Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence for a C-terminal turn in PBAN. An NMR and distance geometry study.

The solution conformation of the pheromone biosynthesis activating neuropeptide (PBAN) of the moth Helicoverpa zea has been determined using homonuclear two-dimensional nuclear magnetic resonance techniques and distance geometry-restrained energy minimization. The insect peptide hormone showed a random distribution of conformers in aqueous solution, whereas in a less polar medium of trifluoroethanol and water, a reordering process was observed. In particular, the C-terminal region (Phe-Ser-Pro-Arg-Leu-NH2) adopts a type I' beta-turn conformation, residues 20-27 are in a helix conformation, and residues 1-19 exhibit a high degree of flexibility. Direct observation of the C-terminal beta-turn configuration of PBAN is consistent with a previous report that showed a rigid, cyclic analog of the C-terminal pentapeptide of PBAN retained pheromonotropic activity [Nachman, R.J., Kuniyoshi, H. , Roberts, V.A. , Holman, G.M. & Suzuki, A. (1993). Biochem. Biophys. Res. Commun. 661-666]. Furthermore, our results show no interaction between the C-terminal turn and the rest of the polypeptide chain, thus providing further evidence that the C-terminal turn is indeed the important conformation recognized by the PBAN receptor.
The phenotype of SDHB germline mutation carriers: a nationwide study.

OBJECTIVE Succinate dehydrogenase B subunit (SDHB) gene germline mutations predispose to pheochromocytomas, sympathetic paragangliomas, head and neck paragangliomas and non-paraganglionic tumors (e.g. renal cell carcinoma, gastrointestinal stromal tumor and pituitary neoplasia). The aim of this study was to determine phenotypical characteristics of a large Dutch cohort of SDHB germline mutation carriers and assess differences in clinical phenotypes related to specific SDHB mutations. DESIGN Retrospective descriptive study. METHODS Retrospective descriptive study in seven academic centers. RESULTS We included 194 SDHB mutation carriers consisting 65 (33.5%) index patients and 129 (66.5%) relatives. Mean age was 44.8 ± 16.0 years. Median duration of follow-up was 2.6 years (range: 0-36). Sixty persons (30.9%) carried the exon 3 deletion and 46 (23.7%) the c.423 + 1G > A mutation. Fifty-four mutation carriers (27.8%) had one or multiple head and neck paragangliomas, 4 (2.1%) had a pheochromocytoma and 26 (13.4%) had one or more sympathetic paragangliomas. Fifteen patients (7.7%) developed metastatic paraganglioma and 17 (8.8%) developed non-paraganglionic tumors. At study close, there were 111 (57.2%) unaffected mutation carriers. Statistical analyses showed no significant differences in the number and location of head and neck paragangliomas, sympathetic paragangliomas or pheochromocytomas, nor in the occurrence of metastatic disease or other tumors between carriers of the two founder SDHB mutations (exon 3 deletion vs c.423 + 1G > A). CONCLUSIONS In this nationwide study of disease-affected and unaffected SDHB mutation carriers, we observed a lower rate of metastatic disease and a relatively high number of head and neck paragangliomas compared with previously reported referral-based cohorts.
Text Detection using Object RecognitionTechniques

In this paper we propose an approach in text detection using object detection technique. Our approach is to deal with letters as objects. We use an object detection method, Retina Net deep leaning, to detect letters and recognize the text in natural scene images. The goal is to achieve high accuracy in text spotting, especially for curved text where the state-of-art methods fail. The Retina Net model architecture was used and modified in different ways to find the best performing model. Retina Net is implemented using Keras with Tensor flow backend. We prepare a model for training using the total-text dataset. The system manages to detect the letters as objects in the images. Then we perform letter candidate grouping to detect text based on distances between neighboring letters. The results exceeded our expectations. The training data was barely sufficient for some letters due to the differences in the frequency of their appearance in the dataset. Moreover, some specific letters, in specific orientations, were confusingly identified as others with a similar pattern. Nevertheless, we obtained a good performance on the test data for some classes, with a mAP of 40%. In order to further develop this method and to improve performance, more training data is needed, containing letters in different fonts. We also consider adding a dictionary to help correct or complete missing letters.
Associations between T1 white matter lesion volume and regional white matter microstructure in aging

