Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites.

O-GalNAc-glycosylation is one of the main types of glycosylation in mammalian cells. No consensus recognition sequence for the O-glycosyltransferases is known, making prediction methods necessary to bridge the gap between the large number of known protein sequences and the small number of proteins experimentally investigated with regard to glycosylation status. From O-GLYCBASE a total of 86 mammalian proteins experimentally investigated for in vivo O-GalNAc sites were extracted. Mammalian protein homolog comparisons showed that a glycosylated serine or threonine is less likely to be precisely conserved than a nonglycosylated one. The Protein Data Bank was analyzed for structural information, and 12 glycosylated structures were obtained. All positive sites were found in coil or turn regions. A method for predicting the location for mucin-type glycosylation sites was trained using a neural network approach. The best overall network used as input amino acid composition, averaged surface accessibility predictions together with substitution matrix profile encoding of the sequence. To improve prediction on isolated (single) sites, networks were trained on isolated sites only. The final method combines predictions from the best overall network and the best isolated site network; this prediction method correctly predicted 76% of the glycosylated residues and 93% of the nonglycosylated residues. NetOGlyc 3.1 can predict sites for completely new proteins without losing its performance. The fact that the sites could be predicted from averaged properties together with the fact that glycosylation sites are not precisely conserved indicates that mucin-type glycosylation in most cases is a bulk property and not a very site-specific one. NetOGlyc 3.1 is made available at www.cbs. dtu.dk/services/netoglyc.
Development of a new real-time polymerase chain reaction assay to detect Duck adenovirus A DNA and application to samples from Swiss poultry flocks

Between 2008 and 2012, commercial Swiss layer and layer breeder flocks experiencing problems in laying performance were sampled and tested for infection with Duck adenovirus A (DAdV-A; previously known as Egg drop syndrome 1976 virus). Organ samples from birds sent for necropsy as well as blood samples from living animals originating from the same flocks were analyzed. To detect virus-specific DNA, a newly developed quantitative real-time polymerase chain reaction method was applied, and the presence of antibodies against DAdV-A was tested using a commercially available enzyme-linked immunosorbent assay. In 5 out of 7 investigated flocks, viral DNA was detected in tissues. In addition, antibodies against DAdV-A were detected in all of the flocks.
The Extracellular Domain of Herpes Simplex Virus gE Is Indispensable for Efficient Cell-to-Cell Spread: Evidence for gE/gI Receptors

ABSTRACT Herpes simplex virus (HSV) spreads rapidly and efficiently within epithelial and neuronal tissues. The HSV glycoprotein heterodimer gE/gI plays a critical role in promoting cell-to-cell spread but does not obviously function during entry of extracellular virus into cells. Thus, gE/gI is an important molecular handle on the poorly understood process of cell-to-cell spread. There was previous evidence that the large extracellular (ET) domains of gE/gI might be important in cell-to-cell spread. First, gE/gI extensively accumulates at cell junctions, consistent with being tethered there. Second, expression of gE/gI in trans interfered with HSV spread between epithelial cells. To directly test whether the gE ET domain was necessary for gE/gI to promote virus spread, a panel of gE mutants with small insertions in the ET domain was constructed. Cell-to-cell spread was reduced when insertions were made within either of two regions, residues 256 to 291 or 348 to 380. There was a strong correlation between loss of cell-to-cell spread function and binding of immunoglobulin. gE ET domain mutants 277, 291, and 348 bound gI, produced mature forms of gE that reached the cell surface, and were incorporated into virions yet produced plaques similar to gE null mutants. Moreover, all three mutants were highly restricted in spread within the corneal epithelium, in the case of mutant 277 to only 4 to 6% of the number of cells compared with wild-type HSV. Therefore, the ET domain of gE is indispensable for efficient cell-to-cell spread. These observations are consistent with our working hypothesis that gE/gI can bind extracellular ligands, so-called gE/gI receptors that are concentrated at epithelial cell junctions. This fits with similarities in structure and function of gE/gI and gD, which is a receptor binding protein.
Beta2‐adrenergic receptor allele frequencies in the Quechua, a high altitude native population

