julilili42/papers huggingface dataset:
The Mutual Relation of Platelet Activation and Innate Immunity
2018-09-25

Abstract Platelets are known to be central regulators of haemostasis, inflammation and immune response. Formed by megakaryocytes in the bone marrow and the lungs, platelets express a broad range of adhesion receptors and release cytokines and platelet microparticles which enable them to interact with both immune cells and pathogens. In bacterial and viral infections, thrombophilia and thrombocytopenia are commonly seen symptoms, indicating the close relationship between haemostasis and immune defence. Indeed, platelets contribute both directly and via immune mediation to pathogen clearance. In sterile inflammation, a pathogen-free process which is often triggered by cell necrosis and autoimmune reactions, platelets are also of central importance. Recently, platelet inflammasome has been extensively studied in this context. Both sterile inflammation and infection are affected by the interactions of platelets and innate immunity, notably the complement system. Although the general elements of this interplay have been known for long, more and more insights into disease-specific mechanisms could be gained recently. This review gives an outline of the current findings in the field of platelet–immune cell interactions and points out possible implications for clinical therapy.
Differential Development of Children’s Understanding of the Cardinality of Small Numbers and Zero
2018-09-25

Counting and the understanding of cardinality are important steps in children's numerical development. Recent studies have indicated that language and visuospatial abilities play an important role in the development of children's cardinal knowledge of small numbers. However, predictors for the knowledge about <i>zero</i> were usually not considered in these studies. Therefore, the present study investigated whether the acquisition of cardinality knowledge on small numbers and the concept of <i>zero</i> share cross-domain and domain-specific numerical predictors. Particular interest was paid to the question whether visuospatial abilities - in addition to language abilities - were associated with children's understanding of small numbers and <i>zero</i>. Accordingly, we assessed kindergarteners aged 4 to 5 years in terms of their understanding of small numbers and <i>zero</i> as well as their visuospatial, general language, counting, Arabic number identification abilities, and their finger number knowledge. We observed significant zero-order correlations of vocabulary, number identification, finger knowledge, and counting abilities with children's knowledge about <i>zero</i> as well as understanding of the cardinality of small numbers. Subsequent regression analyses substantiated the influences of counting abilities on knowledge about <i>zero</i> and the influences of both counting abilities and finger knowledge on children's understanding of the cardinality of small numbers. No significant influences of cross-domain predictors were observed. In sum, these results indicate that domain-specific numerical precursor skills seem to be more important for children's development of an understanding of the cardinality of small numbers as well as of the concept of <i>zero</i> than the more proximal cross-domain abilities such as language and visuospatial abilities.
μ-rhythm extracted with personalized EEG filters correlates with corticospinal excitability in real-time phase-triggered EEG-TMS
2018-09-25

Abstract Ongoing brain activity has been implicated in the modulation of cortical excitability. The combination of electroencephalography (EEG) and transcranial magnetic stimulation (TMS) in a real-time triggered setup is a novel method for testing hypotheses about the relationship between spontaneous neuronal oscillations, cortical excitability, and synaptic plasticity. For this method, a reliable real-time extraction of the neuronal signal of interest from scalp EEG with high signal-to-noise ratio (SNR) is of crucial importance. Here we compare individually tailored spatial filters as computed by spatial-spectral decomposition (SSD), which maximizes SNR in a frequency band of interest, against established local C3-centered Laplacian filters for the extraction of the sensorimotor μ -rhythm. Single-pulse TMS over the left primary motor cortex was synchronized with the surface positive or negative peak of the respective extracted signal, and motor evoked potentials (MEP) were recorded with electromyography (EMG) of a contralateral hand muscle. Both extraction methods led to a comparable degree of MEP amplitude modulation by phase of the sensorimotor μ -rhythm at the time of stimulation. This could be relevant for targeting other brain regions with no working benchmark such as the local C3-centered Laplacian filter, as sufficient SNR is an important prerequisite for reliable real-time single-trial detection of EEG features.
EEG Recordings During a 3D Visuomotor Learning Task
2018-09-25

