of extended gain matrices.
Experiences of Anticholinesterase Pesticide Poisonings in an Australian Tertiary Hospital

There is limited information regarding the management and outcomes of patients presenting with anticholinesterase pesticide poisoning in Australia. Patients presenting to a tertiary referral hospital with anticholinesterase exposures were identified by discharge coding. The medical records of each patient were retrospectively reviewed. Based on clinical outcome, patients were classified as severe or non-severe poisonings. Forty-one presentations were noted between 1990 and 2003. Eight patients (20%) had severe poisoning of which tachycardia, fasciculations with weakness and metabolic acidosis were common manifestations. The diagnosis was delayed in four patients due to the absence of a clear history, which did not influence patient outcomes or put hospital staff at risk of nosocomial poisoning. The median length of hospital stay was prolonged in severe poisonings (20 days) compared to 12 hours in other patients. Two cases of intermediate syndrome were attributed to fenthion and diazinon, and one case of delayed polyneuropathy to trichlorfon. Cholinesterase activities were performed in only 49% of presentations. The overall mortality was 2.4% (1 death) and the mortality in patients with severe poisoning was 12.5%. The incidence of anticholinesterase poisoning in Australia is low. These outcomes were favourable and comparable with other published data. Measures to enhance the knowledge of medical staff supplemented by validated treatment protocols should be developed. For less significant exposures, an emphasis on adequate documentation of cholinergic signs and cholinesterase activities is necessary for rapid triage and may also have potential forensic implications if not performed.
In Situ Capture RT-qPCR: A New Simple and Sensitive Method to Detect Human Norovirus in Oysters

Human noroviruses (HuNoVs) are the major cause worldwide for non-bacterial acute gastroenteritis. In this study, we applied a novel viral receptor mediated in situ capture RT-qPCR (ISC-RT-qPCR) to detect HuNoVs in oysters and compared with the traditional RT-qPCR method. Ten HuNoVs RT-PCR positive and 5 negative clinical samples from gastroenteritis patients were used to compare specificity and sensitivity of ISC-RT-qPCR against that of the RT-qPCR assay. ISC-RT-qPCR had at a one-log and a two-log increase in sensitivity over that of the RT-qPCR assay for genotype I (GI) and GII, respectively. Distributions of HuNoVs in oyster tissues were investigated in artificially inoculated oysters. GI HuNoVs could be detected in all tissues in inoculated oysters by both ISC-RT-qPCR and RT-qPCR. GII HuNoVs could only be detected in gills and digestive glands by both methods. The number of viral genomic copies (vgc) measured by ISC-RT-qPCR was comparable with RT-qPCR in the detection of GI and GII HuNoVs in inoculated oysters. Thirty-six oyster samples from local market were assayed for HuNoVs by both assays. More HuNoVs could be detected by ISC-RT-qPCR in retail oysters. The detection rates of GI HuNoVs in gills, digestive glands, and residual tissues were 33.3, 25.0, and 19.4% by ISC-RT-qPCR; and 5.6, 11.1, and 11.1% by RT-qPCR, respectively. The detection rates of GII HuNoVs in gills were 2.8% by ISC-RT-qPCR; no GII HuNoV was detected in these oysters by RT-qPCR. Overall, all results demonstrated that ISC-RT-qPCR is a promising method for detecting HuNoVs in oyster samples.
Additive Neural Networks for Statistical Machine Translation

Most statistical machine translation (SMT) systems are modeled using a loglinear framework. Although the log-linear model achieves success in SMT, it still suffers from some limitations: (1) the features are required to be linear with respect to the model itself; (2) features cannot be further interpreted to reach their potential. A neural network is a reasonable method to address these pitfalls. However, modeling SMT with a neural network is not trivial, especially when taking the decoding efficiency into consideration. In this paper, we propose a variant of a neural network, i.e. additive neural networks, for SMT to go beyond the log-linear translation model. In addition, word embedding is employed as the input to the neural network, which encodes each word as a feature vector. Our model outperforms the log-linear translation models with/without embedding features on Chinese-to-English and Japanese-to-English translation tasks.
Precipitation and large herbivorous mammals II: application to fossil data