The beta2‐adrenergic receptor is involved in the control of numerous physiological processes and, as the primary catecholamine receptor in the lungs, is of particular importance in the regulation of pulmonary function. There are several polymorphic loci in the beta2‐adrenergic receptor gene that have alleles that alter receptor function, including two (A/G46, G/C79) that increase agonist sensitivity. As such a phenotype may increase vaso and bronchial dilation, thereby facilitating air and blood flow through the lungs, we hypothesized that selection may have favoured these alleles in high altitude populations as part of an adaptive strategy to deal with the hypoxic conditions characteristic of such environments. We tested this hypothesis by determining the allele frequencies for these two polymorphisms, as well one additional missense mutation (C/T491) and two silent mutations (G/A252 and C/A523) in 63 Quechua speaking natives from communities located between 3200 and 4200 m on the Peruvian altiplano. These frequencies were compared with those of two lowland populations, one native American (Na‐Dene from the west coast of Canada) and one Caucasian of Western European descent. The Quechua manifest many of the pulmonary characteristics of high altitude populations and differences in allele frequencies between the Quechua and lowlanders could be indicative of a selective advantage conferred by certain genotypes in high altitude environments. Allele frequencies varied between populations at some loci and patterns of linkage disequilibrium differed between the old‐world and new‐world samples; however, as these populations are not closely related, significant variation would be expected due to stochastic effects alone. Neither of the alleles associated with increased receptor sensitivity (A46, G79) was significantly over‐represented in the Quechua compared with either lowland group. The Quechua were monomorphic for the C allele at base 79. This variant has been associated with body mass index; however no clearly defined metabolic phenotype has been established. In addition, we sequenced the coding region of the gene in three unrelated Quechua to determine if there were any other polymorphisms common in this population. None were detected.
Impact of the Oregon Health Plan on Children With Special Health Care Needs

Objective. Although an increasing number of Medicaid children are enrolled in Medicaid managed care plans, little is known about how children with special health care needs fare under such programs. Of particular concern is the ability of such children to navigate a managed care system and gain access to specialty and other services. This study compares the managed care experiences of children with and without special care needs in the Oregon Health Plan. Methodology. Telephone surveys were conducted with a sample of parents of children enrolled in the Oregon Health Plan. Three groups of children were sampled: Supplemental Security Income (SSI) children with disabilities, children with asthma, and children without special health care needs. Descriptive and multivariate analyses were conducted to determine the impact of Medicaid managed care on access and satisfaction. Results. Children with disabilities in managed care plans did not experience any more difficulty accessing needed specialty care than did those without special health care needs. Children with asthma, however, reported higher levels of unmet need. There were no differences in access between children with disabilities enrolled in managed care and those children with disabilities remaining in fee-for-service. Conclusions. Unlike SSI children with disabilities, children who were not SSI-eligible but had asthma seemed to have difficulty obtaining some services. These children were not eligible for the same consumer protections afforded SSI children by Oregon. If states want to enroll all children with special health care needs into managed care programs, they must develop mechanisms for identifying such children and ensuring that they receive medically necessary services.
Wideband antenna for mobile terminals using a coupled feeding structure

A wideband antenna which consists of a planar inverted F-antenna (PIFA) with a coupled feeding structure for wireless terminals is presented. The operating bandwidth of the proposed antenna is from 820 MHz to 3 GHz, as far as we know, this is the first antenna which covers entire bands of wireless communication applications (GSM850 / GSM900 / GPS / DCS1800 / PCS1900 / WCDMA1700 / WCDMA2100 / WiBro2350 / Bluetooth (BT) / Wi-Fi / WiMAX2500 and Long Term Evolution (LTE) 2600). Therefore, it can be used as current 2G/3G/4G services as well as GPS. In addition, the antenna has small size, 20 × 40 mm2, and can be directly printed on no-ground region of system circuit board. The overall area of Printed Circuit Board (PCB) including antenna area is 40 × 100 × 0.8 mm3. As a result, the proposed antenna is suitable for compact mobile applications and small wireless devices.
A NEW MEASURE TO QUANTIFY HYSTERESIS LOSSES: THE CASE OF ITALIAN WINE EXPORTS TO THE UNITED STATES