&lt;p&gt;This is a data set of EEG recordings and corresponding kinematic data during a 3D visuomotor learning task performed by thirty-four subjects. Alongside a readme, the folder consists of thirty-four .mat files for each participants&#39;&nbsp;data and a channels.csv file for EEG recording channel locations.&nbsp;When using this data please cite:&lt;/p&gt; &lt;p&gt;Ozdenizci, Ozan, et al. &quot;Neural Signatures of Motor Skill in the Resting Brain.&quot; &lt;em&gt;2019 IEEE International Conference on Systems, Man, and Cybernetics (SMC),&lt;/em&gt; 2019.&lt;/p&gt; &lt;p&gt;&nbsp;&lt;/p&gt;
EEG Recordings During a 3D Visuomotor Learning Task
2018-09-25

This is a data set of EEG recordings and corresponding kinematic data during a 3D visuomotor learning task performed by thirty-four subjects. Alongside a readme, the folder consists of thirty-four .mat files for each participants' data and a channels.csv file for EEG recording channel locations. When using this data please cite: Ozdenizci, Ozan, et al. "Neural Signatures of Motor Skill in the Resting Brain." <em>2019 IEEE International Conference on Systems, Man, and Cybernetics (SMC),</em> 2019.
Metallicity effect and planet mass function in pebble-based planet formation models
2018-09-26

Context. One of the main scenarios of planet formation is the core accretion model where a massive core forms first and then accretes a gaseous envelope. This core forms by accreting solids, either planetesimals or pebbles. A key constraint in this model is that the accretion of gas must proceed before the dissipation of the gas disc. Classical planetesimal accretion scenarios predict that the time needed to form a giant planet’s core is much longer than the time needed to dissipate the disc. This difficulty led to the development of another accretion scenario, in which cores grow by accretion of pebbles, which are much smaller and thus more easily accreted, leading to more rapid formation. Aims. The aim of this paper is to compare our updated pebble-based planet formation model with observations, in particular the well-studied metallicity effect. Methods. We adopt the Bitsch et al. (2015a, A&amp;A, 575, A28) disc model and the Bitsch et al. (2015b, A&amp;A, 582, A112) pebble model and use a population synthesis approach to compare the formed planets with observations. Results. We find that keeping the same parameters as in Bitsch et al. (2015b, A&amp;A, 582, A112) leads to no planet growth due to a computation mistake in the pebble flux (2018b). Indeed a large fraction of the heavy elements should be put into pebbles ( Z peb ∕ Z tot = 0.9) in order to form massive planets using this approach. The resulting mass functions show a huge amount of giants and a lack of Neptune-mass planets, which are abundant according to observations. To overcome this issue we include the computation of the internal structure for the planetary atmosphere in our model. This leads to the formation of Neptune-mass planets but no observable giants. Furthermore, reducing the opacity of the planetary envelope more closely matches observations. Conclusions. We conclude that modelling the internal structure for the planetary atmosphere is necessary to reproduce observations.
Dorsal and Ventral Posterior Cingulate Cortex Switch Network Assignment via Changes in Relative Functional Connectivity Strength to Noncanonical Networks
2018-09-26

The posterior cingulate cortex (PCC) is often used as a seed region for probing default-mode network (DMN) connectivity. However, there is evidence for a functional segregation between its dorsal (dPCC) and ventral (vPCC) subregions, which suggests differential involvements of d-/vPCC in regulating cognitive demands. Our paradigm included functional magnetic resonance imaging measures for baseline resting state, affective or cognitive tasks, and post-task resting states. We investigated the effect of task demands on intra-PCC coupling and d-/vPCC network assignment to major intrinsic connectivity networks (ICNs), which was estimated via edge weights of a graph network encompassing DMN, dorsal-attention network, and central-executive network (CEN). Although PCC subregions were functionally coupled during both resting-state conditions and cognitive tasks, they decoupled during affective stimulation. For dPCC, functional connectivity strength (FCS) to CEN was higher than to the other two ICNs; whereas for vPCC, FCS to DMN was the highest. We, hence, defined CEN and DMN as the canonical networks at rest for dPCC and vPCC, respectively. Switching from rest to affective stimulation, however, induced the strongest effects to relative network assignments between non-canonical networks of dPCC and vPCC. Although vPCC showed a durable functional connectivity (FC) to DMN, dPCC played a crucial role during switches of between-network FC depending on cognitive versus affective task requirements. Our results underline that it is crucial for future seed-based FC studies to consider these two subregions separately in terms of seed location and discussion of findings. Finally, our findings highlight the functional importance of connectivity changes toward regions outside the canonical networks.
Exploring Space, Economy, and Interregional Interaction at a Second-Millennium B.C.E. Citadel in Central Western Anatolia: 2014–2017 Research at Kaymakçı
2018-09-26