White matter lesions, typically manifesting as regions of signal intensity abnormality (WMSA) on MRI, increase in frequency with age. However, the role of this damage in cognitive decline and disease is still not clear, as lesion volume has only loosely been associated with clinical status. Diffusion tensor imaging (DTI) has been used to examine the quantitative microstructural integrity of white matter, and has applications in the examination of subtle changes to tissue that appear visually normal on conventional imaging. The primary goal of this study was to determine whether major macrostructural white matter damage, (total WMSA volume), is associated with microstructural integrity of normal appearing white matter, and if these macrostructural changes fully account for microstructural changes. Imaging was performed in 126 nondemented individuals, ages 43–85 years, with no history of cerebrovascular disease. Controlling for age, greater WMSA volume was associated with decreased fractional anisotropy (FA) in widespread brain regions. Patterns were similar for FA and radial diffusivity but in contrast, WMSA was associated with axial diffusivity in fewer areas. Age was associated with FA in several regions, and many of these effects remained even when controlling for WMSA volume, suggesting the etiology of WMSAs does not fully account for all age‐associated white matter deterioration. These results provide evidence that WMSA volume is associated with the integrity of normal‐appearing white matter. In addition, our results suggest that overt lesions may not account for the association of increasing age with decreased white matter tissue integrity. Hum Brain Mapp 35:1085–1100, 2014. © 2013 Wiley Periodicals, Inc.
Exploring the Relationship between Skeletal Mass and Total Body Mass in Birds

Total body mass (TBM) is known to be related to a number of different osteological features in vertebrates, including limb element measurements and total skeletal mass. The relationship between skeletal mass and TBM in birds has been suggested as a way of estimating the latter in cases where only the skeleton is known (e.g., fossils). This relationship has thus also been applied to other extinct vertebrates, including the non-avian pterosaurs, while other studies have used additional skeletal correlates found in modern birds to estimate TBM. However, most previous studies have used TBM compiled from the literature rather than from direct measurements, producing values from population averages rather than from individuals. Here, we report a new dataset of 487 extant birds encompassing 79 species that have skeletal mass and TBM recorded at the time of collection or preparation. We combine both historical and new data for analyses with phylogenetic control and find a similar and well-correlated relationship between skeletal mass and TBM. Thus, we confirm that TBM and skeletal mass are accurate proxies for estimating one another. We also look at other factors that may have an effect on avian body mass, including sex, ontogenetic stage, and flight mode. While data are well-correlated in all cases, phylogeny is a major control on TBM in birds strongly suggesting that this relationship is not appropriate for estimating the total mass of taxa outside of crown birds, Neornithes (e.g., non-avian dinosaurs, pterosaurs). Data also reveal large variability in both bird skeletal and TBM within single species; caution should thus be applied when using published mass to test direct correlations with skeletal mass and bone lengths.
Religiosity and Spiritual Engagement in Two American Indian Populations.

Social scientific investigation into the religiospiritual characteristics of American Indians rarely includes analysis of quantitative data. After reviewing information from ethnographic and autobiographical sources, we present analyses of data from a large, population-based sample of two tribes (n = 3,084). We examine salience of belief in three traditions: aboriginal, Christian, and Native American Church. We then investigate patterns in sociodemographic subgroups, determining the significant correlates of salience with other variables controlled. Finally, we examine frequency with which respondents assign high salience to only one tradition (exclusivity) or multiple traditions (nonexclusivity), again investigating subgroup variations. This first detailed, statistical portrait of American Indian religious and spiritual lives links work on tribal ethnic identity to theoretical work on America's "religious marketplace. " Results may also inform social/behavioral interventions that incorporate religiospiritual elements.
Planar comb filters based on aberration-free elliptical grating facets