This paper introduces a new measure to capture dynamic losses for exporting firms on markets that exhibit hysteresis on the supply side. Our indicator aims to quantify dynamic losses caused by sunk adjustment costs in case of exchange rate fluctuations. While the standard procedure in welfare analysis is to compare two equilibria, we focus on welfare effects that take place during dynamics. We analyze negative dynamic effects on producers' income that are generated due to writing off sunk adjustment costs. As an example, we investigate Italian wine exports to the United States over the period 1995–2013. After testing for hysteresis on the market, we present the indicator of hysteresis losses. It captures a continuous increase of dynamic losses during the period 2003–2008. Moreover, over-proportionately large hysteresis losses are generated in comparison to the exchange rate changes if the pain threshold of the exchange rate (ca. 1.25$/€) is passed.
Findings of multidimensional instruments for determining psychopathology in diabetic and non-diabetic hemodialysis patients.

OBJECTIVE The aim of this study was to expand the research on psychiatric complications of end-stage renal disease (ESRD), as well as to examine the prevalence of a broad range of psychopathology in diabetic and non-diabetic hemodialysis (HD) patients. METHODS One hundred nineteen HD patients were invited to enter the cross-sectional study. To assess quality of life, quality of sleep, mental status and depression and anxiety symptoms, the 36-item Short Form, Pittsburgh Sleep Quality Index (PSQI), Mini-Mental State Examination and Hospital Anxiety and Depression Scale, respectively, were used. RESULTS The mean age of all patients was 56.9±16.1 years; 54 (45.4%) were female. In the diabetic patients group, 84.8% of the patients had low MCS scores, and 89.2% patients had low PCS scores; 73.9% were poor sleepers; 63.0% had cognitive decline; 62.0% patients were depressive symptoms; and 28.3%had symptoms of anxiety. When comparing the diabetic and non-diabetic patients, the diabetic patients had lower role-emotional, sleep duration, and sleep efficiency scores. CONCLUSIONS Incorporating a standard assessment and, eventually, treatment of psychopathologic symptoms into the care provided to diabetic and hemodialysis patients might improve quality of life and sleep, depressive symptoms and, reduce mortality risk.
TRIO a Technique for Reconstruction Using Intensity Order: Application to Undersampled MRI

Long acquisition times are still a limitation for many applications of magnetic resonance imaging (MRI), specially in 3-D and dynamic imaging. Several undersampling reconstruction techniques have been proposed to overcome this problem. These techniques are based on acquiring less samples than specified by the Nyquist criterion and estimating the nonacquired data by using some sort of prior information. Most of these reconstruction methods use prior information based on estimations of the pixel intensities of the images and therefore they are prone to introduce spatial or temporal blurring. Instead of using the pixel intensities, we propose to use information that allows us to sort the pixels of an image from darkest to brightest. The set of order relations which sort the pixels of an image has been called intensity order. The intensity order of an image can be estimated from low-resolution images, adjacent slices in volumetric acquisitions, temporal correlation in dynamic sequences or from prior reconstructions. Our technique for reconstruction using intensity order (TRIO) consists of looking for an image that satisfies the intensity order and minimizes the discrepancy between the acquired and reconstructed data. Results show that TRIO can effectively reconstruct 2-D-cine cardiac MR images (under-sampling factor of 4), estimating correctly the temporal evolution of the objects. Furthermore, TRIO is used as a second stage reconstruction after reconstructing with other techniques, keyhole, sliding window and k-t BLAST, to estimate the order information. In all cases the images are improved by TRIO.
Induction of callose in roots of Norway spruce seedlings after short-term exposure to aluminum.

