julilili42/papers huggingface dataset:
Learning from brain control: clinical application of brain–computer interfaces
2015-10-06

Brain–computer interfaces (BCI) use neuroelectric and metabolic brain activity to activate peripheral devices and computers without mediation of the motor system. In order to activate the BCI patients have to learn a certain amount of brain control. Self-regulation of brain activity was found to follow the principles of skill learning and instrumental conditioning. This review focuses on the clinical application of brain–computer interfaces in paralyzed patients with locked-in syndrome and completely locked-in syndrome (CLIS). It was shown that electroencephalogram (EEG)-based brain–computer interfaces allow selection of letters and words in a computer menu with different types of EEG signals. However, in patients with CLIS without any muscular control, particularly of eye movements, classical EEG-based brain–computer interfaces were not successful. Even after implantation of electrodes in the human brain, CLIS patients were unable to communicate. We developed a theoretical model explaining this fundamental deficit in instrumental learning of brain control and voluntary communication: patients in complete paralysis extinguish goal-directed response-oriented thinking and intentions. Therefore, a reflexive classical conditioning procedure was developed and metabolic brain signals measured with near infrared spectroscopy were used in CLIS patients to answer simple questions with a “yes” or “no”-brain response. The data collected so far are promising and show that for the first time CLIS patients communicate with such a BCI system using metabolic brain signals and simple reflexive learning tasks. Finally, brain machine interfaces and rehabilitation in chronic stroke are described demonstrating in chronic stroke patients without any residual upper limb movement a surprising recovery of motor function on the motor level as well as on the brain level. After extensive combined BCI training with behaviorally oriented physiotherapy, significant improvement in motor function was shown in this previously intractable paralysis. In conclusion, clinical application of brain machine interfaces in well-defined and circumscribed neurological disorders have demonstrated surprisingly positive effects. The application of BCIs to psychiatric and clinical–psychological problems, however, at present did not result in substantial improvement of complex behavioral disorders.
Drosophila chitinous aECM and its cellular interactions during tracheal development
2015-10-07

The morphology of organs, and hence their proper physiology, relies to a considerable extent on the extracellular matrix (ECM) secreted by their cells. The ECM is a structure contributed to and commonly shared by many cells in an organism that plays an active role in morphogenesis. Increasing evidence indicates that the ECM not only provides a passive contribution to organ shape but also impinges on cell behaviour and genetic programmes. The ECM is emerging as a direct modulator of many aspects of cell biology, rather than as a mere physical network that supports cells. Here, we review how the apical chitinous ECM is generated in Drosophila trachea and how cells participate in the formation of this supracellular structure. We discuss recent findings on the molecular and cellular events that lead to the formation of this apical ECM (aECM) and how it is influenced and affects tracheal cell biology. Developmental Dynamics 245:259–267, 2016 . © 2015 Wiley Periodicals, Inc.
Towards the molecular mechanism of the integration of peroxisomal membrane proteins
2015-10-07

The correct topogenesis of peroxisomal membrane proteins is a crucial step for the formation of functioning peroxisomes. Although this process has been widely studied, the exact mechanism with which it occurs has not yet been fully characterized. Nevertheless, it is generally accepted that peroxisomes employ three proteins - Pex3, Pex19 and Pex16 in mammals - for the insertion of peroxisomal membrane proteins into the peroxisomal membrane. Structural biology approaches have been utilized for the elucidation of the mechanistic questions of peroxisome biogenesis, mainly by providing information on the architecture of the proteins significant for this process. This review aims to summarize, compare and put into perspective the structural knowledge that has been generated mainly for Pex3 and Pex19 and their interaction partners in recent years.
Bloodstream Infections and Frequency of Pretreatment Associated With Age and Hospitalization Status in Sub-Saharan Africa
2015-10-07

The proportion of patients with culture-proven BSIs in children compared with adults was similar across the TSAP study population; however, outpatient children were more likely to have Salmonella Typhi infections than outpatient adults. This finding points to the importance of including outpatient facilities in surveillance efforts, particularly for the surveillance of typhoid fever. Strategies to reduce contamination among pediatric blood cultures are needed across the continent to prevent the misdiagnosis of BSI cases in children.
Rotoscoping on Stereoscopic Images and Videos
2015-10-07