A new approach for eliminating aberration effects through introduction of elliptical grating facets in optical comb filters is presented. Simulation results show remarkable improvements of comb filter performance for aberration-free elliptical facets compared to traditional flat facet designs. The proposed theory was validated through design and fabrication of 100-GHz-period planar silica-on-silicon comb filters for use in multiwavelength optical sources. Multimode interference structures were used to achieve both flat-top and Gaussian spectral comb filter responses. All devices showed high extinction ratio, low nonuniformity in insertion loss, and high degree of passband shape control.
The primordial non-Gaussianity of local type (flocalNL) in the WMAP 5-year data: the length distribution of CMB skeleton

We present skeleton studies of non-Gaussianity in the cosmic microwave background temperature anisotropy observed in the 5-yr Wilkinson Microwave Anisotropy Probe (WMAP) data. The local skeleton is traced on the 2D sphere by cubic spline interpolation which leads to more accurate estimation of the intersection positions between the skeleton and the secondary pixels than conventional linear interpolation. We demonstrate that the skeleton-based estimator of non-Gaussianity of the local type (f^(local)_(NL)) – the departure of the length distribution from the corresponding Gaussian expectation – yields an unbiased and sufficiently converged likelihood function for f^(local)_(NL). We analyse the skeleton statistics in the WMAP 5-yr combined V- and W-band data outside the Galactic base-mask determined from the KQ75 sky coverage. The results are consistent with Gaussian simulations of the best-fitting cosmological model, but deviate from the previous results determined using the WMAP 1-yr data. We show that it is unlikely that the improved skeleton tracing method, the omission of Q-band data, the modification of the foreground-template fitting method or the absence of six extended regions in the new mask contribute to such a deviation. However, the application of the Kp0 base-mask in data processing does improve the consistency with the WMAP1 results. The f^(local)_(NL)-likelihood functions of the data are estimated at nine different smoothing levels. It is unexpected that the best-fitting values show positive correlation with the smoothing scales. Further investigation argues against a point source or goodness-of-fit explanation but finds that about 30 per cent of either Gaussian or f_(NL) samples having better goodness-of-fit than the WMAP 5-yr data show a similar correlation. We present the estimate f^(local)_(NL)= 47.3 ± 34.9 (1σ error) determined from the first four smoothing angles and f^(local)_(NL)= 76.8 ± 43.1 for the combination of all nine. The former result may be overestimated at the 0. 21σ level because of point sources.
100 Gbit/s authenticated encryption based on quantum key distribution

We propose a block-cipher-based hardware architecture for authenticated encryption (AE) applications supporting the Ethernet standard IEEE 802.3ba. Our main design goal was to achieve high throughput on FPGA platforms. Compared to previous works aiming at data rates beyond 100 Gbit/s, our design makes use of an alternative block cipher and an alternative mode of operation, namely Serpent and the offset codebook mode of operation, respectively. Using four cipher cores for the encryption part of the AE architecture, we achieve a throughput of 133 Gbit/s on an Altera Stratix IV FPGA. The design requires 30 kALMs and runs at a maximum clock frequency of 260 MHz. This represents, to the best of our knowledge, the fastest full implementation of an AE scheme on FPGAs to date.
Using the concept of ideal cardiovascular health to measure population health: a review

Purpose of review This article describes the recent literature from January 2014 to March 2015 examining the cardiovascular health of populations using the concept of ideal cardiovascular health with a particular focus on cardiovascular health in different countries and the association with subclinical markers of cardiovascular disease (CVD). Recent findings The relatively new concept of ideal cardiovascular health, based on the presence of seven healthy behaviours and factors including nonsmoking, active physical activity, healthy diet, low body mass index, low blood pressure, glucose, and cholesterol, can be used to assess a population's health status and develop an understanding of how cardiovascular health is associated with biological disease processes and clinical outcomes such as CVD incidence and mortality. Recent studies have adapted the American Heart Association definition of ideal cardiovascular health to fit the available data in different countries and have shown that the prevalence of ideal cardiovascular health is low in populations worldwide, including North America, Europe, Asia, and the Middle East. Recent studies have also uncovered strong associations between ideal cardiovascular health metrics and subclinical markers for CVD such as coronary artery calcification, carotid intima-media thickness, and pulse wave velocity. Summary A number of studies have demonstrated the low prevalence of ideal cardiovascular health in several countries and a strong relationship with subclinical CVD and biomarkers. The association with subclinical markers for CVD provides some evidence of the intermediary biological pathways through which ideal cardiovascular health results in a lower incidence of CVD and highlights the importance of improving cardiovascular health metrics in the general population.
Promoting survival, migration, and integration of transplanted Schwann cells by over‐expressing polysialic acid

