julilili42/papers huggingface dataset:
Brain activation in frontotemporal and Alzheimer’s dementia: a functional near-infrared spectroscopy study
2016-12-01

Abstract Background Frontotemporal dementia is an increasingly studied disease, the underlying functional impairments on a neurobiological level of which have not been fully understood. Patients with the behavioral-subtype frontotemporal dementia (bvFTD) are particularly challenging for clinical measurements such as functional imaging due to their behavioral symptoms. Here, an alternative imaging method, functional near-infrared spectroscopy (fNIRS), is introduced to measure task-related cortical brain activation based on blood oxygenation. The current study investigated differences in cortical activation patterns of patients with bvFTD, Alzheimer’s dementia (AD), and healthy elderly subjects measured by fNIRS. Method Eight probable bvFTD patients completed the semantic, phonological, and control conditions of a verbal fluency task. Eight AD patients and eight healthy controls were compared on the same task. Simultaneously, an fNIRS measurement was conducted and analyzed using a correction method based on the expected negative correlation between oxygenated and deoxygenated hemoglobin. Results Healthy controls show an increase in cortical activation measured in frontoparietal areas such as the dorsolateral prefrontal cortex. The activation pattern of patients with AD is similar, but weaker. In contrast, bvFTD patients show a more frontopolar pattern, with activation of Broca’s area, instead of the dorsolateral prefrontal cortex and the superior temporal gyrus. The frontoparietal compensation mechanisms, seen in the healthy elderly, were missing in bvFTD patients. Conclusion Different frontoparietal cortical activation patterns may indicate a correlate of diverse pathophysiological mechanisms of AD and bvFTD during verbal fluency processing. The AD pattern is weaker and more similar to the healthy pattern, whereas the bvFTD pattern is qualitatively different, namely more frontopolar and without frontoparietal compensation activation. It adheres to a change of cortical activation during the course of the disease.
T1 and T2 mapping for evaluation of myocardial involvement in patients with ANCA-associated vasculitides
2016-12-01

AAV patients demonstrated increased T1, ECV, and T2 values, with native T1 and T2 showing the highest prevalence of values beyond the 95% percentile of normal. Since these findings seem to be independent of LGE, mapping techniques may provide complementary information to LGE-CMR in the assessment of myocardial involvement in patients with AAV.
The direct cooling tail method for X-ray burst analysis to constrain neutron star masses and radii
2016-12-01

Determining neutron star (NS) radii and masses can help to understand the properties of matter at supra-nuclear densities. Thermal emission during thermonuclear X-ray bursts from NSs in low-mass X-ray binaries provides a unique opportunity to study NS parameters, because of the high fluxes, large luminosity variations and the related changes in the spectral properties. The standard cooling tail method uses hot NS atmosphere models to convert the observed spectral evolution during cooling stages of X-ray bursts to the Eddington flux F_Edd and the stellar angular size Omega. These are then translated to the constraints on the NS mass M and radius R. Here we present the improved, direct cooling tail method that generalises the standard approach. First, we adjust the cooling tail method to account for the bolometric correction to the flux. Then, we fit the observed dependence of the blackbody normalization on flux with a theoretical model directly on the M-R plane by interpolating theoretical dependences to a given gravity, hence ensuring only weakly informative priors for M and R instead of F_Edd and Omega. <br />The direct cooling method is demonstrated using a photospheric radius expansion burst from SAX J1810.8--2609, which has happened when the system was in the hard state. Comparing to the standard cooling tail method, the confidence regions are shifted by 1 sigma towards larger radii, giving R=11.5-13.0 km at M=1.3-1.8 M_sun for this NS.<br />
Mechanisms behind plant diversity effects on inorganic and organic N leaching from temperate grassland
2016-12-01