Current understandings of the archaeology of second-millennium B.C.E. central western Anatolia are enriched by ongoing research at Kaymakçı, located in the Marmara Lake basin of the middle Gediz River valley in western Turkey. Discovered during regional survey in 2001, the site offers a critical node of exploration for understanding a previously unexamined period in a well-traversed geography thought to be the core of the Late Bronze Age Seha River Land known from Hittite texts. Here we present results from the first three seasons of excavation on the citadel of Kaymakçı plus a study season (2014–2017), introducing the site’s chronology, historical and regional context, and significance through presentation of excavation areas as well as material and subsistence economies. With reference to such evidence, we discuss the site’s development, organization, and interregional interactions, demonstrating its place in local and regional networks that connected Aegean and central Anatolian spheres of interest.
Cyclin D1-positive Mediastinal Large B-Cell Lymphoma With Copy Number Gains of CCND1 Gene
2018-09-26

Primary mediastinal large B-cell lymphoma (PMBL) is a mature large B-cell lymphoma of putative thymic B-cell origin involving the mediastinum with younger age distribution and better prognosis than diffuse large B-cell lymphoma (DLBCL), not otherwise specified. Recently, based on gene expression profile analysis and morphologic findings, cases of PMBL without mediastinal involvement have been reported. In this study, we analyzed 3 cases of nodal DLBCL with morphologic features of PMBL presenting in submandibular or supraclavicular lymph nodes, in middle-aged to elderly patients, 2 of them without clinical or radiologic evidence of mediastinal involvement. The 3 patients presented with stage I/II disease and had excellent response to R-CHOP/R-EPOCH therapy. The 3 cases showed MAL expression and were positive for CD23 and/or CD30. All 3 cases expressed cyclin D1 with copy number gains of CCND1 gene but without rearrangement. There was no rearrangement of CIITA or PDL1/PDL2 . Reverse transcriptase-multiplex ligation-dependent probe amplification, a mRNA-based gene expression profile analysis revealed high probability of PMBL (87.6%, 98.7%, and 99%) in these 3 cases. Targeted next-generation sequencing analysis showed SOCS1 mutations in the 3 cases, and TNFAIP3 and XPO1 mutations in one, further supporting the diagnosis of PMBL. In conclusion, we report 3 cases of nodal PMBL, 2 of them without mediastinal mass, and expression of cyclin D1 due to copy number gains of CCND1 gene, a diagnostic pitfall with mantle cell lymphoma and DLBCL, not otherwise specified.
The evolutionary conserved FOXJ1 target gene Fam183b is essential for motile cilia in Xenopus but dispensable for ciliary function in mice
2018-09-26