Creating an animation based on video footage (rotoscoping) often requires significant manual work. For monoscopic videos diverse publications already feature (semi-)automatic techniques to apply non-photorealistic image abstraction (NPR) to videos. This paper addresses abstraction of 3D stereo content minimizing stereoscopic discomfort in images and videos. We introduce a completely autonomous framework that enhances stereo and temporal consistency. Stereoscopic coherence with consistent textures for both eyes is produced by warping the left and right images into a central disparity domain followed by mapping them back to the left and right view. Smooth movements with reduced flickering are achieved by considering optical flow in the propagation of abstract features between frames. The results show significant improvements of stereo consistency without discomforting artifacts in the depth perception. We extend existing stroke based rendering (SBR) for higher accuracy at strong image gradients. Furthermore, we demonstrate that our stereo framework is easily applicable to other point-based abstraction styles. Finally, we evaluate the stereo consistency of our results in a small user study and show that the comfort of the visual appearance is maintained.
Physiology, Fe(II) oxidation, and Fe mineral formation by a marine planktonic cyanobacterium grown under ferruginous conditions
2015-10-08

Evidence for Fe(II) oxidation and deposition of Fe(III)-bearing minerals from anoxic or redox-stratified Precambrian oceans has received support from decades of sedimentological and geochemical investigation of Banded Iron Formations (BIF). While the exact mechanisms of Fe(II) oxidation remains equivocal, reaction with O2 in the marine water column, produced by cyanobacteria or early oxygenic phototrophs, was likely. In order to understand the role of cyanobacteria in the deposition of Fe(III) minerals to BIF, we must first know how planktonic marine cyanobacteria respond to ferruginous (anoxic and Fe(II)-rich) waters in terms of growth, Fe uptake and homeostasis, and Fe mineral formation. We therefore grew the common marine cyanobacterium Synechococcus PCC 7002 in closed bottles that began anoxic, and contained Fe(II) concentrations that span the range of possible concentrations in Precambrian seawater. These results, along with cell suspension experiments, indicate that Fe(II) is likely oxidized by this strain via chemical oxidation with oxygen produced during photosynthesis, and not via any direct enzymatic or photosynthetic pathway. Imaging of the cell-mineral aggregates with scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM) are consistent with extracellular precipitation of Fe(III) (oxyhydr)oxide minerals, but that >10% of Fe(III) sorbs to cell surfaces rather than precipitating. Proteomic experiments support the role of reactive oxygen species (ROS) in Fe(II) toxicity to Synechococcus PCC 7002. The proteome expressed under low Fe conditions included multiple siderophore biosynthesis and siderophore and Fe transporter proteins, but most siderophores are not expressed during growth with Fe(II). These results provide a mechanistic and quantitative framework for evaluating the geochemical consequences of perhaps life’s greatest metabolic innovation, i.e. the evolution and activity of oxygenic photosynthesis, in ferruginous Precambrian oceans.
Central Nervous Insulin Signaling in Sleep-Associated Memory Formation and Neuroendocrine Regulation
2015-10-08

The neurochemical underpinnings of sleep's contribution to the establishment and maintenance of memory traces are largely unexplored. Considering that intranasal insulin administration to the CNS improves memory functions in healthy and memory-impaired humans, we tested whether brain insulin signaling and sleep interact to enhance memory consolidation in healthy participants. We investigated the effect of intranasal insulin on sleep-associated neurophysiological and neuroendocrine parameters and memory consolidation in 16 men and 16 women (aged 18-30 years), who learned a declarative word-pair task and a procedural finger sequence tapping task in the evening before intranasal insulin (160 IU) or placebo administration and 8 h of nocturnal sleep. On the subsequent evening, they learned interfering word-pairs and a new finger sequence before retrieving the original memories. Insulin increased growth hormone concentrations in the first night-half and EEG delta power during the second 90 min of non-rapid-eye-movement sleep. Insulin treatment impaired the acquisition of new contents in both the declarative and procedural memory systems on the next day, whereas retrieval of original memories was unchanged. Results indicate that sleep-associated memory consolidation is not a primary mediator of insulin's acute memory-improving effect, but that the peptide acts on mechanisms that diminish the subsequent encoding of novel information. Thus, by inhibiting processes of active forgetting during sleep, central nervous insulin might reduce the interfering influence of encoding new information.
Optimized Fast Dynamic Contrast-Enhanced Magnetic Resonance Imaging of the Prostate
2015-10-08