Higher plant diversity reduces nitrate leaching by complementary resource use, while its relation to leaching of other N species is unclear. We determined the effects of plant species richness, functional group richness, and the presence of specific functional groups on ammonium, dissolved organic N (DON), and total dissolved N (TDN) leaching from grassland in the first 4 years after conversion from fertilized arable land to unfertilized grassland. On 62 experimental plots in Jena, Germany, with 1-60 plant species and 1-4 functional groups (legumes, grasses, tall herbs, small herbs), nitrate, ammonium, and TDN concentrations in soil solution (0-0.3 m soil layer) were measured fortnightly during 4 years. DON concentrations were calculated by subtracting inorganic N from TDN. Nitrogen concentrations were multiplied with modeled downward water fluxes to obtain N leaching. DON leaching contributed most to TDN leaching (64 +/- SD 4% of TDN). Ammonium leaching was unaffected by plant diversity. Increasing species richness decreased DON leaching in the fourth year. We attribute this finding to enhanced use of DON as a C and N source and enhanced mineralization of DON by soil microorganisms. An increase of species richness decreased TDN leaching likely driven by the complementary use of nitrate by diverse mixtures. Legumes increased DON and TDN leaching likely because of their N-fixing ability and higher litter production. Grasses decreased TDN leaching because of more exhaustive use of nitrate and water. Our results demonstrate that increasing plant species richness decreases leaching of DON and TDN.
Universal dependencies for Turkish
2016-12-01

The Universal Dependencies (UD) project was conceived after the substantial recent interest in unifying annotation schemes across languages. With its own annotation principles and abstract inventory for parts of speech, morphosyntactic features and dependency relations, UD aims to facilitate multilingual parser development, cross-lingual learning, and parsing research from a language typology perspective. This paper presents the Turkish IMST-UD Treebank, the first Turkish treebank to be in a UD release. The IMST-UD Treebank was automatically converted from the IMST Treebank, which was also recently released. We describe this conversion procedure in detail, complete with mapping tables. We also present our evaluation of the parsing performances of both versions of the IMST Treebank. Our findings suggest that the UD framework is at least as viable for Turkish as the original annotation framework of the IMST Treebank.
RiboTagger: fast and unbiased 16S/18S profiling using whole community shotgun metagenomic or metatranscriptome surveys
2016-12-01

RiboTagger permits fast recovery of SSU-RNA sequences from shotgun nucleic acid surveys of complex microbial communities. The program targets all three domains of life, exhibits high sensitivity and specificity and is substantially faster than comparable programs.
Informational benefits from social media use for professional purposes: Results from a longitudinal study
2016-12-01

Using data from four waves of a longitudinal study among Dutch internet users, we examined whether and how the use of social network sites (SNS) for professional purposes is related to informational benefits. Building on a social capital framework and taking into account the affordances of social media, we specifically looked at users’ activities and the structure of their online networks. Users of LinkedIn or other professional SNS consistently reported higher informational benefits than non-users. The number of ties on the SNS used for professional purposes predicted informational benefits half a year later, and strong ties became more important over time. We also found evidence for a reciprocal relationship between strategic networking and informational benefits. For the use variables (frequency of login, reading, activity in groups, posting professional content), we mainly found concurrent associations with informational benefits. The results shed light on the complex interplay of concurrent and longitudinal processes in the relationship between SNS use and professional informational benefits.
Morphology of the peritoneal cavity and pathophysiological consequences
2016-12-01