The poor survival and migration of transplanted Schwann cells (SCs) are major drawbacks for their clinical application in cell therapy for neurotrauma. To overcome such drawbacks we genetically modified SCs to over‐express polysialic acid (PSA) by lentiviral delivery of polysialyltransferase (PST) to study whether over‐expression of PSA could enhance their survival, migration, and integration when transplanted into the spinal cord. It was found that more PSA‐expressing SCs (PST/SCs) survived than GFP‐expressing SCs (GFP/SCs) after transplantation, although cell loss was still quite significant. PSA expression did not enhance the motility of transplanted SCs in uninjured spinal cord. However, in a spinal cord crush injury model PST/SCs transplanted caudal to the lesion showed that increased number of PST/SCs migrated to the injury site compared with that of GFP/SCs. Induced expression of PSA in spinal cord can further facilitate the infiltration of PST/SCs into the lesion site. PST/SCs were also shown to intermingle well with host spinal cells while GFP/SCs formed boundaries with host tissue. This was confirmed by an in vitro confrontation assay showing that more PST/SCs crossed over to astrocyte territory than GFP/SCs. Furthermore, PST/SCs induced much less expression of glial fibrillary acidic protein and chondroitin sulfate proteoglycan in the surrounding tissues than GFP/SCs, indicating that expression of PSA on SCs do not cause significant stress response of astrocytes. These results demonstrate that expression of PSA on SCs significantly changes their biological properties and makes them more feasible for neural repair after neurotrauma. © 2010 Wiley‐Liss, Inc.
The PiggyBac transposon enhances the frequency of CHO stable cell line generation and yields recombinant lines with superior productivity and stability

Generating stable, high‐producing mammalian cell lines is a major bottleneck in the manufacture of recombinant therapeutic proteins. Conventional gene transfer methods for cell line generation rely on random plasmid integration, resulting in unpredictable and highly variable levels of transgene expression. As a consequence, a large number of stably transfected cells must be analyzed to recover a few high‐producing clones. Here we present an alternative gene transfer method for cell line generation based on transgene integration mediated by the piggyBac (PB) transposon. Recombinant Chinese hamster ovary (CHO) cell lines expressing a tumor necrosis factor receptor:Fc fusion protein were generated either by PB transposition or by conventional transfection. Polyclonal populations and isolated clonal cell lines were characterized for the level and stability of transgene expression for up to 3 months in serum‐free suspension culture. Pools of transposed cells produced up to fourfold more recombinant protein than did the pools generated by standard transfection. For clonal cell lines, the frequency of high‐producers was greater following transposition as compared to standard transfection, and these clones had a higher volumetric productivity and a greater number of integrated transgenes than did those generated by standard transfection. In general, the volumetric productivity of the cell pools and individual cell lines generated by transposition was stable for up to 3 months in the absence of selection. Our results indicate that the PB transposon supports the generation of cell lines with high and stable transgene expression at an elevated frequency relative to conventional transfection. Thus, PB‐mediated gene delivery is expected to reduce the extent of recombinant cell line screening. Biotechnol. Bioeng. 2011;108:2141–2150. © 2011 Wiley Periodicals, Inc.
The dimensionality of DSM-IV alcohol use disorders among adolescent and adult drinkers and symptom patterns by age, gender, and race/ethnicity.