Using fast optimized DCE-MRI of the prostate, a minimum sampling duration of 150 seconds is required for sufficient pharmacokinetic parameter estimates, providing a high diagnostic accuracy regarding the discrimination between benign and potentially malignant lesions.
Pattern recognition receptor mediated downregulation of microRNA‐650 fine‐tunes MxA expression in dendritic cells infected with influenza A virus
2015-10-08

MicroRNAs are important posttranscriptional regulators of gene expression, which have been shown to fine‐tune innate immune responses downstream of pattern recognition receptor (PRR) signaling. This study identifies miR‐650 as a novel PRR‐responsive microRNA that is downregulated upon stimulation of primary human monocyte‐derived dendritic cells (MDDCs) with a variety of different microbe‐associated molecular patterns. A comprehensive target search combining in silico analysis, transcriptional profiling, and reporter assays reveals that miR‐650 regulates several well‐known interferon‐stimulated genes, including IFIT2 and MXA. In particular, downregulation of miR‐650 in influenza A infected MDDCs enhances the expression of MxA and may therefore contribute to the establishment of an antiviral state. Together these findings reveal a novel link between miR‐650 and the innate immune response in human MDDCs.
Foam Stabilized by Fly-Ash Nanoparticles for Enhancing Oil Recovery
2015-10-08

Abstract Foam has been employed as an Improved/Enhanced oil recovery (IOR/EOR) method to overcome gravity override and the channeling and fingering of the injected gas, which arises due to the low density and viscosity of the injected fluid combined with the rock heterogeneity. A major challenge; however, is the stability of the generated foam when it contacts the oil. Foam boosters, which are generally costly surfactants, have been co-injected together with the main foaming surfactant to create stable foams in the presence oil. Similar to surfactants, particles can also accumulate at the gas-liquid and liquid-liquid interfaces. The difference is that the energy of adsorption and desorption of particles to the interface is so large that their adsorption is considered irreversible. Nanoparticles are orders of magnitude smaller than pore throats and therefore can easily flow through porous media. In this study we investigate the possibility of replacing the expensive foam boosters with inexpensive nanoparticles made of coal fly-ash, which is abundantly available as a by-product of coal power plants. We investigate the viability of reducing the size of fly-ash particles using high frequency ultrasonic grinding. We also study the foaminess (foamability) and stability of the foams made with minor concentrations of fly-ash nanoparticles and surfactant both in bulk and porous media. The effect of monovalent and divalent ion concentration on the foaminess of the nano-ash suspension combined with very low concentrations of a commercial alpha olefin sulfonate (AOS) surfactant, in presence and absence of oil, is studied. We observe that bulk foam that contains very small amounts of nano-ash particles shows a higher stability in presence of model oils. Furthermore, experiments in porous media exhibit remarkably stronger foam with mixtures of nano-ash and surfactant, such that the amount of produced liquids from the cores significantly increases. In presence of oil, the nano-ash-AOS foam shows a higher stability, although crude oil tends to form stable emulsions in water in presence of nano-ash.
Me, myself, and I: self-referent word use as an indicator of self-focused attention in relation to depression and anxiety
2015-10-09