Abstract The peritoneal cavity (cavum peritonei) is incompletely divided into spaces and recessus (or fossae), which are playing an important role in health and disease. Peritoneal subspaces are determined by the parietal attachments of the abdominal organs, the ligaments and mesenteries. These include the splenorenal, the falciform, the triangular, the gastrosplenic, the phrenicocolic and the gastrocolic ligaments; the greater omentum and the lesser omentum (formed by the gastrohepatic and hepatoduodenal ligaments); the small bowel mesenterium and the mesocolon. These ligaments and mesenteries divide the peritoneal cavity into several distinct anatomic and functional regions. The supramesocolic compartment is divided into a bilateral subphrenic space and a subhepatic space continuing into the lesser sac (bursa omentalis). The inframesolic compartment is divided into a left and right region by the mesentery. The right paracolic gutter communicates with the pelvis and with the right suphrenic space. The left paracolic gutter is separated from the left subphrenic space by the phrenocolic ligament. The peritoneal space is virtual, is completely occupied by the intraabdominal organs and can only be visualized by radiological means in the presence of air (organ perforation), liquid (ascites, pus, bile, gastrointestinal fluids) or tumor invasion. Peritoneal morphology has numerous pathophysiological implications: it impacts on the propagation of intraabdominal infections, determines the spreading of peritoneal metastasis and can cause bowel volvulus. Internal hernias can arise at the junction between intraperitoneal and extraperitoneal bowel segments, in particular into the left paraduodenal recessus. Knowledge of peritoneal morphology is a precondition for developing locoregional therapeutic strategies in peritoneal disease and for effective peritoneal dialysis.
Siamese Convolutional Networks for Cognate Identification
2016-12-01

In this paper, we present phoneme level Siamese convolutional networks for the task of pair-wise cognate identification. We represent a word as a two-dimensional matrix and employ a siamese convolutional network for learning deep representations. We present siamese architectures that jointly learn phoneme level feature representations and language relatedness from raw words for cognate identification. Compared to previous works, we train and test on larger and realistic datasets; and, show that siamese architectures consistently perform better than traditional linear classifier approach.
Discriminating Similar Languages with Linear SVMs and Neural Networks.
2016-12-01

This paper describes the systems we experimented with for participating in the discriminating between similar languages (DSL) shared task 2016. We submitted results of a single system based on support vector machines (SVM) with linear kernel and using character ngram features, which obtained the first rank at the closed training track for test set A. Besides the linear SVM, we also report additional experiments with a number of deep learning architectures. Despite our intuition that non-linear deep learning methods should be advantageous, linear models seems to fare better in this task, at least with the amount of data and the amount of effort we spent on tuning these models.
A Dermal Equivalent Engineered with TGF‐β3 Expressing Bone Marrow Stromal Cells and Amniotic Membrane: Cosmetic Healing of Full‐Thickness Skin Wounds in Rats
2016-12-01

Abstract Transforming growth factor beta‐3 (TGF‐β3) has been shown to decrease scar formation after scheduled topical applications to the cutaneous wounds. This study aimed to continuously deliver TGF‐β3, during the early phase of wound healing, by engineering a dermal equivalent (DE) using TGF‐β3 expressing bone marrow stromal cells (BM‐SCs) and human dehydrated amniotic membrane (hDAM). To engineer a DE, rat BM‐SCs were seeded on the hDAM and TGF‐β3 was transiently transfected into the BM‐SCs using a plasmid vector. Pieces of the dermal equivalent were transplanted onto the full‐thickness excisional skin wounds in rats. The process of wound healing was assessed by image analysis, Manchester Scar Scale (MSS), and histopathological studies 7, 14, 21, and 85 days after the excision. The results confirmed accurate construction of recombinant pcDNA3.1‐TGF‐β3 expression system and showed that the transfected BM‐SCs seeded on hDAM expressed TGF‐β3 mRNA and protein from day 3 through day 7 after transfection. After implantation of the DE, contraction of the wounds was measured from day 7 through 21 and analyzed by linear regression, which revealed that the rate of wound contraction in all experimental groups was similar. Histologic evaluation demonstrated that transfected BM‐SCs decreased retention and recruitment of the cells during the early stage of wound healing, decreased the formation of vascular structures and led to formation of uniformly parallel collagen bundles. MSS scores showed that TGF‐β3 secreting cells significantly improved the cosmetic appearance of the healed skin and decreased the scar formation. From these results, it could be concluded that transient secretion of TGF‐β3, during the early phase of healing, by BM‐SCs seeded on hDAM can improve the cosmetic appearance of the scar in cutaneous wounds without negatively affecting the process of wound repair.
“My Muslim sister, indeed you are a mujahidah” - Narratives in the propaganda of the Islamic State to address and radicalize Western Women. An Exemplary analysis of the online magazine Dabiq
2016-12-01