Background: We developed a method to estimate precipitation using mammalian ecomorphology, specifically the relative height of the molars of herbivores (see companion paper, this issue). Question: If we apply the new method to paleoenvironments, do the results agree with previous results from fossil mammals and paleobotanical proxies? Data: Large herbivorous fossil mammals of Eurasia. Data from NOW database covers 23–22 Ma and is Eurasia-wide. Method: We apply the new precipitation estimation method (based on present-day mammalian ecomorphology) to fossil assemblages from different localities. Conclusions: The early Miocene retained the overall humid conditions of the late Paleogene. A shift to more arid conditions began during the middle Miocene. The late Miocene as a whole was a time of large changes, and there was continent-wide restructuring of the distribution of environments. Our new results agree with previous investigations and the mammal proxy data are in good agreement with palaeovegetation data. Mammals and vegetation produce similar precipitation values and large-scale patterns.
House dust mite allergen avoidance and self-management in allergic patients with asthma: randomised controlled trial.

BACKGROUND The efficacy of bed covers that are impermeable to house dust mites has been disputed. AIM The aim of the present study was to investigate whether the combination of 'house dust mite impermeable' covers and a self-management plan, based on peak flow values and symptoms, leads to reduced use of inhaled corticosteroids (ICS) than self-management alone. DESIGN OF STUDY Prospective, randomised, double blind, placebo-controlled trial. SETTING Primary care in a south-eastern region of the Netherlands. METHOD Asthma patients aged between 16 and 60 years with a house dust mite allergy requiring ICS were randomised to intervention and placebo groups. They were trained to use a self-management plan based on peak flow and symptoms. After a 3-month training period, the intervention commenced using house dust mite impermeable and placebo bed covers. The follow-up period was 2 years. Primary outcome was the use of ICS; secondary outcomes were peak expiratory flow parameters, asthma control, and symptoms. RESULTS One hundred and twenty-six patients started the intervention with house dust mite impermeable or placebo bed covers. After 1 and 2 years, significant differences in allergen exposure were found between the intervention and control groups (P<0.001). No significant difference between the intervention and control groups was found in the dose of ICS (P = 0.08), morning peak flow (P = 0.52), peak flow variability (P = 0.36), dyspnoea (P = 0.46), wheezing (P = 0.77), or coughing (P = 0.41). There was no difference in asthma control between the intervention and control groups. CONCLUSION House dust mite impermeable bed covers combined with self-management do not lead to reduced use of ICS compared with self-management alone.
Neurokinin receptor modulation of respiratory activity in the rabbit

The respiratory role of neurokinin (NK) receptors was investigated in α‐chloralose‐urethane‐anaesthetized, vagotomized, paralysed and artificially ventilated rabbits by using bilateral microinjections (30–50 nL) of NK receptor agonists and antagonists. Microinjections were performed in a region located just caudal to the rostral expiratory neurons. This region displayed features similar to those of the pre‐Bötzinger complex (pre‐BötC) of adult cats and rats, and proved to produce excitatory respiratory effects in response to microinjections of d,l‐homocysteic acid. We used as agonists (0.1, 0.5 and 5 mm) substance P (SP), the NK1 receptor agonists [Sar9, Met(O2)11]‐SP and GR 73632, the NK2 receptor agonist NKA, the NK3 receptor agonist senktide, and as antagonists (5 mm) the NK1 receptor antagonist CP‐99,994 and the NK2 receptor antagonist MEN 10376. SP always increased respiratory frequency, but NK1 receptor agonists did not change respiratory variables. NKA and senktide at 5 mm increased respiratory frequency. CP‐99,994 caused increases in respiratory frequency and did not antagonize the effects of SP. MEN 10376 prevented the respiratory responses induced by NKA and reduced those provoked by SP. SP or the NK1 receptor agonists (5 mm) injected (1 μL) into the IV ventricle caused marked excitatory effects on respiration. The results suggest that NK2 and NK3, but not NK1, receptors are involved in the excitatory modulation of inspiratory activity within the investigated region and are consistent with the notion that the pre‐BötC neurons are important components of the inspiratory rhythm‐generating mechanisms.
Small and Large-Sample Behavior of Two Detectors Against Envelope-Detected

The mean and median detectors are compared at both small- and large-(ARE)-sample sizes for use with envelope-detected data. For the Rayleigh distribution, the mean is the better detector for all sample sizes. However, for the noncoherent contaminated-normal distribution, the mean is the better small-sample detector, whereas the median is the better large-sample detector. Hence, the ARE cannot always be used to deduce the small-sample behavior of detectors.
Sea ice assimilation into a coupled ocean–sea ice model using its adjoint