Callose (1,3-beta-glucan) is a suggested physiological indicator of aluminum (Al) toxicity in crop plants. It is not known if callose serves a similar function in forest trees, because quantitative data on callose formation in tree roots are limited, particularly under controlled conditions. To evaluate callose as a physiological indicator of Al toxicity in tree roots, we quantified callose formation in roots of Norway spruce (Picea abies (L.) Karst. ) seedlings. Seedlings were grown in simulated soil solutions in the presence or absence (control) of Al under controlled conditions. In seedlings grown in solutions containing 280 microM Al, callose concentrations in roots were twice as high as control values after 6 h of Al treatment and 5 times higher than control values after 1 day. Thereafter, root callose concentrations gradually decreased and were only twice as high as control values after 7 days. The presence of various Al concentrations in the simulated soil solutions indicated that callose was induced by a relatively low Al concentration (84 microM). We conclude that callose in tree roots is an indicator of Al toxicity.
Using c‐Fos/c‐Jun as hetero‐dimer interaction model to optimize donor to acceptor concentration ratio range for three‐filter fluorescence resonance energy transfer (FRET) measurement

Sensitized emission FRET detection method based on three‐filter fluorescence microscopy is widely used and more suitable for live cell FRET imaging and dynamic protein–protein interaction analysis. But when it is applied to detect two proteins interaction in living cells, this intensity‐based detection method is complicated by many experimental factors such as spectral crosstalk and spectral bleed‐through and variable donor to acceptor concentration ratio. There are several FRET algorithms developed recently to correct those factors in order to quantitatively gauge and compare FRET signals between different experimental groups. But the algorithms are often difficult to choose when they are applied to certain experiments. In this research, we use c‐Fos/c‐Jun as a simple hetero‐dimer interaction model to quantitatively detect and compare the FRET signals based on the following widely used sensitized emission FRET algorithms: NFRET, FRETN, FR, FRETR, Eapp and EEFF. We optimized the donor to acceptor concentration ratio range for the above FRET algorithms and facilitate their use in accurate FRET signal determination based on the three‐filter FRET microscopy.
Axonal atrophy in aging is associated with a decline in neurofilament gene expression

Neurofilaments (Nfs) are major determinants of axonal caliber. Nf transcript levels increase during development and maturation, and are associated with an increase in Nf protein, Nf numbers, and caliber of axons. With aging there is axonal atrophy. In this study we asked whether the axonal atrophy of aging was associated with a decline in Nf transcript expression, Nf protein levels, and Nf numbers. Expression of transcripts for the three Nf subunits was evaluated in dorsal root ganglia (DRG) of Fischer‐344 rats aged 3–32 months by Northern and in situ hybridization. There was an approximately 50% decrease in Nf subunit mRNA levels in DRG of aged (>23 months) as compared to young and mature (3 and 12 months) rats, whereas expression of another neuronal mRNA, GAP‐43, showed no decline. Western analysis showed a corresponding decrease in Nf subunit proteins and no decline in GAP‐43. Morphometric analysis showed a 50% decrease in Nf numbers within axons. The decrease in Nf gene expression and Nf numbers was accompanied by a decrease in cross‐sectional area and circularity of all myelinated fibers, with the largest fibers showing the most marked changes, and a shrinkage in the perikaryal area of large neurons. Furthermore, we found a concomitant decrease in the expression of transcripts for the nerve growth factor receptors trkA and p75 with aging. Although the mechanisms leading to the decrease in Nf gene expression with aging are not known, a decrease in the availability of growth factors, or the neuron's ability to respond to them, may play a role in this process. © 1995 Wiley‐Liss, Inc.
Engineering tendon and ligament tissues: present developments towards successful clinical products

Musculoskeletal diseases are one of the leading causes of disability worldwide. Among them, tendon and ligament injuries represent an important aspect to consider in both athletes and active working people. Tendon and ligament damage is an important cause of joint instability, and progresses into early onset of osteoarthritis, pain, disability and eventually the need for joint replacement surgery. The social and economical burden associated with these medical conditions presents a compelling argument for greater understanding and expanding research on this issue. The particular physiology of tendons and ligaments (avascular, hypocellular and overall structural mechanical features) makes it difficult for currently available treatments to reach a complete and long‐term functional repair of the damaged tissue, especially when complete tear occurs. Despite the effort, the treatment modalities for tendon and ligament are suboptimal, which have led to the development of alternative therapies, such as the delivery of growth factors, development of engineered scaffolds or the application of stem cells, which have been approached in this review. Copyright © 2012 John Wiley & Sons, Ltd.
Trip Outfits Advisor: Location-Oriented Clothing Recommendation

