julilili42/papers huggingface dataset:
MR‐based field‐of‐view extension in MR/PET: B0 homogenization using gradient enhancement (HUGE)
2012-11-30

In whole‐body MR/PET, the human attenuation correction can be based on the MR data. However, an MR‐based field‐of‐view (FoV) is limited due to physical restrictions such as B 0 inhomogeneities and gradient nonlinearities. Therefore, for large patients, the MR image and the attenuation map might be truncated and the attenuation correction might be biased. The aim of this work is to explore extending the MR FoV through B 0 homogenization using gradient enhancement in which an optimal readout gradient field is determined to locally compensate B 0 inhomogeneities and gradient nonlinearities. A spin‐echo‐based sequence was developed that computes an optimal gradient for certain regions of interest, for example, the patient's arms. A significant distortion reduction was achieved outside the normal MR‐based FoV. This FoV extension was achieved without any hardware modifications. In‐plane distortions in a transaxially extended FoV of up to 600 mm were analyzed in phantom studies. In vivo measurements of the patient's arms lying outside the normal specified FoV were compared with and without the use of B 0 homogenization using gradient enhancement. In summary, we designed a sequence that provides data for reducing the image distortions due to B 0 inhomogeneities and gradient nonlinearities and used the data to extend the MR FoV. Magn Reson Med, 70:1047–1057, 2013. © 2012 Wiley Periodicals, Inc.
Visual Analysis of Cardiac 4D MRI Blood Flow Using Line Predicates
2012-11-30

Four-dimensional MRI is an in vivo flow imaging modality that is expected to significantly enhance the understanding of cardiovascular diseases. Among other fields, 4D MRI provides valuable data for the research of cardiac blood flow and with that the development, diagnosis, and treatment of various cardiac pathologies. However, to gain insights from larger research studies or to apply 4D MRI in the clinical routine later on, analysis techniques become necessary that allow to robustly identify important flow characteristics without demanding too much time and expert knowledge. Heart muscle contractions and the particular complexity of the flow in the heart imply further challenges when analyzing cardiac blood flow. Working toward the goal of simplifying the analysis of 4D MRI heart data, we present a visual analysis method using line predicates. With line predicates precalculated integral lines are sorted into bundles with similar flow properties, such as velocity, vorticity, or flow paths. The user can combine the line predicates flexibly and by that carve out interesting flow features helping to gain overview. We applied our analysis technique to 4D MRI data of healthy and pathological hearts and present several flow aspects that could not be shown with current methods. Three 4D MRI experts gave feedback and confirmed the additional benefit of our method for their understanding of cardiac blood flow.
Glycosylation of Candida albicans Cell Wall Proteins Is Critical for Induction of Innate Immune Responses and Apoptosis of Epithelial Cells
2012-11-30

C. albicans is one of the most common fungal pathogen of humans, causing local and superficial mucosal infections in immunocompromised individuals. Given that the key structure mediating host-C. albicans interactions is the fungal cell wall, we aimed to identify features of the cell wall inducing epithelial responses and be associated with fungal pathogenesis. We demonstrate here the importance of cell wall protein glycosylation in epithelial immune activation with a predominant role for the highly branched N-glycosylation residues. Moreover, these glycan moieties induce growth arrest and apoptosis of epithelial cells. Using an in vitro model of oral candidosis we demonstrate, that apoptosis induction by C. albicans wild-type occurs in early stage of infection and strongly depends on intact cell wall protein glycosylation. These novel findings demonstrate that glycosylation of the C. albicans cell wall proteins appears essential for modulation of epithelial immunity and apoptosis induction, both of which may promote fungal pathogenesis in vivo.
Unionidae (Bivalvia; Palaeoheterodonta) from the Palaeogene of northern Vietnam: exploring the origins of the modern East Asian freshwater bivalve fauna
2012-11-30