Self-focused attention (SFA) is considered a cognitive bias that is closely related to depression. However, it is not yet well understood whether it represents a disorder-specific or a trans-diagnostic phenomenon and which role the valence of a given context is playing in this regard. Computerized quantitative text-analysis offers an integrative psycho-linguistic approach that may help to provide new insights into these complex relationships. The relative frequency of first-person singular pronouns in natural language is regarded as an objective, linguistic marker of SFA. Here we present two studies that examined the associations between SFA and symptoms of depression and anxiety in two different contexts (positive vs. negative valence), as well as the convergence between pronoun-use and self-reported aspects of SFA. In the first study, we found that the use of first-person singular pronouns during negative but not during positive memory recall was positively related to symptoms of depression and anxiety in patients with anorexia nervosa with varying levels of co-morbid depression and anxiety. In the second study, we found the same pattern of results in non-depressed individuals. In addition, use of first-person singular pronouns during negative memory recall was positively related to brooding (i.e., the assumed maladaptive sub-component of rumination) but not to reflection. These findings could not be replicated in two samples of depressed patients. However, non-chronically depressed patients used more first-person singular pronouns than healthy controls, irrespective of context. Taken together, the findings lend partial support to theoretical models that emphasize the effects of context on self-focus and consider SFA as a relevant trans-diagnostic phenomenon. In addition, the present findings point to the construct validity of pronoun-use as a linguistic marker of maladaptive self-focus.
The Elucidation of the Interactome of 16 Arabidopsis bZIP Factors Reveals Three Independent Functional Networks
2015-10-09

The function of the bZIP transcription factors is strictly dependent on their ability to dimerize. Heterodimerization has proven to be highly specific and is postulated to operate as a combinatorial mechanism allowing the generation of a large variety of dimers with unique qualities by specifically combining a small set of monomers; an assumption that has not yet been tested systematically. Here, the interaction pattern and the transactivation properties of 16 Arabidopsis thaliana bZIPs are examined in transiently transformed Arabidopsis protoplasts to deliver a perspective on the relationship between bZIP dimerization and function. An interaction matrix of bZIPs belonging to the C, G, H, and S1 bZIP groups was resolved by Bimolecular Fluorescent Complementation (BiFC) coupled to quantitative flow cytometric analysis, while an extensive GUS reporter gene assay was carried out to determine the effect of different bZIP pairs on the expression of four different known bZIP-targeted promoters. Statistical data treatment and complementary bioinformatic analysis were performed to substantiate the biological findings. According to these results, the 16 bZIPs interact in three isolated networks, within which their members dimerize non-specifically and exhibit a significant level of functional redundancy. A coherent explanation for these results is supported by in silico analysis of differences in the length, structure and composition of their leucine zippers and appears to explain their dimerization specificity and dynamics observed in vivo quite well. A model in which the bZIP networks act as functional units is proposed.
Synthesis and Spectroscopic Evaluation of Two Novel Glycosylated Zinc(II)-Phthalocyanines
2015-10-09

In continuation of our work on glycoconjugated phthalocyanines, two new water soluble, non-ionic zinc(II) phthalocyanines have been prepared and fully characterized by means of 1H-NMR, 13C-NMR, MALDI-TOF, ESI-TOF, UV-Vis spectroscopy, emission spectroscopy and fluorescence lifetime measurements. The carbohydrate-containing phthalonitrile precursors were synthesized through a copper-catalyzed azide-alkyne cycloaddition (CuAAC). The 2-methoxyethoxymethyl protecting group (MEM) was used to protect the carbohydrate moieties. It resisted the harsh basic cyclotetramerization conditions and could be easily cleaved under mild acidic conditions. The glycoconjugated zinc(II) phthalocyanines described here have molar extinction coefficents εmax &gt; 105 m−1 cm−1 and absorption maxima λ &gt; 680 nm, which make them attractive photosensitizers for photo-dynamic therapy.
The International Criminal Court in Ongoing Intrastate Conflicts: Navigating the Peace–Justice Divide
2015-10-09