The terrorist group Islamic State succeeds in radicalizing thousands of young people from the West, among them a large number of women. Although the phenomenon of female members in terrorist groups is not entirely new, the massive commitment of females for the Islamic State is surprising. The group makes strong use of the internet, especially social media, to spread its propaganda which contributes to female radicalization and might even lead to their recruitment. By now it is known that the push and especially the pull factors appearing in the radicalization process are different than those in male radicalization. Howeverresearch does barely take the gender-specific dynamics into account when it comes to the development of measures that counter Islamic radicalization. At this point, I argue that a deeper understanding of the gender-specific narratives of the group serves as a key point to develop effective measures. In the propaganda of the Islamic State that directly addresses women from the West, certain narratives can be found. With the analysis of articles that address women taken from the online magazine Dabiq, I identified nine narratives outlined in this paper. The investigation of both images and the strategic use of language in the considered articles indicate how the narratives are constructed. The emphasis on religious and gender-specific narratives in the articles leads me to argue in favor of a stronger focus on female-specific counter-radicalization measures. The involvement of the findings from this paper into radicalization research may help to develop effective counter-narratives and adjust them gender-specifically.
In Vitro Variant Surface Antigen Expression in Plasmodium falciparum Parasites from a Semi-Immune Individual Is Not Correlated with Var Gene Transcription
2016-12-01

Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is considered to be the main variant surface antigen (VSA) of Plasmodium falciparum and is mainly localized on electron-dense knobs in the membrane of the infected erythrocyte. Switches in PfEMP1 expression provide the basis for antigenic variation and are thought to be critical for parasite persistence during chronic infections. Recently, strain transcending anti-PfEMP1 immunity has been shown to develop early in life, challenging the role of PfEMP1 in antigenic variation during chronic infections. In this work we investigate how P. falciparum achieves persistence during a chronic asymptomatic infection. The infected individual (MOA) was parasitemic for 42 days and multilocus var gene genotyping showed persistence of the same parasite population throughout the infection. Parasites from the beginning of the infection were adapted to tissue culture and cloned by limiting dilution. Flow cytometry using convalescent serum detected a variable surface recognition signal on isogenic clonal parasites. Quantitative real-time PCR with a field isolate specific var gene primer set showed that the surface recognition signal was not correlated with transcription of individual var genes. Strain transcending anti-PfEMP1 immunity of the convalescent serum was demonstrated with CD36 selected and PfEMP1 knock-down NF54 clones. In contrast, knock-down of PfEMP1 did not have an effect on the antibody recognition signal in MOA clones. Trypsinisation of the membrane surface proteins abolished the surface recognition signal and immune electron microscopy revealed that antibodies from the convalescent serum bound to membrane areas without knobs and with knobs. Together the data indicate that PfEMP1 is not the main variable surface antigen during a chronic infection and suggest a role for trypsin sensitive non-PfEMP1 VSAs for parasite persistence in chronic infections.
Robotic intracorporeal urinary diversion: practical review of current surgical techniques
2016-12-01

In this practical review, we discuss current surgical techniques reported in the literature to perform intracorporeal urinary diversion (ICUD) after robotic radical cystectomy (RARC), emphasizing criticisms of single approaches and making comparisons with extracorporeal urinary diversion (ECUD). Although almost 97% of all RARCs use an ECUD, ICUD is gaining in popularity, in view of its potential benefits (i.e., decreased bowel exposure, etc.), although there are a few studies comparing ICUD and ECUD. Analyzing single experiences and the data from recent metanalyses, we emphasize the current critiques to ICUD, stressing particular technical details which could reduce operative time, lowering the postoperative complications rate, and improving functional outcomes. Only analysis of long-term follow-up data from large-scale homogeneous series can ascertain whether robotic intracorporeal urinary diversion is superior to other approaches.
Structural incorporation of W6+into hematite and goethite: A combined study of natural and synthetic iron oxides developed from precursor ferrihydrite and the preservation of ancient fluid compositions in hematite
2016-12-01