Abstract. Satellite sea ice concentrations (SICs), together with several ocean parameters, are assimilated into a regional Arctic coupled ocean–sea ice model covering the period of 2000–2008 using the adjoint method. There is substantial improvement in the representation of the SIC spatial distribution, in particular with respect to the position of the ice edge and to the concentrations in the central parts of the Arctic Ocean during summer months. Seasonal cycles of total Arctic sea ice area show an overall improvement. During summer months, values of sea ice extent (SIE) integrated over the model domain become underestimated compared to observations, but absolute differences of mean SIE to the data are reduced in nearly all months and years. Along with the SICs, the sea ice thickness fields also become closer to observations, providing added value by the assimilation. Very sparse ocean data in the Arctic, corresponding to a very small contribution to the cost function, prevent sizable improvements of assimilated ocean variables, with the exception of the sea surface temperature.
A Novel Image Encryption Scheme based on Multiple Parameter Discrete Fractional Fourier Transform

is one of the most challenging aspects in internet and Multimedia applications. Encryption is a process which is used to secure data. The Encryption algorithms and suitable transforms play a crucial role to form efficient security systems. In this regard the original information in the existing security system based on the fractional Fourier transform (FRFT) is protected by only a certain order of FRFT. In this paper, we propose a novel method to encrypt an image by using multiple parameters discrete fractional Fourier transform (DFRFT) with random phase matrices. The multiple-parameter discrete fractional Fourier transform (MPDFRFT) possesses all the desired properties of discrete fractional Fourier transform. The MPDFRFT converts to the DFRFT when all of its order parameters are the same. We exploit the properties of multiple-parameter DFRFT and propose a novel encryption scheme using the double random phase in the MPDFRFT domain for encrypting digital data. The proposed encoding scheme with MPDFRFT significantly enhances the data security compared to DFRFT and FRFT and it shows consistent performance with different images. The scheme offers a high degree of resistance towards bruteforce attack.
The NewProt Self-Service Portal for Protein Engineering

The NewProt portal is a platform that gives users access to a broad range of protein engineering tools and services. On an embedded website users can interactively work with these tools and perform their computations supported by integrated workflows. The portal provides a tight integration of standard tools for protein engineering and workflow development. The concept of the NewProt project is to combine and integrate the best European softwares into a homogeneous portal for in silico protein engineering. The predictions made by the portal regarding the effect of mutations on protein stability, selectivity, activity, production level, etcetera, will be experimentally validated to iteratively improve the quality of the software.
Foliage of Oaks Grown Under Elevated CO2 Reduces Performance of Antheraea polyphemus (Lepidoptera: Saturniidae)

Abstract To understand how the increase in atmospheric CO2 from human activity may affect leaf damage by forest insects, we examined host plant preference and larval performance of a generalist herbivore, Antheraea polyphemus Cram. , that consumed foliage developed under ambient or elevated CO2. Larvae were fed leaves from Quercus alba L. and Quercus velutina Lam. grown under ambient or plus 200 μl/liter CO2 using free air carbon dioxide enrichment (FACE). Lower digestibility of foliage, greater protein precipitation capacity in frass, and lower nitrogen concentration of larvae indicate that growth under elevated CO2 reduced the food quality of oak leaves for caterpillars. Consuming leaves of either oak species grown under elevated CO2 slowed the rate of development of A. polyphemus larvae. When given a choice, A. polyphemus larvae preferred Q. velutina leaves grown under ambient CO2; feeding on foliage of this species grown under elevated CO2 led to reduced consumption, slower growth, and greater mortality. Larvae compensated for the lower digestibility of Q. alba leaves grown under elevated CO2 by increasing the efficiency of conversion of ingested food into larval mass. Despite equivalent consumption rates, larvae grew larger when they consumed Q. alba leaves grown under elevated compared with ambient CO2. Reduced consumption, slower growth rates, and increased mortality of insect larvae may explain lower total leaf damage observed previously in plots in this forest exposed to elevated CO2. By subtly altering aspects of leaf chemistry, the ever-increasing concentration of CO2 in the atmosphere will change the trophic dynamics in forest ecosystems.
Sprite Generation From Mpeg Video Using Motion Information