Eocene/Oligocene sediments deposited in two Cenozoic pull-apart basins in northern Vietnam, i.e. the Na Duong and Cao Bang basins, yield several rich and well-preserved assemblages of unionid bivalves. This study outlines the taxonomy of the Unionidae from these communities, and all taxa are described and illustrated in detail. As far as we are aware, this is the first comprehensive treatment of Cenozoic Unionidae from South-East Asia. Eight of the nine taxa are described as new to science. Four species – Cuneopsis quangi sp. nov., Cristaria mothanica sp. nov., Cristaria falcatocostata sp. nov. and Lamprotula hungi sp. nov. – can be confidently assigned to modern genera. The generic position of the remaining species is equivocal (?Nodularia cunhatia sp. nov., ?Cuneopsis sp., ?Lanceolaria sp., ?Lamprotula sp.) or remains tentative (Anodontini sp.). The phyletic relationships of the fossil taxa to modern species are discussed and interpreted in light of the Cenozoic tectonic history of South-East Asia and the intimately associated evolution of drainage systems. The results confirm a close relationship of the fossil unionids to the modern mussel fauna of the Yangtze, Pearl and Red River catchment areas. Moreover, the fossils from Cao Bang and Na Duong are among the earliest confirmed records of all genera identified, and thus document an important, early stage in the development of the modern East and South-East Asian bivalve faunas. http://zoobank.org/urn:lsid:zoobank.org:pub:D52F10F0-1AFF-4EFD-B724-692E982143E4
Recognition Memory for High and Low Associative Stimuli in Autistic Individuals with Outstanding Memory Skill
2012-11-30

Abstract Background: Individuals with autism exhibit typical recognition memory performance, but they show a reduced use of context and relational processing in more complex memory tasks. It is unclear whether the same is true for autistic individuals with exceptional memory skill for whom superior rote memory skill has been assumed. Objective: In this study, we investigated recognition memory for high and low associative stimuli in autistic memory experts. In accord with the rote memory notion, we expected an equal recognition performance for high and low associative stimuli and superior memorizing of nonsense material compared to control participants. Method: Seven autistic memory experts and seven typically developed control subjects, matched according to age, sex, handedness, and full-scale intelligence quotient (IQ), were examined on a continuous old-new recognition paradigm, including high or low associative pseudowords and shapes. Memory expertise was characterized as a currently present outstanding memory skill above the subject’s general level of ability and above the general population and was validated through direct clinical observation or some form of credible evidence. Results: Our hypotheses were partially corroborated with autistic memory experts recognizing high and low associative shapes equally well in contrast to control participants who showed superior recognition of high associative shapes. However, memory experts did not outperform control participants in the recognition of low associative shapes. There were no differences for the recognition of pseudowords. Conclusions: Findings do not indicate enhanced memory for nonsense material, but a failure to make use of semantic features of abstract stimuli as assumed for autism as a whole.
In tight junctions, claudins regulate the interactions between occludin, tricellulin and marvelD3, which, inversely, modulate claudin oligomerization
2012-12-01

Summary Tight junctions seal the paracellular cleft of epithelia and endothelia, form vital barriers between tissue compartments and consist of tight-junction-associated marvel proteins (TAMPs) and claudins. The function of TAMPs and the interaction with claudins are not understood. We therefore investigated the binding between the TAMPs occludin, tricellulin, and marvelD3 and their interaction with claudins in living tight-junction-free human embryonic kidney-293 cells. In contrast to claudins and occludin, tricellulin and marvelD3 showed no enrichment at cell–cell contacts indicating lack of homophilic trans-interaction between two opposing cell membranes. However, occludin, marvelD3 and tricellulin exhibited homophilic cis-interactions, along one plasma membrane, as measured by fluorescence resonance energy transfer. MarvelD3 also cis-interacted with occludin and tricellulin heterophilically. Classic claudins, such as claudin-1 to -5 may show cis-oligomerization with TAMPs, whereas the non-classic claudin-11 did not. Claudin-1 and -5 improved enrichment of occludin and tricellulin at cell–cell contacts. The low mobile claudin-1 reduced the membrane mobility of the highly mobile occludin and tricellulin, as studied by fluorescence recovery after photobleaching. Co-transfection of claudin-1 with TAMPs led to changes of the tight junction strand network of this claudin to a more physiological morphology, depicted by freeze-fracture electron microscopy. The results demonstrate multilateral interactions between the tight junction proteins, in which claudins determine the function of TAMPs and vice versa, and provide deeper insights into the tight junction assembly.
Readability Classification for German using Lexical, Syntactic, and Morphological Features
2012-12-01