Hematite (a-Fe2O3) and goethite (a-FeOOH) can incorporate considerable amounts of tungsten (W). Although W concentrations up to several wt% in hematite and goethite have been reported in the literature, none of the proposed models for a structural incorporation has been generally accepted yet. Here, the first combination of X-ray absorption fine structure (XAFS) measurements with X-ray diffraction (XRD), Raman spectroscopy (RS), electron microprobe (EMPA) and total reflection X-ray fluorescence (TXRF) provides a general relation between W content and its structural incorporation into hematite and goethite.
Advancing linguistic features and insights by label-informed feature grouping : an exploration in the context of native language identification
2016-12-01

We propose a hierarchical clustering approach designed to group linguistic features for supervised machine learning that is inspired by variationist linguistics. The method makes it possible to abstract away from the individual feature occurrences by grouping features together that behave alike with respect to the target class, thus providing a new, more general perspective on the data. On the one hand, it reduces data sparsity, leading to quantitative performance gains. On the other, it supports the formation and evaluation of hypotheses about individual choices of linguistic structures. We explore the method using features based on verb subcategorization information and evaluate the approach in the context of the Native Language Identification (NLI) task.
Infrared Colorization Using Deep Convolutional Neural Networks
2016-12-01

This paper proposes a method for transferring the RGB color spectrum to near-infrared (NIR) images using deep multi-scale convolutional neural networks. A direct and integrated transfer between NIR and RGB pixels is trained. The trained model does not require any user guidance or a reference image database in the recall phase to produce images with a natural appearance. To preserve the rich details of the NIR image, its high frequency features are transferred to the estimated RGB image. The presented approach is trained and evaluated on a real-world dataset containing a large amount of road scene images in summer. The dataset was captured by a multi-CCD NIR/RGB camera, which ensures a perfect pixel to pixel registration.
Study protocol for a prospective, non-controlled, multicentre clinical study to evaluate the diagnostic accuracy of a stepwise two-photon excited melanin fluorescence in pigmented lesions suspicious for melanoma (FLIMMA study)
2016-12-01

Introduction Non-invasive, nanosecond, stepwise two-photon laser excitation of skin tissue was shown to induce melanin fluorescence spectra that allow for the differentiation of melanocytic nevi from cutaneous melanoma. Methods and analysis This prospective, non-controlled, multicentre clinical study is performed to evaluate the diagnostic performance of the stepwise two-photon excited melanin fluorescence in the detection of cutaneous melanoma. The comparator will be the histopathological diagnosis. A total of 620 pigmented skin lesions suspicious for melanoma and intended for excision will be enrolled. Ethics and dissemination Ethics approval was provided by the local ethics committees of the medical faculties of the University of Tuebingen, Heidelberg and Berlin. Study registration The FLIMMA study NCT02425475 .
Towards grounding computational linguistic approaches to readability: Modeling reader-text interaction for easy and difficult texts
2016-12-01

Computational approaches to readability assessment are generally built and evaluated using gold standard corpora labeled by publishers or teachers rather than being grounded in observations about human performance. Considering that both the reading process and the outcome can be observed, there is an empirical wealth that could be used to ground computational analysis of text readability. This will also support explicit readability models connecting text complexity and the reader’s language proficiency to the reading process and outcomes.\\nThis paper takes a step in this direction by reporting on an experiment to study how the relation between text complexity and reader’s language proficiency affects the reading process and performance outcomes of readers after reading We modeled the reading process using three eye tracking variables: fixation count, average fixation count, and second pass reading duration. Our models for these variables explained 78.9%, 74% and 67.4% variance, respectively. Performance outcome was modeled through recall and comprehension questions, and these models explained 58.9% and 27.6% of the variance, respectively. While the online models give us a better understanding of the cognitive correlates of reading with text complexity and language proficiency, modeling of the offline measures can be particularly relevant for incorporating user aspects into readability models.