When packing for a journey, have you ever asked “what clothes should I take with me? ” Wearing appropriate and aesthetically pleasing clothing when traveling is a concern for many of us. Our data observation of photos from several popular travel websites reveals that people's choice of clothing items and their color combinations have strong correlations with the weather, the season, and the main type of attraction at the destination. This leads to an interesting and novel problem: can the correlation between clothing and locations be automatically learned from social photos and leveraged for location-oriented clothing recommendations? In this paper, we systematically study this problem and propose a hybrid multilabel convolutional neural network combined with the support vector machine (mCNN-SVM) approach to capture the intrinsic and complex correlations between clothing attributes and location attributes. Specifically, we adapt the CNN architecture to multilabel learning and fine-tune it using each fine-grained clothing item. Then, the recognized items are fed to the SVM to learn the correlations. Experiments on three fashion datasets and a benchmark journey outfit dataset show that our proposed approach outperforms several baselines by over 10.52–16.38% in terms of the mAP for clothing item recognition and outperforms several alternative methods by over 9.59–29.41% in terms of the mAP when ranking clothing by appropriateness for travel destinations. Finally, an interesting case study demonstrates the effectiveness of our method by answering what items to wear, how to match them, and how to dress in an aesthetically pleasing manner for a journey.
Influence of Matching for Exposure Time on Estimates of Attributable Mortality Caused by Nosocomial Bacteremia in Critically Ill Patients

Abstract Objective: To evaluate the influence of matching on exposure time on estimates of attributable mortality of nosocomial bacteremia as assessed by matched cohort studies. Design: Two retrospective, pairwise-matched (1:2) cohort studies. Setting: A 54-bed intensive care unit (ICU) in a university hospital. Patients: Patients with nosocomial Escherichia coli bacteremia (n = 68) and control-patients without nosocomial bacteremia (n = 136 for each matched cohort study). Intervention: In both matched cohort studies, the same set of bacteremic patients was matched with control-patients using the APACHE II system. In the first study, control-patients were required to have an ICU stay at least as long as the respective bacteremic patient prior to onset of bacteremia (matching on exposure time). In the second study, control-patients were required to have an ICU stay shorter than the stay prior to the development of bacteremia in the respective bacteremic patient (no matching on exposure time). Results: For bacteremic patients, the mean ICU stay before onset of the bacteremia was 9 days (median, 6 days). In the first matched cohort study, hospital mortality was not different between bacteremic patients and control-patients (44.1% vs 43.4%; P = .999). In the second study, mortality of bacteremic patients and control-patients was also not different (44.1% vs 47.8%; P = .657). Mortality rates between control groups were not different (43.4% vs 47.8%; P = .543). Conclusion: Matching or not matching on exposure time did not alter the estimate of attributable mortality for ICU patients with E. coli bacteremia.
Small worlds in the tree topologies of wireless sensor networks

In this study, the characteristics of small worlds are investigated in the context of the tree topologies of wireless sensor networks. Tree topologies, which construct spatial graphs with larger characteristic path lengths than random graphs and small clustering coefficients, are ubiquitous in wireless sensor networks. Suffering from the link rewiring or the link addition, the characteristic path length of the tree topology reduces rapidly and the clustering coefficient increases greatly. The variety of characteristic path length influences the time synchronization characteristics of wireless sensor networks greatly. With the increase of the link rewiring or the link addition probability, the time synchronization error decreases drastically. Two novel protocols named LEACH-SW and TREEPSI-SW are proposed to improve the performances of the sensor networks, in which the small world characteristics are taken into use to reduce the time synchronization errors.