We investigate the problem of reading level assessment for German texts on a newly compiled corpus of freely available easy and difficult articles, targeted at adult and child readers respectively. We adapt a wide range of syntactic, lexical and language model features from previous research on English and combined them with new features that make use of the rich morphology of German. We show that readability classification for German based on these features is highly successful, reaching 89.7 % accuracy, with the new morphological features making an important contribution. TITLE AND ABSTRACT IN GERMAN
Skipping breakfast: morningness-eveningness preference is differentially related to state and trait food cravings.
2012-12-01

Eveningness preference is associated with unhealthy eating behaviors. We measured state and trait food cravings in chronotypes in the morning and in the evening. Less Evening (E)- than Morning (M)-types reported to have had breakfast. Accordingly, hours that had elapsed since the last meal were higher in E- than M-types in the morning, but did not differ between groups in the evening. E-types reported higher anticipation of positive reinforcement that may result from eating than M-types in the morning, but both had the same hunger levels. On a trait level, M-types reported more feelings of guilt for giving into cravings compared to E-types. Results suggest that E-types skip breakfast more often than M-types, but this eating pattern does not inevitably lead to more food cravings in the evening or more pronounced habitual cravings. Furthermore, E-types did not experience more hunger in the morning although they had not been eating for a longer time period. Results support findings about a different lifestyle in E-types compared to M-types.
Native Language Identification using Recurring $n$-grams -- Investigating Abstraction and Domain Dependence
2012-12-01

Native Language Identification tackles the problem of determining the native language of an author based on a text the author has written in a second language. In this paper, we discuss the systematic use of recurring n-grams of any length as features for training a native language classifier. Starting with surface n-grams, we investigate two degrees of abstraction incorporating parts-of-speech. The approach outperforms previous work employing a comparable data setup, reaching 89.71% accuracy for a task with seven native languages using data from the International Corpus of Learner English (ICLE). We then investigate the claim by Brooke and Hirst (2011) that a content bias in ICLE seems to result in an easy classification by topic instead of by native language characteristics. We show that training our model on ICLE and testing it on three other, independently compiled learner corpora dealing with other topics still results in high accuracy classification.
Mineralogy and Geochemistry of the Sedimentary Kaolin Deposits from Sinai, Egypt: Implications for Control by the Source Rocks
2012-12-01

Abstract Mineralogical and geochemical variations among the Carboniferous and Cretaceous sedimentary kaolin deposits from Sinai provided an opportunity to examine the effect of the source area on compositions of the deposits. The Carboniferous kaolin deposits are mineralogically and geochemically heterogeneous. The Khaboba and Hasbar deposits consist of kaolinite, quartz, anatase, illite, chlorite, zircon, and leucoxene. The shale-normalized rare earth element ( REE ) patterns of the Khaboba deposit showed a slight LREE over HREE enrichment ((La/Yb) SN = 1.19–1.51) with a MREE depletion (Gd/Gd* SN = 0.51–0.75), while the Hasbar kaolin had a MREE enrichment. The Abu Natash kaolin deposit consisted of kaolinite, anatase, and a little quartz with larger TiO2, Cr, and V and smaller Zr and Nb contents compared to other Carboniferous deposits. The shale-normalized REE patterns of the Abu Natash deposit exhibited a positive Eu anomaly (Eu/Eu* SN = 1.28–1.40) and a MREE enrichment (Gd/Gd* SN = 1.41–2.05). The Cretaceous deposits were relatively homogeneous in terms of mineralogical composition and geochemistry and are composed of kaolinite, quartz, anatase, rutile, zircon, and leucoxene. The Cretaceous kaolin deposits showed mostly flat shale-normalized REE patterns with a variable LREE depletion. The presence of illite and chlorite, the absence of rutile, large Zr and Nb contents, and the REE patterns suggested a component of weathered low-grade metasediments as a source for the Carboniferous deposits in the Khaboba and Hasbar areas, while the large Ti, Cr, and V, and small quartz contents indicated mafic source rocks for the Abu Natash deposit. The abundance of high-Cr rutile and the absence of illite and chlorite, and large Zr, Ti, Cr, and V contents suggested a mixture of medium- to high-grade metamafic and granitic rocks as source rocks for the Cretaceous kaolin deposits. The occurrence of alkaline rocks in the source of the deposits studied was identified by high-Nb contents and the presence of bastnaesite. The mineralogical and geochemical heterogeneity and lesser maturity of the Carboniferous deposits suggested local sources for each deposit and their deposition in basins close to the sources. The mineralogical and geochemical homogeneity and maturity of the Cretaceous deposits, on the other hand, indicated common sources for all deposits and their deposition in relatively remote basins.
Dormancy in breast cancer
2012-12-01