In recent decades, international courts have increasingly started investigating armed conflicts. However, the impact of this remains under-researched. Patrick S. Wegner closes this gap via a comprehensive analysis of the impact of the International Criminal Court in the Darfur and Lord's Resistance Army conflicts. He offers a fresh approach to peace and conflict studies, while avoiding the current quantitative focus of the literature and polarisation between critics and supporters of applying justice in conflicts. This is the first time that the impact of an international criminal court has been analysed in all its facets in two conflicts. The consequences of these investigations are much more complex and difficult to predict than most of the existing literature suggests. Recurrent claims, such as the deterrent effect of trials and the danger of blocking negotiations by the issuing of arrest warrants, are put to the test here with some surprising results
Is LinkedIn making you more successful? The informational benefits derived from public social media
2015-10-10

This article uses a social capital framework to examine whether and how the use of three types of publicly accessible social media (LinkedIn, Twitter, Facebook) is related to professional informational benefits among a representative sample of Dutch online users. Professional informational benefits were conceptualized as the (timely) access to relevant information and being referred to career opportunities. The effect of content and structure of the respective online network on professional informational benefits was examined on the general (users vs. non-users of a platform) and more fine-grained level (within users of a specific platform). Overall, users of LinkedIn and Twitter reported higher informational benefits than non-users, whereas the Facebook users reported lower informational benefits. Posting about work and strategically selecting ties consistently predicted informational benefits. The network composition mattered most on LinkedIn; strong and weak ties predicted informational benefits. The results demonstrate the usefulness of the social capital framework.
Mutagenic Deimmunization of Diphtheria Toxin for Use in Biologic Drug Development
2015-10-10

Background: Targeted toxins require multiple treatments and therefore must be deimmunized. We report a method of protein deimmunization based on the point mutation of highly hydrophilic R, K, D, E, and Q amino acids on the molecular surface of truncated diphtheria-toxin (DT390). Methods: Based on their surface position derived from an X-ray-crystallographic model, residues were chosen for point mutation that were located in prominent positions on the molecular surface and away from the catalytic site. Mice were immunized with a targeted toxin containing either a mutated DT390 containing seven critical point mutations or the non-mutated parental toxin form. Results: Serum analysis revealed a significant 90% reduction in anti-toxin antibodies in mice immunized with the mutant, but not the parental drug form despite multiple immunizations. The experiment was repeated in a second strain of mice with a different MHC-haplotype to address whether point mutation removed T or B cell epitopes. Findings were identical indicating that B cell epitopes were eliminated from DT. The mutant drug form lost only minimal activity in vitro as well as in vivo. Conclusion: These findings indicate that this method may be effective for deimmunizing of other proteins and that discovery of a deimmunized form of DT may lead to the development of more effective targeted toxin.
Absence of Early Neuronal Death in the Olivocochlear System Following Acoustic Overstimulation
2015-10-10

ABSTRACT This study was conducted to examine possible effects of noise trauma on olivocochlear (OC) neurons. Anesthetized rats were exposed to a continuous 10 kHz pure tone at 120 dB sound pressure level for 2 hrs. The effects of treatment were verified by recordings of auditory brainstem response and distortion product otoacoustic emission. Three or 8 days after acoustic trauma, rats received unilateral injections of an aqueous solution of the retrograde neuronal tracer Fluorogold (FG) into the scala tympani to identify OC neurons (OCN). Five days after FG injection, brains were perfusion‐fixed, and brainstem sections were cut and analyzed with respect to FG‐labeled neurons. We found that, in both groups, numbers of OCN were similar to that of controls. The incubation of a second set of sections with antibodies against choline‐acetyltransferase (the enzyme responsible for acetylcholine synthesis) showed the cholinergic neurons of the brainstem, however, without suggesting differences between groups. Our study, the first to investigate noise trauma effects on identified OCN, revealed that no visible alterations occurred in 2 weeks following trauma, neither in identified OCN nor in choline‐acetyltransferase‐immunofluorescence. At this time, auditory brainstem response and distortion product otoacoustic emission measurements showed severe signs of hearing loss. The mechanisms leading to hearing loss upon noise trauma apparently do not involve degeneration of OCN. Anat Rec, 299:103–110, 2016. © 2015 Wiley Periodicals, Inc.