Sprite coding, accepted by the emerging MPEG-4 standard is a very efficient method for representing the background video object. Still this sprite generation is an open issue due to the foreground objects which obstructs the accuracy of camera motion estimation and blurs the generated sprite. In this paper we propose a method for constructing the background sprite with partial decoding of the MPEG stream. Initially the Independently Moving Objects (IMO) are segmented out from the background by clustering the pre-processed motion vectors of MPEG video. The camera motion parameters are obtained from the motion information corresponding to the background region which is used for frame alignment.
Schwann cells promote endothelial cell migration

Directed cell migration is a crucial orchestrated process in embryonic development, wound healing, and immune response. The underlying substrate can provide physical and/or chemical cues that promote directed cell migration. Here, using electrospinning we developed substrates of aligned poly(lactic-co-glycolic acid) nanofibres to study the influence of glial cells on endothelial cells (ECs) in a 3-dimensional (3D) co-culture model. ECs build blood vessels and regulate their plasticity in coordination with neurons. Likewise, neurons construct nerves and regulate their circuits in coordination with ECs. In our model, the neuro-vascular cross-talk was assessed using a direct co-culture model of human umbilical vein endothelial cells (HUVECs) and rat Schwann cells (rSCs). The effect of rSCs on ECs behavior was demonstrated by earlier and higher velocity values and genetic expression profiles different of those of HUVECs when seeded alone. We observed 2 different gene expression trends in the co-culture models: (i) a later gene expression of angiogenic factors, such as interleukin-8 (IL-8) and vascular endothelial growth factor (VEGF), and (ii) an higher gene expression of genes involved in actin filaments rearrangement, such as focal adhesion kinase (FAK), Mitogen-activated protein kinase-activated protein kinase 13 (MAPKAPK13), Vinculin (VCL), and Profilin (PROF). These results suggested that the higher ECs migration is mainly due to proteins involved in the actin filaments rearrangement and in the directed cell migration rather than the effect of angiogenic factors. This co-culture model provides an approach to enlighten the neurovascular interactions, with particular focus on endothelial cell migration.
To randomize or not to randomize: space optimal summaries for hyperlink analysis

Personalized PageRank expresses link-based page quality around user selected pages. The only previous personalized PageRank algorithm that can serve on-line queries for an unrestricted choice of pages on large graphs is our Monte Carlo algorithm [WAW 2004]. In this paper we achieve unrestricted personalization by combining rounding and randomized sketching techniques in the dynamic programming algorithm of Jeh and Widom [WWW 2003]. We evaluate the precision of approximation experimentally on large scale real-world data and find significant improvement over previous results. As a key theoretical contribution we show that our algorithms use an optimal amount of space by also improving earlier asymptotic worst-case lower bounds. Our lower bounds and algorithms apply to the SimRank as well; of independent interest is the reduction of the SimRank computation to personalized PageRank.
Microscopy of in situ DNA and RNA-containing structures

M.L. Segura-Valdez, R. Chávez-Rosales, L.T. Agredano-Moreno, E. Ubaldo, E.F. del Toro-Rangel, R. Lara-Martínez, C.E. Villegas-Mercado, G. Zavala, P.F. Islas-Morales and L.F. Jiménez-García 1 Cell Nanobiology Laboratory, Department of Cell Biology, Faculty of Sciences, National Autonomous University of Mexico (Universidad Nacional Autónoma de México-UNAM), Circuito Exterior, C.U. 04510 Coyoacán, México D.F. , Mexico 2 Institute of Biotechnology, National Autonomous University of Mexico (Universidad Nacional Autónoma de MéxicoUNAM), Cuernavaca, Morelos, Mexico
Design and simulation of three wavelength terahertz GaN quantum cascade laser

Quantum cascade laser (QCL) is a promising candidate for comparatively less developed terahertz spectral range. GaN based QCLs provide significant advantages over traditional GaAs based QCLs due to their higher LO phonon energy. Multiple wavelength hetero active region cavity offers various advantages like multiple emission wavelength for spectroscopy, nonlinear optical phenomena, and second harmonic generation. In this paper, we propose and design a multiple wavelength hetero cavity terahertz GaN based QCL emitting at 1.7 THz, 4.3 THz, and 7.2 THz. We present detail modeling of the system and final gain spectrum. We observe high gain (~ 250 cm-1) with multiple wavelength output emission. We also observe the sensitivity of the emission on temperature and find that the gain decreases sharply with increase in the temperature.