Tumor dormancy describes a prolonged quiescent state in which tumor cells are present, but disease progression is not yet clinically apparent. Breast cancer is especially known for long asymptomatic periods, up to 25 years, with no evidence of the disease, followed by a relapse. Factors that determine the cell's decision to enter a dormant state and that control its duration remain unclear. In recent years, considerable progress has been made in understanding how tumor cells circulating in the blood interact and extravasate into secondary sites and which factors might determine whether these cells survive, remain dormant, or become macrometastases. The mechanisms of tumor cell dormancy are still not clear. Two different hypotheses are currently discussed: tumor cells persist either by completely withdrawing from the cell cycle or by continuing to proliferate at a slow rate that is counterbalanced by cell death. Because dormant disseminated tumor cells may be the founders of metastasis, one hypothesis is that dormant tumor cells, or at least a fraction of them, share stem cell-like characteristics that may be responsible for their long half-lives and their suggested resistance to standard chemotherapy. Therefore, knowledge of the biology of tumor cell dormancy may be the basis from which to develop innovative targeted therapies to control or eliminate this tumor cell fraction. In this review, we discuss biological mechanisms and clinical implications of tumor dormancy in breast cancer patients.
Recycling of Arabidopsis plasma membrane PEN1 syntaxin
2012-12-01

Penetration resistance against powdery mildews is one of the best-studied processes of plant innate immunity. One vital component is the plant syntaxin, PEN1, which is required for timely deposition of callose and extracellular membrane material, as well as PEN1 itself, at the attack sites. Recently, we reported that the ARF-GEF GNOM also is required for penetration resistance, mediating transport of recycled material, including PEN1, to the site of attack. The close relative of PEN1, SYP122, does not accumulate at the sites of attack nor does it affect penetration resistance. In support of this, we show here that in contrast to PEN1, SYP122 does not continuously recycle. Furthermore, by using a PEN1 transgene that is only transcribed in dividing cells, we show that papillary PEN1 accumulation is not dependent on de-novo protein synthesis. This emphasizes the involvement of recycling in penetration resistance, which possibly relates to the differences in function of the two syntaxins.
Confocal sample-scanning microscope for single-molecule spectroscopy and microscopy with fast sample exchange at cryogenic temperatures
2012-12-01

The construction of a microscope with fast sample transfer system for single-molecule spectroscopy and microscopy at low temperatures using 2D/3D sample-scanning is reported. The presented construction enables the insertion of a sample from the outside (room temperature) into the cooled (4.2 K) cryostat within seconds. We describe the mechanical and optical design and present data from individual Photosystem I complexes. With the described setup numerous samples can be investigated within one cooling cycle. It opens the possibility to investigate biological samples (i) without artifacts introduced by prolonged cooling procedures and (ii) samples that require preparation steps like plunge-freezing or specific illumination procedures prior to the insertion into the cryostat.
Higher estimates of daily dietary net endogenous acid production (NEAP) in the elderly as compared to the young in a healthy, free-living elderly population of Pakistan
2012-12-01