BACKGROUND There is limited information on the validity of Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV) alcohol use disorders (AUD) symptom criteria among adolescents in the general population. The purpose of this study is to assess the DSM-IV AUD symptom criteria as reported by adolescent and adult drinkers in a single representative sample of the U.S. population aged 12 years and older. This design avoids potential confounding due to differences in survey methodology when comparing adolescents and adults from different surveys. METHODS A total of 133,231 current drinkers (had at least 1 drink in the past year) aged 12 years and older were drawn from respondents to the 2002 to 2005 National Surveys on Drug Use and Health. DSM-IV AUD criteria were assessed by questions related to specific symptoms occurring during the past 12 months. Factor analytic and item response theory models were applied to the 11 AUD symptom criteria to assess the probabilities of symptom item endorsements across different values of the underlying trait. RESULTS A 1-factor model provided an adequate and parsimonious interpretation for the 11 AUD criteria for the total sample and for each of the gender-age groups. The MIMIC model exhibited significant indication for item bias among some criteria by gender, age, and race/ethnicity. Symptom criteria for "tolerance,""time spent," and "hazardous use" had lower item thresholds (i.e., lower severity) and low item discrimination, and they were well separated from the other symptoms, especially in the 2 younger age groups (12 to 17 and 18 to 25). "Larger amounts,""cut down,""withdrawal," and "legal problems" had higher item thresholds but generally lower item discrimination, and they tend to exhibit greater dispersion at higher AUD severity, particularly in the youngest age group (12 to 17). CONCLUSIONS Findings from the present study do not provide support for the 2 separate DSM-IV diagnoses of alcohol abuse and dependence among either adolescents or adults. Variations in criteria severity for both abuse and dependence offer support for a dimensional approach to diagnosis which should be considered in the ongoing development of DSM-V.
Characterization of hydrophobic interaction and antioxidant properties of the phenothiazine nucleus in mitochondrial and model membranes

Abstract The antioxidant properties of the phenothiazine nucleus (PHT) associated with mitochondrial membranes and liposomes were investigated. PHT exhibited hydrophobic interaction with lipid bilayers, as shown by the quenching of excited states of 1-palmitoyl-2[10-pyran-1-yl)]-decanoyl-sn-glycero-3-phophocholine (PPDPC) incorporated in phosphatidylcholine/phosphatidylethanolamine/cardiolipin liposomes, observed even in high ionic strength; and by the spectral changes of PHT following the addition of mitochondrial membranes. Inserted into bilayers, 5 μM PHT was able to protect lipids and cytochrome c against pro-oxidant agents and exhibited spectral changes suggestive of oxidative modifications promoted by the trapping of the reactive species. In this regard, PHT exhibited the ability to scavenge DPPH (2,2-diphenyl-1-picryl-hydrazyl-hydrate) free radical. PHT was also able to protect rat liver mitochondria against peroxide- and iron-induced oxidative damage and consequent swelling. At the concentration range in which the antioxidant properties were observed, PHT did not cause alterations in the membrane structure and function. This study contributes to the comprehension of the correlation structure and function of phenothiazines and antioxidant properties.
Antigen-Specific Primary Activation of CD8+ T Cells Within the Liver1

It is generally accepted that naive T cells recirculate via the blood and lymph, but do not enter nonlymphoid tissues without prior activation and differentiation. In this study, we demonstrate that the liver is an exception to this rule. Naive Des-TCR transgenic CD8+ T cells specific for H-2Kb were selectively retained in the liver within a few minutes of adoptive transfer into transgenic Met-Kb mice expressing H-2Kb in the liver. Activated CD8+ cells were found in the liver, but not the blood, as soon as 2 h after transfer and underwent cell division and started to recirculate within 24 h of transfer. In contrast, CD8+ cells activated in the lymph nodes remained sequestered at that site for 2 days before entering the blood. Our results therefore suggest that, in addition to its previously described role as a non Ag-specific activated T cell graveyard, the liver is involved in Ag-specific activation of naive recirculating CD8+ T cells. This particular property of the liver, combined with the previously demonstrated ability of hepatocytes to induce tolerance by means of premature CD8+ T cell death, may be a major mechanism contributing to the acceptance of liver allografts and the chronicity of viral hepatitis.