Abstract The transcription factor FOXJ1 is essential for the formation of motile cilia throughout the animal kingdom. Target genes therefore likely constitute an important part of the motile cilia program. Here, we report on the analysis of one of these targets, Fam183b , in Xenopus and mice. Fam183b encodes a protein with unknown function which is conserved from the green algae Chlamydomonas to humans. Fam183b is expressed in tissues harbouring motile cilia in both mouse and frog embryos. FAM183b protein localises to basal bodies of cilia in mIMCD3 cells and of multiciliated cells of the frog larval epidermis. In addition, FAM183b interacts with NUP93, which also localises to basal bodies. During frog embryogenesis, Fam183b was dispensable for laterality specification and brain development, but required for ciliogenesis and motility of epidermal multiciliated cells and nephrostomes, i.e. the embryonic kidney. Surprisingly, mice homozygous for a null allele did not display any defects indicative of disrupted motile ciliary function. The lack of a cilia phenotype in mouse and the limited requirements in frog contrast with high sequence conservation and the correlation of gene expression with the presence of motile cilia. This finding may be explained through compensatory mechanisms at sites where no defects were observed in our FAM183b-loss-of-function studies.
Molecular and clinical analysis of 27 German patients with Leber congenital amaurosis
2018-09-26

Abstract Leber congenital amaurosis (LCA) is the earliest and most severe form of all inherited retinal dystrophies (IRD) and the most frequent cause of inherited blindness in children. The phenotypic overlap with other early-onset and severe IRDs as well as difficulties associated with the ophthalmic examination of infants can complicate the clinical diagnosis. To date, 25 genes have been implicated in the pathogenesis of LCA. The disorder is usually inherited in an autosomal recessive fashion, although rare dominant cases have been reported. We report the mutation spectra and frequency of genes in 27 German index patients initially diagnosed with LCA. A total of 108 LCA- and other genes implicated in IRD were analysed using a cost-effective targeted next-generation sequencing procedure based on molecular inversion probes (MIPs). Sequencing and variant filtering led to the identification of putative pathogenic variants in 25 cases, thereby leading to a detection rate of 93%. The mutation spectrum comprises 34 different alleles, 17 of which are novel. In line with previous studies, the genetic results led to a revision of the initial clinical diagnosis in a substantial proportion of cases, demonstrating the importance of genetic testing in IRD. In addition, our detection rate of 93% shows that MIPs are a cost-efficient and sensitive tool for targeted next-generation sequencing in IRD.
Visualizing metabolic network dynamics through time-series metabolomics data
2018-09-26

ABSTRACT New technologies have given rise to an abundance of -omics data, particularly metabolomics data. The scale of these data introduces new challenges for the interpretation and extraction of knowledge, requiring the development of new computational visualization methodologies. Here, we present a new method for the visualization of time-course metabolomics data within the context of metabolic network maps. We demonstrate the utility of this method by examining previously published data for two cellular systems—the human platelet and erythrocyte under cold storage for use in transfusion medicine. The results comprise two animated videos that allow for new insights into the metabolic state of both cell types. In the case study of the platelet metabolome during storage, the new visualization technique elucidates a nicotinamide accumulation which mirrors that of hypoxanthine and might, therefore, reflect similar pathway usage. This visual analysis provides a possible explanation for why the salvage reactions in purine metabolism exhibit lower activity during the first few days of the storage period. The second case study displays drastic changes in specific erythrocyte metabolite pools at different times during storage at different temperatures. In conclusion, this new visualization technique introduced in this article constitutes a well-suitable approach for large-scale network exploration and advances hypothesis generation. This method can be applied to any system with data and a metabolic map to promote visualization and understand physiology at the network level. More broadly, we hope that our approach will provide the blueprints for new visualizations of other longitudinal -omics data types. AUTHOR SUMMARY Profiling the dynamic state of a metabolic network through the use of time-course metabolomics technologies allows insights into cellular biochemistry. Interpreting these data together at the systems level provides challenges that can be addressed through the development of new visualization approaches. Here, we present a new method for the visualization of time-course metabolomics data that integrates data into an existing metabolic network map. In brief, the metabolomics data are visualized directly on a network map with dynamic elements (nodes that either change size, fill level, or color corresponding with the concentration) while the user controls the time series (i.e., which time point is being displayed) through a graphical interface. We provide short videos that illustrate the utility of this method through its application to existing data sets for the human platelet and erythrocyte. The results presented here give blueprints for the development of visualization methods for other time-course -omics data types that attempt to understand systems-level physiology.
Urban water supply in Punic and Roman Sardinia
2018-09-26