Dietary intake has been shown to influence the acid-base balance in human subjects; however, this phenomenon is poorly understood and rarely reported for the least well-studied segment of older people in a developing country. The aims of the present study were to: (1) quantify estimates of daily net endogenous acid production (NEAP) (mEq/d) in a sample of otherwise healthy elderly aged 50 years and above; and (2) compare NEAP between the elderly and young to determine the effects of aging, which could contribute to changes in the acid-base balance. Analyses were carried out among 526 elderly and 131 young participants (aged 50-80 and 23-28 years, respectively), all of whom were free of discernible disease, nonsmokers, and not on any chronic medication. Selected anthropometric factors were measured and 24-hour dietary recall was recorded. We used two measures to characterize dietary acid load: (1) NEAP estimated as the dietary potential renal acid load plus organic acid excretion, the latter as a multiple of estimated body surface area; and (2) estimated NEAP based on protein and K. For the young and elderly, the ranges of NEAP were 12.1-67.8 mEq/d and 2.0-78.3 mEq/d, respectively. Regardless of the method used, the mean dietary acid-base balance (NEAP) was significantly higher for the elderly than the young (P = 0.0035 for NEAP [elderly, 44.1 mEq/d versus young 40.1 mEq/d]; and P = 0.0035 for the protein:potassium ratio [elderly, 1.4 mEq/d versus young 1.1 mEq/d]). A positive and significant correlation was found between NEAP and energy, protein, and phosphorus (P < 0.05 for all trends). The findings from this study provide evidence of the relatively higher production of NEAP in older people, possibly as an effect of higher consumption of certain acid-producing foods by the elderly.
Cardiovascular magnetic resonance imaging of isolated perfused pig hearts in a 3T clinical MR scanner
2012-12-01

Abstract Purpose An isolated perfused pig heart model has recently been proposed for the development of novel methods in standard clinical magnetic resonance (MR) scanners. The original set-up required the electrical system to be within the safe part of the MR-room, which introduced significant background noise. The purpose of the current work was to refine the system to overcome this limitation so that all electrical parts are completely outside the scanner room. Methods Four pig hearts were explanted under terminal anaesthesia from large white cross landrace pigs. All hearts underwent cardiovascular magnetic resonance (CMR) scanning in the MR part of a novel combined 3T MR and x-ray fluoroscopy (XMR) suite. CMR scanning included real-time k-t SENSE functional imaging, k-t SENSE accelerated perfusion imaging and late gadolinium enhancement imaging. Interference with image quality was assessed by spurious echo imaging and compared to noise levels acquired while operating the electrical parts within the scanner room. Results Imaging was performed successfully in all hearts. The system proved suitable for isolated heart perfusion in a novel 3T XMR suite. No significant additional noise was introduced into the scanner room by our set-up. Conclusions We have substantially improved a previous version of an isolated perfused pig heart model and made it applicable for MR imaging in a state of the art clinical 3T XMR imaging suite. The use of this system should aid novel CMR sequence development and translation into clinical practice.
Semi-automatic Annotation of Chinese Word Structure
2012-12-01

Chinese word structure annotation is potentially useful for many NLP tasks, especially for Chinese word segmentation. Li and Zhou (2012) have presented an annotation for word structures in the Penn Chinese Treebank. But they only consider words that have productive affixes, which covers 35% of word types in that corpus. In this paper, we propose a linguistically inspired annotation that covers various morphological derivations of Chinese in a more general way, such that almost all multiple-character words can be structurally analyzed. As manual annotation is expensive, we propose a semi-supervised approach to automatic annotation, which combines the maximum entropy learning and the EM iteration for the Gaussian mixture model. The proposed method has achieved an accuracy of 90% on the testing set.
Admittance matrix of a trapezoidal piezoelectric heterogeneous bimorph
2012-12-01

Bimorph structures are a standard method for transforming the high force of piezoelectric materials into a large deflection. In micro electromechanical systems (MEMS) applications, it is preferable to use structures consisting of a passive substrate (usually silicon) and one or more piezoelectric layers on the top. Such structures are called heterogeneous bimorphs or enakemesomorphs. In some MEMS applications- for example, for use as acoustic transducers-it is desirable to arrange such heterogeneous bimorphs in a circular shape, which results in trapezoidal cantilever structures. In this paper, an analytic dynamic description of such actuators is obtained. The resulting model is proved to be compatible with existing models for heterogeneous bimorphs with constant width. A comparison to a finite element analysis model of an exemplary layout shows divergences wholly within the same range as found for published models for constant-width structures.