The study of Punic and Roman water supply systems in Sardinia (Western Mediterranean) has developed significantly over the last few decades of research. Due to the particular climatic conditions, the problem of water supply in the island has always been strongly felt. Water management systems were therefore of vital importance in the organization of private and public spaces in antiquity. Methods of planning and construction became quite precise, as did systems for control and maintenance; their use and evolution over the centuries could be seen in relation to expansion of urban centers and to demographic increase, to higher urban living standards, to enlarge of production systems and, maybe, to climatic variations. The purpose of this article is to provide a comparative overview of the most significant urban areas of Sardinia during the Punic and Roman period. The description of water works (wells, cisterns, tanks, channels), of techniques of water usage, of construction technologies, also with regards on public buildings directly fed by them, will give a comprehensive framework regarding these fundamental types of structures. This article is categorized under: Engineering Water &gt; Water, Health, and Sanitation Human Water &gt; Water Governance Science of Water &gt; Water Extremes
The augmentation of retinogeniculate communication during thalamic burst mode
2018-09-26

Abstract Retinal signals are transmitted to cortex via neurons in the lateral geniculate nucleus (LGN), where they are processed in burst or tonic response mode. Burst mode occurs when LGN neurons are sufficiently hyperpolarized for T-Type Ca 2+ channels to de-inactivate, allowing them to open in response to a depolarization which can trigger a high-frequency sequence of Na+-based spikes (i.e. burst). In contrast, T-type channels are inactivated during tonic mode and do not contribute to spiking. Although burst mode is commonly associated with sleep and the disruption of retinogeniculate communication, bursts can also be triggered by visual stimulation, thereby transforming the retinal signals relayed to the cortex. To determine how burst mode affects retinogeniculate communication, we made recordings from monosynaptically connected retinal ganglion cells and LGN neurons in the cat during visual stimulation. Our results reveal a robust augmentation of retinal signals within the LGN during burst mode. Specifically, retinal spikes were more effective and often triggered multiple LGN spikes during periods likely to have increased T-Type Ca 2+ activity. Consistent with the biophysical properties of T-Type Ca 2+ channels, analysis revealed that effect magnitude was correlated with the duration of the preceding thalamic interspike interval and occurred even in the absence of classically defined bursts. Importantly, the augmentation of geniculate responses to retinal input was not associated with a degradation of visual signals. Together, these results indicate a graded nature of response mode and suggest that, under certain conditions, bursts facilitate the transmission of visual information to the cortex by amplifying retinal signals. Significance The thalamus is the gateway for retinal information traveling to the cortex. The lateral geniculate nucleus (LGN), like all thalamic nuclei, has two classically defined categories of spikes—tonic and burst—that differ in their underlying cellular mechanisms. Here we compare retinogeniculate communication during burst and tonic response modes. Our results show that retinogeniculate communication is enhanced during burst mode and visually evoked thalamic bursts, thereby augmenting retinal signals transmitted to cortex. Further, our results demonstrate that the influence of burst mode on retinogeniculate communication is graded and can be measured even in the absence of classically defined thalamic bursts.
Founding of the International Society for the Study of Pleura and Peritoneum (ISSPP)
2018-09-26

The International Society for the Study of Pleura and Peritoneum (ISSPP) has been founded on Saturday, September 2018 at the Institut de France, Fondation Dosne-Thiers in the 9th arrondissement in Paris.The clinical demand for knowledge and improved management of patients with peritoneal diseases, in particular cancer, has never been greater.However, results from recent randomized studies have shown that therapy-focused research based on the trial and error principle carries a high risk of failure.We need to apply evidence and rigor to the treatment of these patients.
Draft Genome Sequence of the Extensively Drug-Resistant Pseudomonas aeruginosa Clinical Isolate TUEPA7472
2018-09-26

Pseudomonas aeruginosa TUEPA7472 is extensively drug resistant (XDR) and is a representative Gram-negative rod that is multiresistant toward 4 classes of clinically relevant antibiotics (4MRGN). The 6.8-Mb draft genome sequence of this strain provides insight into these resistance mechanisms and the potential of the strain to produce virulence factors.